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7w67

The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide

Method: X-RAY DIFFRACTION Dmax: 81.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Set1/Ash2 histone methyltransferase complex subunit ASH2

Homo sapiens

UniProt Q9UBL3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 380–496 Chain A； UniProt 539–598 Not recorded Histone-lysine N-methyltransferase 2A × 1 （Q03164） Retinoblastoma-binding protein 5 × 1 （Q15291） Histone H3.3C × 1 （Q6NXT2） SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350 Resolution 2.19 Å R-free 0.222

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7W67 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3RSN Crystal Structure of the N-terminal region of Human Ash2L Deposited 2011-05-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 96–271（176 aa） Fragment：Ash2L N-terminal domain, UNP residues 96-271
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；100 mM Tris-HCl pH8.5, 20% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.254
3S32 Crystal structure of Ash2L N-terminal domain Deposited 2011-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 95–280（186 aa） Fragment：N-terminal domain residues 95-280
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M MgAcetate and 17-20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.45 Å R-free 0.263
3TOJ Structure of the SPRY domain of human Ash2L Deposited 2011-09-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 370–496（127 aa） Fragment：Ash2L SPRY domain, UNP residues 370-496, 539-617
Chain A 539–617（79 aa） Fragment：Ash2L SPRY domain, UNP residues 370-496, 539-617
Chain B 370–496（127 aa） Fragment：Ash2L SPRY domain, UNP residues 370-496, 539-617
Chain B 539–617（79 aa） Fragment：Ash2L SPRY domain, UNP residues 370-496, 539-617
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20% PEG4000, 0.15 M Li2SO4, 0.1 M Tris, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.07 Å R-free 0.206
4RIQ Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI) Deposited 2014-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 603–618（16 aa） Fragment：UNP residues 603-618
Chain F 603–618（16 aa） Fragment：UNP residues 603-618
Chain L 603–618（16 aa） Fragment：UNP residues 603-618
Chain X 603–618（16 aa） Fragment：UNP residues 603-618
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；323 K；0.2M MgCl2, 25% PEG 3350, 0.1M Tris pH 8.5 and 10 mM spermidine, VAPOR DIFFUSION, SITTING DROP, temperature 323K
Resolution 2.23 Å R-free 0.284
4RIQ Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI) Deposited 2014-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 603–618（16 aa） Fragment：UNP residues 603-618
Chain O 603–618（16 aa） Fragment：UNP residues 603-618
Chain R 603–618（16 aa） Fragment：UNP residues 603-618
Chain U 603–618（16 aa） Fragment：UNP residues 603-618
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；323 K；0.2M MgCl2, 25% PEG 3350, 0.1M Tris pH 8.5 and 10 mM spermidine, VAPOR DIFFUSION, SITTING DROP, temperature 323K
Resolution 2.23 Å R-free 0.284
4X8N Crystal structure of Ash2L SPRY domain in complex with phosphorylated RbBP5 Deposited 2014-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 380–495（116 aa） Fragment：UNP residues 380-495, 539-598
Chain A 539–598（60 aa） Fragment：UNP residues 380-495, 539-598
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol
Resolution 2.10 Å R-free 0.277
4X8P Crystal structure of Ash2L SPRY domain in complex with RbBP5 Deposited 2014-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 380–495（116 aa） Fragment：UNP residues 380-495, 539-598
Chain A 539–598（60 aa） Fragment：UNP residues 380-495, 539-598
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol
Resolution 2.20 Å R-free 0.271
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain A 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain B 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain B 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain A 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain B 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6L The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L Deposited 2015-12-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain B 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；200mM NaCl, 20% PEG 3350
Resolution 1.90 Å R-free 0.213
6E2H Crystal structure of human Ash2L (SPRY domain and SDI motif) in complex with full length DPY-30 Deposited 2018-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 380–622（243 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20mM citrate pH 4.7 and polyethylene glycol (PEG) 6000
Resolution 2.24 Å R-free 0.200
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain T 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain T 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain T 95–628（534 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain T 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain T 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain D 2–534（533 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6W5I Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01) Deposited 2020-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7BRE The crystal structure of MLL2 in complex with ASH2L and RBBP5 Deposited 2020-03-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 286–402（117 aa） Fragment：UNP residues 286-402 and UNP residues 445-504
Chain A 445–504（60 aa） Fragment：UNP residues 286-402 and UNP residues 445-504
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.265
7BRE The crystal structure of MLL2 in complex with ASH2L and RBBP5 Deposited 2020-03-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 286–402（117 aa） Fragment：UNP residues 286-402 and UNP residues 445-504
Chain D 445–504（60 aa） Fragment：UNP residues 286-402 and UNP residues 445-504
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.265
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain M 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7W6A Crystal structure of the MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L complex Deposited 2021-12-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5 25% w/v polyethylene glycol 3350
Resolution 2.21 Å R-free 0.229
7W6I The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide Deposited 2021-12-01 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3,350
Resolution 2.56 Å R-free 0.244
7W6J The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me2 peptide Deposited 2021-12-01 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.68 Å R-free 0.252
7W6L The crystal structure of MLL3-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Chain B 380–496（117 aa）
Chain B 539–598（60 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM sodium cacodylate, pH 6.5, 10% polyethylene glycol 3350, 0.1 M MgCl2
Resolution 2.26 Å R-free 0.223
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.63 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

31 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ASH2L_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–118； UniProt 380–496 Author chain A； PDBConstruct 125–184； UniProt 539–598

Histone-lysine N-methyltransferase 2A

Homo sapiens

UniProt Q03164

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 3813–3969 Mutation：N3861I,Q3867L,C3882SS Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Retinoblastoma-binding protein 5 × 1 （Q15291） Histone H3.3C × 1 （Q6NXT2） SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350 Resolution 2.19 Å R-free 0.222

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7W67 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2AGH Structural basis for cooperative transcription factor binding to the CBP coactivator Deposited 2005-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2839–2869（31 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Pressure 1
NMR sample composition 0.5-0.8 mM 15N,13C-labeled protein (e.g. CBP) + 3 fold excess of unlabeled binding partners (MYB + MLL), 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O | 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O
NMR sample composition 13C,15N-MYB + UNLABELED CBP & MYB, 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O | 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O
NMR sample composition 13C,15N-MLL + UNLABELED CBP & MLL, 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O | 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O
Resolution not provided
2J2S Solution structure of the nonmethyl-CpG-binding CXXC domain of the leukaemia-associated MLL histone methyltransferase Deposited 2006-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1143–1214（72 aa） Fragment：RESIDUES 1146-1214
Mutation：YES ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.5；290 K
NMR sample composition 90% WATER, 10% D2O
Resolution not provided
2JYI Solution structure of MLL CXXC domain Deposited 2007-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1147–1203（57 aa） Fragment：CXXC domain
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.1；298 K；Ionic strength (raw mmCIF value) 0.3；Pressure ambient
NMR measurement conditions pH 7.1；298 K；Ionic strength (raw mmCIF value) 0.3；Pressure ambient
NMR measurement conditions pH 7.1；298 K；Ionic strength (raw mmCIF value) 0.3；Pressure ambient
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] CXXC, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] CXXC, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] CXXC, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2KKF Solution structure of MLL CXXC domain in complex with palindromic CPG DNA Deposited 2009-06-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1147–1203（57 aa） Fragment：CXXC DOMAIN: UNP RESIDUES 1147-1203
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 25；Pressure Ambient
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] CXXC domain-1, 1 mM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-2, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] CXXC domain-3, 1 mM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-4, 100% D2O | 100% D2O
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] CXXC domain-5, 1 mM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-6, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-98% 15N] CXXC domain-7, 1 mM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-8, 100% D2O | 100% D2O
Resolution not provided
2KU7 Solution structure of MLL1 PHD3-Cyp33 RRM chimeric protein Deposited 2010-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1585–1628（44 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298.2 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.3-0.5 mM [U-100% 13C; U-100% 15N] MLL PHD3-Cyp33 RRM, 20 mM sodium phosphate, 50 mM sodium chloride, 0.4 mM DSS, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
2KYU The solution structure of the PHD3 finger of MLL Deposited 2010-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1564–1628（65 aa） Fragment：PHD3 finger (UNP residues 1564-1628)
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.9；303 K
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] PHD3, 100 uM ZINC ION, 25 mM potassium phosphate, 3 mM DTT, 50 mM sodium chloride, 1 mM sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2LXS Allosteric communication in the KIX domain proceeds through dynamic re-packing of the hydrophobic core Deposited 2012-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2840–2858（19 aa） Fragment：UNP RESIDUES 2840-2858
Mutation：C841A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；300 K；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-1, 2 mM [U-100% 13C; U-100% 15N] entity_2-2, 25 mM sodium chloride-3, 50 mM potassium phosphate-4, 1 mM sodium azide-5, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LXT Allosteric communication in the KIX domain proceeds through dynamic re-packing of the hydrophobic core Deposited 2012-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2840–2858（19 aa） Fragment：UNP RESIDUES 2840-2858
Mutation：C841A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；300 K；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-1, 2 mM entity_2-2, 2 mM [U-100% 13C; U-100% 15N] entity_3-3, 25 mM sodium chloride-4, 50 mM potassium phosphate-5, 1 mM sodium azide-6, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MSR Solution structure of LEDGF/p75 IBD in complex with MLL1 peptide (140-160) Deposited 2014-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 140–160（21 aa） Fragment：UNP residues 140-160
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 125；Pressure ambient
NMR sample composition 0.5 mM MLL1_140, 0.5 mM [U-13C; U-15N] IBD, 25 mM HEPES, 100 mM sodium chloride, 0.05 % beta-mercaptoethanol, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2MTN Solution structure of MLL-IBD complex Deposited 2014-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–160（51 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 50 mM potassium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2W5Y Binary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine. Deposited 2008-12-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3785–3969（185 aa） Fragment：METHYLTRANSFERASE DOMAIN, RESIDUES 3785-3969
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；0.1 M SODIUM CACODYLATE, PH6.5, 2 % PEG 8000, 30 % 2-METHYL-2,4-PENTANDIOL, pH 6.8
Resolution 2.00 Å R-free 0.264
2W5Z Ternary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine and histone peptide. Deposited 2008-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 3785–3969（185 aa） Fragment：METHYLTRANSFERASE DOMAIN, RESIDUES 3785-3969
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；0.1 M SODIUM CACODYLATE PH6.8, 2 % PEG 5000, 30 % 2-METHYL-2, 4-PENTANDIOL
Resolution 2.20 Å R-free 0.247
3EG6 Structure of WDR5 bound to MLL1 peptide Deposited 2008-09-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 3762–3773（12 aa） Fragment：MLL-1 Win motif
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；298 K；30% PEG 3350, 30 mM (NH4)2SO4, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.72 Å R-free 0.240
3LQH Crystal structure of MLL1 PHD3-Bromo in the free form Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1566–1665（100 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Chain A 1703–1784（82 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.3；293 K；0.1M Sodium acetate, 50 mM NaCl, 15% PEG3350, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.72 Å R-free 0.234
3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1566–1665（100 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Chain A 1703–1784（82 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.92 Å R-free 0.241
3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1566–1665（100 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Chain B 1703–1784（82 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.92 Å R-free 0.241
3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1566–1665（100 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Chain C 1703–1784（82 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.92 Å R-free 0.241
3LQJ Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me3 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1566–1665（100 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Chain A 1703–1784（82 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；0.1 M Tris, 0.2 M Li2SO4, 15% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.274
3LQJ Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me3 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1566–1665（100 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Chain B 1703–1784（82 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；0.1 M Tris, 0.2 M Li2SO4, 15% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.274
3P4F Structural and biochemical insights into MLL1 core complex assembly and regulation. Deposited 2010-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 3761–3770（10 aa） Fragment：unp residues 3761-3770
Mutation：S3763A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；0.2 M ammonium citrate (buffered with hydrochloric acid/sodium hydroxide to pH 7.0) and 18% PEG3350, VAPOR DIFFUSION, HANGING DROP
Resolution 2.35 Å R-free 0.249
3U85 Crystal structure of human menin in complex with MLL1 Deposited 2011-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 6–25（20 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3 M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K
Resolution 3.00 Å R-free 0.258
3U85 Crystal structure of human menin in complex with MLL1 Deposited 2011-10-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 6–25（20 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3 M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K
Resolution 3.00 Å R-free 0.258
3U88 Crystal structure of human menin in complex with MLL1 and LEDGF Deposited 2011-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain M 103–153（51 aa）
Not recorded CHD CHOLIC ACID × 1 GGB L-CANAVANINE × 4 0BR (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLV GLYOXYLIC ACID × 4 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；277 K；1.6 M ammonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 277K
Resolution 3.00 Å R-free 0.233
3U88 Crystal structure of human menin in complex with MLL1 and LEDGF Deposited 2011-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain N 103–153（51 aa）
Not recorded CHD CHOLIC ACID × 1 GGB L-CANAVANINE × 1 0BR (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLV GLYOXYLIC ACID × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；277 K；1.6 M ammonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 277K
Resolution 3.00 Å R-free 0.233
4ESG X-ray structure of WDR5-MLL1 Win motif peptide binary complex Deposited 2012-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 3755–3771（17 aa） Fragment：UNP residues 3755-3771
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.2；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.2, hanging drop, temperature 294K
Resolution 1.70 Å R-free 0.193
4ESG X-ray structure of WDR5-MLL1 Win motif peptide binary complex Deposited 2012-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 3755–3771（17 aa） Fragment：UNP residues 3755-3771
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.2；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.2, hanging drop, temperature 294K
Resolution 1.70 Å R-free 0.193
4GQ6 Human menin in complex with MLL peptide Deposited 2012-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 6–15（10 aa） Fragment：unp residues 6-15
Not recorded SO4 SULFATE ION × 3 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), NBm1 peptide, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, 1:1 molar ratio with MBM1 peptide, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 1.55 Å R-free 0.189
4NW3 Crystal structure of MLL CXXC domain in complex with a CpG DNA Deposited 2013-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1147–1204（58 aa） Fragment：CXXC zinc finger domain (UNP residues 1147-1204)
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；20% PEG3350, 0.05 M sodium tartrate, VAPOR DIFFUSION, temperature 291K
Resolution 2.82 Å R-free 0.266
5F5E The Crystal Structure of MLL1 SET domain with N3816I/Q3867L mutation Deposited 2015-12-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3813–3969（157 aa） Fragment：MLL1 SET domain (UNP RESIDUES 3813-3969)
Mutation：N3861I, Q3867L ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；35% Tacsimate, pH 7.0
Resolution 1.80 Å R-free 0.236
5F6L The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 3813–3969（157 aa） Fragment：UNP RESIDUES 3813-3969
Mutation：N3861I, Q3867L SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；200mM NaCl, 20% PEG 3350
Resolution 1.90 Å R-free 0.213
5SVH Crystal structure of the KIX domain of CBP in complex with a MLL/c-Myb chimera Deposited 2016-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2839–2869（31 aa） Fragment：;UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315,UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315 ;
Not recorded GOL GLYCEROL × 2 CL CHLORIDE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M potassium sulfate 2.3M Ammonium sulphate
Resolution 2.05 Å R-free 0.242
5SVH Crystal structure of the KIX domain of CBP in complex with a MLL/c-Myb chimera Deposited 2016-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 2839–2869（31 aa） Fragment：;UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315,UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315 ;
Not recorded GOL GLYCEROL × 12 CL CHLORIDE ION × 42 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M potassium sulfate 2.3M Ammonium sulphate
Resolution 2.05 Å R-free 0.242
5SVH Crystal structure of the KIX domain of CBP in complex with a MLL/c-Myb chimera Deposited 2016-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2839–2869（31 aa） Fragment：;UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315,UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315 ;
Not recorded GOL GLYCEROL × 4 CL CHLORIDE ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M potassium sulfate 2.3M Ammonium sulphate
Resolution 2.05 Å R-free 0.242
6EMQ Solution structure of the LEDGF/p75 IBD - MLL1 (aa 111-160) complex Deposited 2017-10-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–160（51 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure arbitrary
NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-MLL1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain K 3754–3969（216 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain K 3754–3969（216 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 3754–3969（216 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 3754–3969（216 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 3762–3969（208 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6PWW Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Deposited 2019-07-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 3762–3969（208 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6W5I Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01) Deposited 2020-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 3762–3969（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 3762–3969（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 3762–3969（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 3762–3969（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 3762–3969（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7RZD CRYSTAL STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PEPTIDE Deposited 2021-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 747–755（9 aa）
Not recorded GOL GLYCEROL × 2 CL CHLORIDE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18-24%PEG4000, 0.1M SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
Resolution 1.82 Å R-free 0.236
7RZJ CRYSTAL STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PHOSPHOPEPTIDE Deposited 2021-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 747–755（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；18-24%PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 1.80 Å R-free 0.217
7S79 STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH SYNTHETIC PHOSPHONO-MLL PEPTIDE ANALOG Deposited 2021-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 747–755（9 aa） Fragment：PHOSPHONO-MLL(747-755) PEPTIDE
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；18-24% PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
Resolution 1.53 Å R-free 0.196
7S7D STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH SYNTHETIC SULFO-MLL PEPTIDE ANALOG Deposited 2021-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 747–755（9 aa） Fragment：SULFO-MLL(747-755) PEPTIDE
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；18-24% PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
Resolution 1.56 Å R-free 0.195
7S8A STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PHOSPHOPEPTIDE, CUBIC CRYSTAL FORM Deposited 2021-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 747–755（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 12P DODECAETHYLENE GLYCOL × 1 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 1 PGE TRIETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 PG4 TETRAETHYLENE GLYCOL × 1 ACT ACETATE ION × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；35% PEG4000, 0.1M TRIS-HCL, PH 8.5, 0.2M SODIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
Resolution 2.10 Å R-free 0.206
7S8E STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PHOSPHOPEPTIDE AND BOUND GLYCEROL Deposited 2021-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 747–755（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；18-24%PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
Resolution 1.60 Å R-free 0.195
7S8F STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PEPTIDE AND BOUND GLYCEROL Deposited 2021-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 747–755（9 aa）
Not recorded GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；18-26%PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
Resolution 1.80 Å R-free 0.206
7U5V Crystal structure of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine and Borealin peptide Deposited 2022-03-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 3811–3969（159 aa） Fragment：SET Domain
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；60% Tacsimate pH 7.0
Resolution 2.59 Å R-free 0.304
7W6A Crystal structure of the MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L complex Deposited 2021-12-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 3813–3969（157 aa）
Mutation：N3861I,Q3867L,C3882SS SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5 25% w/v polyethylene glycol 3350
Resolution 2.21 Å R-free 0.229
7W6I The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide Deposited 2021-12-01 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 3813–3969（157 aa）
Mutation：N3861I,Q3867L,C3882SS SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3,350
Resolution 2.56 Å R-free 0.244
7W6J The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me2 peptide Deposited 2021-12-01 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 3813–3969（157 aa）
Mutation：N3861I,Q3867L,C3882SS SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.68 Å R-free 0.252
7ZEY Complex Cyp33-RRM : MLL1-PHD3 Deposited 2022-03-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1564–1627（64 aa） Fragment：PHD ZINC FINGER (UNP RESIDUES 1564-1627)
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；310.15 K；Ionic strength (raw mmCIF value) 80；Pressure AMBIENT
NMR sample composition 1 mM [U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7ZEZ Trimolecular complex Cyp33-RRMdelta alpha : MLL1-PHD3 : H3K4me3 Deposited 2022-03-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1564–1627（64 aa） Fragment：PHD ZINC FINGER (UNP RESIDUES 1564-1627)
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；310.15 K；Ionic strength (raw mmCIF value) 80；Pressure AMBIENT
NMR sample composition 1 mM [U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 10 uM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 10 uM zinc chloride, 100% D2O | 100% D2O
NMR sample composition 1 mM PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 10 uM zinc chloride, 100% D2O | 100% D2O
Resolution not provided
9C4S Menin mutant G331R in complex with MLL peptide Deposited 2024-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 4–15（12 aa）
Mutation：C5A Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.54 Å R-free 0.202
9C4T menin mutant M327I in complex with MLL peptide Deposited 2024-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 4–15（12 aa）
Mutation：C5A Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.46 Å R-free 0.184
9C4U Menin mutant T349M in complex with MLL peptide Deposited 2024-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 4–15（12 aa）
Mutation：C5A Non-standard monomer：Yes (specific site not provided by mmCIF) PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.57 Å R-free 0.197
9C4V Menin mutant G331D in complex with MLL peptide Deposited 2024-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 4–15（12 aa）
Mutation：C5A Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.47 Å R-free 0.188

54 other PDB entries and 62 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KMT2A_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–158； UniProt 3813–3969

Retinoblastoma-binding protein 5

Homo sapiens

UniProt Q15291

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain F； UniProt 330–356 Not recorded Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone-lysine N-methyltransferase 2A × 1 （Q03164） Histone H3.3C × 1 （Q6NXT2） SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350 Resolution 2.19 Å R-free 0.222

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7W67 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3P4F Structural and biochemical insights into MLL1 core complex assembly and regulation. Deposited 2010-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 371–381（11 aa） Fragment：unp residues 371-381
Mutation：Y381D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；0.2 M ammonium citrate (buffered with hydrochloric acid/sodium hydroxide to pH 7.0) and 18% PEG3350, VAPOR DIFFUSION, HANGING DROP
Resolution 2.35 Å R-free 0.249
4X8N Crystal structure of Ash2L SPRY domain in complex with phosphorylated RbBP5 Deposited 2014-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 347–356（10 aa） Fragment：UNP residues 347-356
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol
Resolution 2.10 Å R-free 0.277
4X8P Crystal structure of Ash2L SPRY domain in complex with RbBP5 Deposited 2014-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 344–355（12 aa） Fragment：UNP residues 344-355
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol
Resolution 2.20 Å R-free 0.271
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Chain F 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6L The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L Deposited 2015-12-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；200mM NaCl, 20% PEG 3350
Resolution 1.90 Å R-free 0.213
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain N 1–538（538 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6KM7 The structural basis for the internal interaction in RBBP5 Deposited 2019-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 10–325（316 aa）
Chain C 390–480（91 aa） Fragment：C-terminal distal domain
Not recorded SO4 SULFATE ION × 2 2PE NONAETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.1 M HEPES-Na, pH 7.5, 2% w/v PEG 400, 2.0 M ammonium sulfate
Resolution 1.80 Å R-free 0.194
6KM7 The structural basis for the internal interaction in RBBP5 Deposited 2019-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 10–325（316 aa）
Chain D 390–480（91 aa） Fragment：C-terminal distal domain
Not recorded SO4 SULFATE ION × 6 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.1 M HEPES-Na, pH 7.5, 2% w/v PEG 400, 2.0 M ammonium sulfate
Resolution 1.80 Å R-free 0.194
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain A 2–538（537 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6PWW Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Deposited 2019-07-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 2–538（537 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6PWX Cryo-EM structure of RbBP5 bound to the nucleosome Deposited 2019-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6W5I Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01) Deposited 2020-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7BRE The crystal structure of MLL2 in complex with ASH2L and RBBP5 Deposited 2020-03-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 330–356（27 aa）
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.265
7BRE The crystal structure of MLL2 in complex with ASH2L and RBBP5 Deposited 2020-03-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 330–356（27 aa）
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.265
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7W6A Crystal structure of the MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L complex Deposited 2021-12-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 330–356（27 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5 25% w/v polyethylene glycol 3350
Resolution 2.21 Å R-free 0.229
7W6I The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide Deposited 2021-12-01 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 330–356（27 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3,350
Resolution 2.56 Å R-free 0.244
7W6J The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me2 peptide Deposited 2021-12-01 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 330–356（27 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.68 Å R-free 0.252
7W6L The crystal structure of MLL3-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 330–356（27 aa）
Chain F 330–356（27 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM sodium cacodylate, pH 6.5, 10% polyethylene glycol 3350, 0.1 M MgCl2
Resolution 2.26 Å R-free 0.223
8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.63 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

31 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RBBP5_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain F； PDBConstruct 1–27； UniProt 330–356

Histone H3.3C

OrganismNot specified

UniProt Q6NXT2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain M； UniProt 2–10 Not recorded Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone-lysine N-methyltransferase 2A × 1 （Q03164） Retinoblastoma-binding protein 5 × 1 （Q15291） SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350 Resolution 2.19 Å R-free 0.222

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7W67 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
21GE Solution structures of BRD9 bromodomain in complex with histone H3 acetyl-lysine 18 (H3K18ac) peptide Deposited 2025-12-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 12–26（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) Null；Pressure 1
NMR sample composition 500 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 500 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 2 mM DTT, 100% D2O | 100% D2O
Resolution not provided
21HJ Solution structures of BRD9 bromodomain in complex with histone H3 lactyl-lysine 18 (H3K18la) peptide Deposited 2025-12-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 12–26（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) null；Pressure 1
NMR sample composition 500 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 500 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 2 mM DTT, 100% D2O | 100% D2O
Resolution not provided
3KV4 Structure of PHF8 in complex with histone H3 Deposited 2009-11-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–25（24 aa） Fragment：UNP Residues 2-25
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 FE2 FE (II) ION × 1 NI NICKEL (II) ION × 1 EDO 1,2-ETHANEDIOL × 13 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；25% (v/v) polyethylene glycol 3350, 0.2 M NaCl, and 0.1 M NaCitrate pH 5.6, VAPOR DIFFUSION, HANGING DROP
Resolution 2.19 Å R-free 0.255
4Z5T The nucleosome containing human H3.5 Deposited 2015-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–135（135 aa）
Chain E 1–135（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.80 Å R-free 0.269
7W6I The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide Deposited 2021-12-01 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–10（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3,350
Resolution 2.56 Å R-free 0.244
7W6J The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me2 peptide Deposited 2021-12-01 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–10（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.68 Å R-free 0.252
7W6L The crystal structure of MLL3-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain M 2–10（9 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM sodium cacodylate, pH 6.5, 10% polyethylene glycol 3350, 0.1 M MgCl2
Resolution 2.26 Å R-free 0.223
8Q1G LSD1-CoREST bound to Acetylated K14 of Histone H3 Deposited 2023-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–22（21 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartrate 1.2M, ADA 0.1M,
Resolution 2.60 Å R-free 0.255
8Q1H LSD1 Y391K-CoREST bound to Histone H3 N-terminal tail Deposited 2023-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–22（21 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartrate 1.2 M, ADA 0.1M
Resolution 2.90 Å R-free 0.254
8Q1J LSD1 Y391K-CoREST bound to Acetylated K14 of Histone H3 Deposited 2023-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–22（21 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartate 1.2 M, ADA 0.1M
Resolution 2.87 Å R-free 0.272
8RBX Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Deposited 2023-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 43 PDB declaration: 46-meric
Chain M 1–135（135 aa）
Chain S 1–135（135 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8SR6 Crystal structure of legAS4 from Legionella pneumophila subsp. pneumophila with histone H3 (3-17)peptide Deposited 2023-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 4–18（15 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Bis-Tris 6.5 and 38% PPG P400
Resolution 2.22 Å R-free 0.230
8T4F Transporter associated with antigen processing (TAP) bound to the 9-mer peptide RRYQKSTEL Deposited 2023-06-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 52–60（9 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8VLD Crystal structure of Ash1L PHD finger in complex with histone H3K4me2 Deposited 2024-01-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 2–12（11 aa）
Chain T 2–12（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1.6 M sodium citrate pH 6.5
Resolution 1.92 Å R-free 0.249
8VLF Crystal structure of Ash1L PHD finger in complex with histone H3K4me3 Deposited 2024-01-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 2–13（12 aa）
Chain T 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1.6 M sodium citrate pH 6.5
Resolution 1.34 Å R-free 0.188
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4M Sodium Malonate
Resolution 2.91 Å R-free 0.221
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4M Sodium Malonate
Resolution 2.91 Å R-free 0.221
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4M Sodium Malonate
Resolution 2.91 Å R-free 0.221
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4M Sodium Malonate
Resolution 2.91 Å R-free 0.221
8ZXC NMR solution structures of ASH1L BRD-PHD domain in complex with H3K4me2 peptide Deposited 2024-06-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) null；Pressure 1
NMR sample composition 100 mM sodium phosphate, 2 mM DTT, 50 mM potassium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 100 mM sodium phosphate, 2 mM DTT, 50 mM potassium chloride, 100% D2O | 100% D2O
Resolution not provided
9C0O Crystal structure of DmCfp1 PHD finger bound to H3K4me3 Deposited 2024-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) DMS DIMETHYL SULFOXIDE × 1 ZN ZINC ION × 3 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；15% PEG3350, 0.01M Tris pH8.5, 0.2M Ammonium sulfate
Resolution 1.53 Å R-free 0.194
9DZN KAT6A MYST domain complexed with a H3K14-CoA bisubstrate inhibitor Deposited 2024-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 6–24（19 aa）
Not recorded CMC CARBOXYMETHYL COENZYME *A × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；294.15 K；1.25 M NH4SO4, 0.28 M NaCl, and 0.1 M HEPES pH 6.4
Resolution 1.72 Å R-free 0.245
9IM4 Crystal Structure of AF9 YEATS domain F28R mutant in complex with histone H3K9la Deposited 2024-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.1M DL Malic acid pH7.0
Resolution 2.79 Å R-free 0.315
9IM4 Crystal Structure of AF9 YEATS domain F28R mutant in complex with histone H3K9la Deposited 2024-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.1M DL Malic acid pH7.0
Resolution 2.79 Å R-free 0.315
9N61 Transporter associated with antigen processing (TAP) bound to the 9-mer peptide RRYQKSTEL and ATP Deposited 2025-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 52–60（9 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9V5M The crystal structure of RBBP4-H3 complex Deposited 2025-05-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–15（14 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.211

22 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H3C_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain M； PDBConstruct 1–9； UniProt 2–10

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7w67

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7w67
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7w67
Deposition date deposition_date2021-12-01
Structure title titleThe crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide
Keywords keywordsMLL family methyltransferases, product specificity, F/Y switch, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.30 Å
Radius of gyration Rg (electron density) rg_electron24.47 Å
Forward intensity I(0) i028949500.00
Molecular weight molecular_weight41391.0 kDa
Excluded volume excluded_volume51748 ų
Envelope volume envelope_volume63671 ų
Hydration-shell volume shell_volume22320 ų
Envelope diameter envelope_diameter84.0 Å
Shell Rg shell_rg31.08 Å
Envelope Rg envelope_rg24.17 Å
Shape Rg shape_rg24.42 Å
Total Rg total_rg25.43 Å
Total atoms total_atoms2909
Residues n_residues360
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax81.6 Å
Rg (real space) rg_real25.36 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real2.8950e+07
I(0) uncertainty (real space) i0_real_error3.7740e+05
Rg (reciprocal space) rg_reciprocal25.35 Å
I(0) (reciprocal space) i0_reciprocal28950000.0000
Solution quality estimate total_estimate0.8803
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.3 Å
Skewness Skewness skewness0.334
Kurtosis Kurtosis kurtosis-0.617
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7413000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.883; Smooth: 0.958
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)