SAXSdb — 7d8a

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

PHD finger protein 14

Danio rerio

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 278–487	Fragment：PHF14-PZP	Gene for histone H3 (germline gene) × 1 （V9H1G0） ZN ZINC ION × 5 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Hepes pH 7.5, 18% PEG4000, 12% isopropanol .	Resolution 2.00 Å R-free 0.212

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 7D8A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7D86 Crystal Structure of zebrafishPHF14-PZP Deposited 2020-10-07	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 278–487（210 aa） Fragment：PHF14-PZP	Not recorded	ZN ZINC ION × 5 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.2 M Magnesium chloride, 0.1 M Bis-Tris, 25 % v/v PEG 3350	Resolution 1.84 Å R-free 0.225
7D87 Crystal Structure of zebrafish PHF14-PZP in complex with H3(1-25) Deposited 2020-10-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 278–487（210 aa） Fragment：PHF14-PZP	Not recorded	ZN ZINC ION × 5 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1 M Carboxylic acids,0.1 M Buffer System 2, 37.50% % v/v MPD_P1K_P3350 (morpheus).	Resolution 2.11 Å R-free 0.204

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A286Y9D1_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–210； UniProt 278–487

Gene for histone H3 (germline gene)

Homo sapiens

UniProt V9H1G0

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 E； UniProt 2–13	Fragment：H3(1-13)	PHD finger protein 14 × 1 （A0A286Y9D1） ZN ZINC ION × 5 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Hepes pH 7.5, 18% PEG4000, 12% isopropanol .	Resolution 2.00 Å R-free 0.212

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 7D8A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5SZB Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with acetylated K14 Deposited 2016-08-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–19（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.2 M tri-sodium citrate, 0.1 M HEPES pH 7.5, 4% MPD	Resolution 1.20 Å R-free 0.155
5SZB Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with acetylated K14 Deposited 2016-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 2–19（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.2 M tri-sodium citrate, 0.1 M HEPES pH 7.5, 4% MPD	Resolution 1.20 Å R-free 0.155
5SZC Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with monomethylated K4 and acetylated K14 Deposited 2016-08-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–19（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.2 M tri-sodium citrate, 0.1 M HEPES pH 7.5, 4% MPD	Resolution 1.19 Å R-free 0.167
5Z93 Crystal Structure of SIRT3 in complex with H3K9bhb peptide Deposited 2018-02-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 7–16（10 aa） Fragment：UNP residues 7-16	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M MES pH 6.5, 25% PEG 1000	Resolution 1.95 Å R-free 0.210
5Z94 Crystal Structure of SIRT3 in complex with H3K4bhb peptide Deposited 2018-02-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–16（15 aa） Fragment：UNP residues 2-16	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Li2SO4, 0.1M sodium citrate, pH 6.0, 19% PEG 3,350	Resolution 1.90 Å R-free 0.191
5Z94 Crystal Structure of SIRT3 in complex with H3K4bhb peptide Deposited 2018-02-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–16（15 aa） Fragment：UNP residues 2-16	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Li2SO4, 0.1M sodium citrate, pH 6.0, 19% PEG 3,350	Resolution 1.90 Å R-free 0.191
7D87 Crystal Structure of zebrafish PHF14-PZP in complex with H3(1-25) Deposited 2020-10-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–26（25 aa） Fragment：histone H3(1-25)	Not recorded	ZN ZINC ION × 5 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1 M Carboxylic acids,0.1 M Buffer System 2, 37.50% % v/v MPD_P1K_P3350 (morpheus).	Resolution 2.11 Å R-free 0.204
8DS8 Crystal structure of human TNRC18 BAH domain in complex with H3K9me3 peptide Deposited 2022-07-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–24（23 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 6.5；277 K；0.1 M Sodium Cacodylate, pH 6.5, 0.2 M Magnesium Acetate, 16-20% PEG 8000	Resolution 1.84 Å R-free 0.235
8DS8 Crystal structure of human TNRC18 BAH domain in complex with H3K9me3 peptide Deposited 2022-07-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–24（23 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 6.5；277 K；0.1 M Sodium Cacodylate, pH 6.5, 0.2 M Magnesium Acetate, 16-20% PEG 8000	Resolution 1.84 Å R-free 0.235
8F8Z PHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide Deposited 2022-11-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–25（24 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 3.30 Å R-free 0.256
8F8Z PHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide Deposited 2022-11-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 2–25（24 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 SO4 SULFATE ION × 10 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 3.30 Å R-free 0.256
8UNI LSD1-CoREST with N-formyl-FAD in complex with H3K4M histone tail Deposited 2023-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–22（21 aa） Fragment：residues 1-21 (2-22 Uniprot numbering)	Mutation：K4M	HUF [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.2 M Sodium Potassium Tartrate, 100 mM ADA pH 6.5	Resolution 3.40 Å R-free 0.252
8UOM LSD1-CoREST with N-formyl-FAD in complex with H3dimeK4 histone tail Deposited 2023-10-20	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） Fragment：residues 1-21 (2-22 Uniprot numbering)	Non-standard monomer：Yes (specific site not provided by mmCIF)	HUF [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5	Resolution 3.20 Å R-free 0.240

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	V9H1G0_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–12； UniProt 2–13

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	7d8a
Deposition date deposition_date	2020-10-07
Structure title title	Crystal Structure of H3(1-13)/PHF14-PZP fusion protein
Keywords keywords	H3(1-13)/PHF14-PZP, GENE REGULATION; GENE REGULATION
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	18.51 Å
Radius of gyration Rg (electron density) rg_electron	17.48 Å
Forward intensity I(0) i0	11953200.00
Molecular weight molecular_weight	23618.0 kDa
Excluded volume excluded_volume	28601 Å³
Envelope volume envelope_volume	34639 Å³
Hydration-shell volume shell_volume	16807 Å³
Envelope diameter envelope_diameter	65.6 Å
Shell Rg shell_rg	23.42 Å
Envelope Rg envelope_rg	17.88 Å
Shape Rg shape_rg	17.50 Å
Total Rg total_rg	18.32 Å
Total atoms total_atoms	1622
Residues n_residues	210
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	65.5 Å
Rg (real space) rg_real	18.47 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.1950e+07
I(0) uncertainty (real space) i0_real_error	1.4710e+05
Rg (reciprocal space) rg_reciprocal	18.48 Å
I(0) (reciprocal space) i0_reciprocal	11950000.0000
Solution quality estimate total_estimate	0.8518
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.4 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	-0.109
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1692000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.697; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.995

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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 14
Molecular weight formula_weight	23262.2 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	1737

SSQRMEHILICCVCLGDNSEDADEIIQCDNCGVTVHEGCYGVDGESDSIMSSASENSTEPWFCDACKNGVSPSCELCPSQDGIFKETDAGRWVHVVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKECSLCEDTRFARTGVCISCDAGMCRSFFHVTCAQREGLLSEAAAEEDIADPFFAYCKQHADRFDRKWKRKNYLALQSYCKVS

来源 Source

来源生物 organism	Danio rerio
通用名 common_name	Zebrafish
NCBI Class编号 ncbi_taxonomy_id	7955
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Gene for histone H3 (germline gene)
Molecular weight formula_weight	1740.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

ARTKQTARKSTGGSGSGS

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 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	5

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 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	115

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8. Citations (1)

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Unit-cell length a length_a	41.781 Å
Unit-cell length b length_b	150.423 Å
Unit-cell length c length_c	81.420 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	40.710 Å
R factor r_factor	0.1810
R_work r_work	0.1774
R_free r_free	0.2123

fit	/app/data/saxs_computation/d8/7d8a/7d8a.fit
pddf	/app/data/pr_computation/d8/7d8a/7d8a.pr.out
profile	/app/data/saxs_computation/d8/7d8a/7d8a.dat

Crystal Structure of H3(1-13)/PHF14-PZP fusion protein

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

PHD finger protein 14

State in the Current Structure

Other States of the Same Protein in the Database

Gene for histone H3 (germline gene)

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

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)