SAXSdb — 3o7a

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

PHD finger protein 13 variant

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 250–301	Fragment：UNP Residues 250-301	H3K4ME3 HISTONE 11MER-PEPTIDE × 1 （Q92133） GOL GLYCEROL × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1M Tris-HCl pH 8.5; 1.5M Na-Citrate, PEG400 6%, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.67 Å R-free 0.224

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q59FB6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–52； UniProt 250–301

H3K4ME3 HISTONE 11MER-PEPTIDE

OrganismNot specified

UniProt Q92133

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 2–12	Non-standard monomer：Yes (specific site not provided by mmCIF)	PHD finger protein 13 variant × 1 （Q59FB6） GOL GLYCEROL × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1M Tris-HCl pH 8.5; 1.5M Na-Citrate, PEG400 6%, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.67 Å R-free 0.224

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 3O7A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2HUE Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4 Deposited 2006-07-26	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 62–136（75 aa） Fragment：residues 62-136	Mutation：G103A	ZN ZINC ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M potassium sulfate, 0.1M Tris-HCl, 14.5% PEG 4K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.70 Å R-free 0.239
2HUE Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4 Deposited 2006-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 62–136（75 aa） Fragment：residues 62-136	Mutation：G103A	ZN ZINC ION × 2 GOL GLYCEROL × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M potassium sulfate, 0.1M Tris-HCl, 14.5% PEG 4K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.70 Å R-free 0.239
2HUE Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4 Deposited 2006-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 62–136（75 aa） Fragment：residues 62-136	Mutation：G103A	ZN ZINC ION × 2 GOL GLYCEROL × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M potassium sulfate, 0.1M Tris-HCl, 14.5% PEG 4K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.70 Å R-free 0.239
2HUE Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4 Deposited 2006-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 62–136（75 aa） Fragment：residues 62-136	Mutation：G103A	ZN ZINC ION × 2 GOL GLYCEROL × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M potassium sulfate, 0.1M Tris-HCl, 14.5% PEG 4K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.70 Å R-free 0.239
2L11 Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide Deposited 2010-07-22	Different construct 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 2–16（15 aa） Fragment：UNP Residues 2-16	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) 200；Pressure ambient NMR sample composition 20 mM sodium phosphate, 200 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.5 mM PMSF, 1 mM Benzamidine, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L12 Solution NMR structure of the chromobox protein 7 with H3K9me3 Deposited 2010-07-22	Different construct 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 2–16（15 aa） Fragment：UNP Residues 2-16	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) 300；Pressure ambient NMR sample composition 10 mM sodium phosphate, 300 mM sodium chloride, 1 mM TCEP, 1 mM Benzamidine, 0.5 mM PMSF, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L1B Solution NMR structure of the chromobox protein Cbx7 with H3K27me3 Deposited 2010-07-27	Different construct 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 20–34（15 aa） Fragment：UNP Residues 20-34	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) 300；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N] protein, 2.7 mM peptide, 10 mM sodium phosphate, 300 mM sodium chloride, 0.5 mM PMSF, 0.5 mM TCEP, 1 mM Benzamidine, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3GV6 Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide Deposited 2009-03-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–15（15 aa） Fragment：UNP residues 2-16	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 7.5；297 K；14% PEG 3350, 0.2M MgCl2, 0.1M HEPES, pH7.5 , VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 1.76 Å R-free 0.266
3ME9 Crystal structure of SGF29 in complex with H3K4me3 peptide Deposited 2010-03-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 2–12（11 aa） Fragment：UNP Residues 2-9 Chain D 2–12（11 aa） Fragment：UNP Residues 2-9	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	UNX UNKNOWN LIGAND × 11 GOL GLYCEROL × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% PEG3350, 0.1M ammonium sulfate, 0.1M Bis-Tris, pH 5.5, vapor diffusion, sitting drop, temperature 291K	Resolution 1.37 Å R-free 0.214
3ME9 Crystal structure of SGF29 in complex with H3K4me3 peptide Deposited 2010-03-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–12（11 aa） Fragment：UNP Residues 2-9	Non-standard monomer：Yes (specific site not provided by mmCIF)	UNX UNKNOWN LIGAND × 6 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% PEG3350, 0.1M ammonium sulfate, 0.1M Bis-Tris, pH 5.5, vapor diffusion, sitting drop, temperature 291K	Resolution 1.37 Å R-free 0.214
3ME9 Crystal structure of SGF29 in complex with H3K4me3 peptide Deposited 2010-03-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–12（11 aa） Fragment：UNP Residues 2-9	Non-standard monomer：Yes (specific site not provided by mmCIF)	UNX UNKNOWN LIGAND × 5 GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% PEG3350, 0.1M ammonium sulfate, 0.1M Bis-Tris, pH 5.5, vapor diffusion, sitting drop, temperature 291K	Resolution 1.37 Å R-free 0.214
3MEA Crystal structure of the SGF29 in complex with H3K4me3 Deposited 2010-03-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–12（11 aa） Fragment：UNP Residues 2-4	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 7.5；291 K；22% peg3350, 0.1M HEPES. 0.004M trimethylated H3K3 peptide was present in the protein stock solution, pH 7.5, vapor diffusion, hanging drop, temperature 291K	Resolution 1.26 Å R-free 0.200
3MET Crystal structure of SGF29 in complex with H3K4me2 Deposited 2010-03-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–12（11 aa） Fragment：UNP Residues 2-12	Non-standard monomer：Yes (specific site not provided by mmCIF)	UNX UNKNOWN LIGAND × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；20-28% PEG3350, 0.1M Bis-Tris pH 5.5, vapor diffusion, Sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP	Resolution 2.00 Å R-free 0.243
3MET Crystal structure of SGF29 in complex with H3K4me2 Deposited 2010-03-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–12（11 aa） Fragment：UNP Residues 2-12	Non-standard monomer：Yes (specific site not provided by mmCIF)	UNX UNKNOWN LIGAND × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；20-28% PEG3350, 0.1M Bis-Tris pH 5.5, vapor diffusion, Sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP	Resolution 2.00 Å R-free 0.243
3MEU Crystal structure of SGF29 in complex with H3R2me2sK4me3 Deposited 2010-03-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 2–14（13 aa） Fragment：UNP Residues 2-14 Chain D 2–14（13 aa） Fragment：UNP Residues 2-14	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；20-28% PEG3350, 0.1M Bis-Tris pH 5.5, vapor diffusion, Sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP	Resolution 1.28 Å R-free 0.228
3MEV Crystal structure of SGF29 in complex with R2AK4me3 Deposited 2010-03-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 2–9（8 aa） Fragment：UNP Residues 2-9 Chain D 2–9（8 aa） Fragment：UNP Residues 2-9	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；20-28% PEG3350, 0.1M Bis-Tris pH 5.5, vapor diffusion, Sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP	Resolution 1.83 Å R-free 0.282
4HSU Crystal structure of LSD2-NPAC with H3(1-26)in space group P21 Deposited 2012-10-30	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 2–31（30 aa） Fragment：UNP residues 2-31	Mutation：K4M	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.99 Å R-free 0.232
4QEO crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH Deposited 2014-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain P 2–16（15 aa） Fragment：unp residues 2-16	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；30% PEG200, 5% PEG3000, and 0.1 M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.226
5OY7 Structure of the 4_601_157 tetranucleosome (P1 form) Deposited 2017-09-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric	Chain A 2–136（135 aa） Chain E 2–136（135 aa） Chain I 2–136（135 aa） Chain M 2–136（135 aa） Chain Q 2–136（135 aa） Chain U 2–136（135 aa） Chain Y 2–136（135 aa） Chain c 2–136（135 aa）	Not recorded	CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodyalte, pH 6.0	Resolution 5.77 Å R-free 0.238
6G0L Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome Deposited 2018-03-19	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 × 10 PDB declaration: dodecameric	Chain A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.00 Å
6UGM Structural basis of COMPASS eCM recognition of an unmodified nucleosome Deposited 2019-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain A 2–136（135 aa） Chain E 2–136（135 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
6UH5 Structural basis of COMPASS eCM recognition of the H2Bub nucleosome Deposited 2019-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric	Chain A 2–136（135 aa） Chain E 2–136（135 aa）	Not recorded	ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6VZ4 Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state Deposited 2020-02-27	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 A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；4 second blot time, blot force 20	Resolution 3.90 Å
7CRO NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP Deposited 2020-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain E 2–136（135 aa） Chain M 2–136（135 aa）	Mutation：K36Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K36Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF)	SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane	Resolution 3.75 Å
7CRP NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode) Deposited 2020-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain E 2–136（135 aa） Chain M 2–136（135 aa）	Mutation：K36Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K36Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF)	SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7CRQ NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode) Deposited 2020-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain E 2–136（135 aa） Chain M 2–136（135 aa）	Mutation：K36Nle,M90Nle,M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K36Nle,M90Nle,M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF)	SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane	Resolution 3.15 Å
7CRR Native NSD3 bound to 187-bp nucleosome Deposited 2020-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain E 2–136（135 aa） Chain M 2–136（135 aa）	Mutation：K36Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K36Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF)	SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane	Resolution 3.48 Å
7UNK Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex Deposited 2022-04-11	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 × 4 PDB declaration: tetrameric	Chain C 1–136（136 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å

22 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q92133_XENLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–11； UniProt 2–12

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3o7a
Deposition date deposition_date	2010-07-30
Structure title title	Crystal structure of PHF13 in complex with H3K4me3
Keywords keywords	PHF13; ZINC FINGER; PHD DOMAIN, NUCLEAR PROTEIN, Structural Genomics, Structural Genomics Consortium, SGC, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	12.16 Å
Radius of gyration Rg (electron density) rg_electron	10.87 Å
Forward intensity I(0) i0	1219460.00
Molecular weight molecular_weight	6972.0 kDa
Excluded volume excluded_volume	8558 Å³
Envelope volume envelope_volume	9482 Å³
Hydration-shell volume shell_volume	7736 Å³
Envelope diameter envelope_diameter	36.9 Å
Shell Rg shell_rg	16.05 Å
Envelope Rg envelope_rg	11.29 Å
Shape Rg shape_rg	10.91 Å
Total Rg total_rg	12.12 Å
Total atoms total_atoms	475
Residues n_residues	57
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

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

Maximum dimension Dmax dmax	39.5 Å
Rg (real space) rg_real	12.10 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.2190e+06
I(0) uncertainty (real space) i0_real_error	1.1170e+04
Rg (reciprocal space) rg_reciprocal	12.10 Å
I(0) (reciprocal space) i0_reciprocal	1219000.0000
Solution quality estimate total_estimate	0.8904
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.5 Å
Skewness Skewness skewness	0.159
Kurtosis Kurtosis kurtosis	-0.312
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	117900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PHD finger protein 13 variant
Molecular weight formula_weight	6058.2 kDa
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	535

SWDLVTCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRDS

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	H3K4ME3 HISTONE 11MER-PEPTIDE
Molecular weight formula_weight	1293.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ARTKQTARKST

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	60

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3o7aA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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8. Citations (1)

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Unit-cell length a length_a	21.232 Å
Unit-cell length b length_b	44.334 Å
Unit-cell length c length_c	60.330 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.670 Å
Low-resolution limit resolution_low	35.730 Å
R factor r_factor	0.1851
R_work r_work	0.1832
R_free r_free	0.2243

fit	/app/data/saxs_computation/o7/3o7a/3o7a.fit
pddf	/app/data/pr_computation/o7/3o7a/3o7a.pr.out
profile	/app/data/saxs_computation/o7/3o7a/3o7a.dat

Crystal structure of PHF13 in complex with H3K4me3

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

PHD finger protein 13 variant

State in the Current Structure

Other States of the Same Protein in the Database

H3K4ME3 HISTONE 11MER-PEPTIDE

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)