2kkf

Solution structure of MLL CXXC domain in complex with palindromic CPG DNA

Method: SOLUTION NMR D_max: 45.9 Å Quality: GOOD

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone-lysine N-methyltransferase HRX

Homo sapiens

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1147–1203	Fragment：CXXC DOMAIN: UNP RESIDUES 1147-1203	5'-D(CPCPCPTPGPCPGPCPAPGPGPG)-3' × 2 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(DCPDCPDCPDTPDGPDCPDGPDCPDAPDGPDGPDG)-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(DCPDCPDCPDTPDGPDCPDGPDCPDAPDGPDGPDG)-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(DCPDCPDCPDTPDGPDCPDGPDCPDAPDGPDGPDG)-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(DCPDCPDCPDTPDGPDCPDGPDCPDAPDGPDGPDG)-3')-8, 100% D2O \| 100% D2O	Resolution not provided

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 2KKF	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 oligomeric state Different ligand/ion Different experimental conditions	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 experimental conditions	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 oligomeric state Different experimental conditions	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
2KU7 Solution structure of MLL1 PHD3-Cyp33 RRM chimeric protein Deposited 2010-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	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 oligomeric state Different experimental conditions	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 conditions	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 conditions	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 oligomeric state Different ligand/ion Different experimental conditions	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 oligomeric state Different ligand/ion Different experimental conditions	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 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 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 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 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 method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 method 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental conditions	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 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 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	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 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 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	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 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 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 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 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 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 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 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 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 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 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 method 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 method 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 method 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 method 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 method 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 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 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 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 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
7W67 The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein 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 3350	Resolution 2.19 Å R-free 0.222
7W6A Crystal structure of the MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L complex Deposited 2021-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein 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 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 × 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 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 × 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 oligomeric state Different experimental conditions	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 oligomeric state Different experimental conditions	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 method 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 method 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 method 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 method 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	HRX_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–59； UniProt 1147–1203

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2kkf
Deposition date deposition_date	2009-06-18
Structure title title	Solution structure of MLL CXXC domain in complex with palindromic CPG DNA
Keywords keywords	;PROTEIN-DNA COMPLEX, CXXC DOMAIN, MLL, CPG DNA, CHROMOSOMAL REARRANGEMENT, DNA-BINDING, METAL-BINDING, NUCLEUS, ZINC-FINGER, DNA BINDING PROTEIN-DNA COMPLEX, Alternative splicing, Apoptosis, Bromodomain, Chromatin regulator, Isopeptide bond, Methyltransferase, Phosphoprotein, Polymorphism, Proto-oncogene, S-adenosyl-L-methionine, Transcription, Transcription regulation, Transferase, Ubl conjugation, Zinc ;; DNA BINDING PROTEIN/DNA
Experimental Method method	SOLUTION NMR

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.12 Å
Radius of gyration Rg (electron density) rg_electron	14.08 Å
Forward intensity I(0) i0	565240000.00
Molecular weight molecular_weight	139770.0 kDa
Excluded volume excluded_volume	150090 Å³
Envelope volume envelope_volume	25089 Å³
Hydration-shell volume shell_volume	14024 Å³
Envelope diameter envelope_diameter	48.5 Å
Shell Rg shell_rg	20.92 Å
Envelope Rg envelope_rg	15.31 Å
Shape Rg shape_rg	14.05 Å
Total Rg total_rg	14.26 Å
Total atoms total_atoms	16580
Residues n_residues	810
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	45.9 Å
Rg (real space) rg_real	14.02 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	5.6520e+08
I(0) uncertainty (real space) i0_real_error	6.2770e+06
Rg (reciprocal space) rg_reciprocal	14.03 Å
I(0) (reciprocal space) i0_reciprocal	565200000.0000
Solution quality estimate total_estimate	0.8886
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.2 Å
Skewness Skewness skewness	0.081
Kurtosis Kurtosis kurtosis	-0.451
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	384600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.995

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase HRX
Molecular weight formula_weight	6678.0 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	16580

GSKKGRRSRRCGQCPGCQVPEDCGVCTNCLDKPKFGGRNIKKQCCKMRKCQNLQWMPSK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(CPCPCPTPGPCPGPCPAPGPGPG)-3'
Molecular weight formula_weight	3664.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,C

CCCTGCGCAGGG

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

▶

8. Citations (1)

▶

fit	/app/data/saxs_computation/kk/2kkf/2kkf.fit
pddf	/app/data/pr_computation/kk/2kkf/2kkf.pr.out
profile	/app/data/saxs_computation/kk/2kkf/2kkf.dat

Solution structure of MLL CXXC domain in complex with palindromic CPG DNA

1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone-lysine N-methyltransferase HRX

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)