← Back to search
1weq

Solution structure of PHD domain in PHD finger protein 7

Method: SOLUTION NMR Dmax: 46.1 Å Quality: REASONABLE
▼

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

PHD finger protein 7

Mus musculus

UniProt Q9DAG9

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 232–303 Fragment：PHD domain ZN ZINC ION × 2 SOLUTION NMR NMR measurement conditions：pH 7；293 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：0.8mM U-15, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 0.1mM ZnCl2; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% 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 1WEQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8JWJ PHD Finger Protein 7 (PHF7) in complex with UBE2D2 Deposited 2023-06-29 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 28–307（280 aa）
Not recorded ZN ZINC ION × 7 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；277 K；MPD, Tris
Resolution 2.96 Å R-free 0.222
8JWJ PHD Finger Protein 7 (PHF7) in complex with UBE2D2 Deposited 2023-06-29 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 28–307（280 aa）
Not recorded ZN ZINC ION × 7 SO4 SULFATE ION × 1 GOL GLYCEROL × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；277 K；MPD, Tris
Resolution 2.96 Å R-free 0.222
8JWS ePHD domain of PHD Finger Protein 7 (PHF7) Deposited 2023-06-29 Different construct 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 28–149（122 aa）
Not recorded ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.7；277 K；PEG 3350, LiCl, Bicine
Resolution 2.00 Å R-free 0.223
8JWS ePHD domain of PHD Finger Protein 7 (PHF7) Deposited 2023-06-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–149（122 aa）
Not recorded ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.7；277 K；PEG 3350, LiCl, Bicine
Resolution 2.00 Å R-free 0.223
8JWS ePHD domain of PHD Finger Protein 7 (PHF7) Deposited 2023-06-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 28–149（122 aa）
Not recorded ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.7；277 K；PEG 3350, LiCl, Bicine
Resolution 2.00 Å R-free 0.223
8JWU PHD Finger Protein 7 (PHF7) fused to UBE2D2 via a (GSGG)3 linker Deposited 2023-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–307（280 aa）
Mutation：S346R,C409K ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG8000, DMSO, MOPS
Resolution 3.58 Å R-free 0.265
8JWU PHD Finger Protein 7 (PHF7) fused to UBE2D2 via a (GSGG)3 linker Deposited 2023-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–307（280 aa）
Mutation：S346R,C409K ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG8000, DMSO, MOPS
Resolution 3.58 Å R-free 0.265
8JWU PHD Finger Protein 7 (PHF7) fused to UBE2D2 via a (GSGG)3 linker Deposited 2023-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 28–307（280 aa）
Mutation：S346R,C409K ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG8000, DMSO, MOPS
Resolution 3.58 Å R-free 0.265

3 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PHF7_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–79； UniProt 232–303

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

SAXS scattering curve SAXS Profile

SAXS profile for 1weq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1weq
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1weq
Deposition date deposition_date2004-05-25
Structure title titleSolution structure of PHD domain in PHD finger protein 7
Keywords keywordsstructural genomics, PHD domain, PHD finger protein 7, RIKEN Structural Genomics/Proteomics Initiative, RSGI, GENE REGULATION; GENE REGULATION
Experimental Method methodSOLUTION NMR
▼

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

Radius of gyration Rg (Guinier) rg_guinier16.43 Å
Radius of gyration Rg (electron density) rg_electron16.44 Å
Forward intensity I(0) i0664341000.00
Molecular weight molecular_weight188780.0 kDa
Excluded volume excluded_volume224120 ų
Envelope volume envelope_volume61912 ų
Hydration-shell volume shell_volume21347 ų
Envelope diameter envelope_diameter82.7 Å
Shell Rg shell_rg31.05 Å
Envelope Rg envelope_rg28.40 Å
Shape Rg shape_rg16.49 Å
Total Rg total_rg16.71 Å
Total atoms total_atoms24800
Residues n_residues1700
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax46.1 Å
Rg (real space) rg_real14.97 Å
Rg uncertainty (real space) rg_real_error0.10 Å
I(0) (real space) i0_real6.3140e+08
I(0) uncertainty (real space) i0_real_error5.4640e+06
Rg (reciprocal space) rg_reciprocal16.98 Å
I(0) (reciprocal space) i0_reciprocal664300000.0000
Solution quality estimate total_estimate0.6615
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.5 Å
Skewness Skewness skewness0.559
Kurtosis Kurtosis kurtosis-0.083
Angular range angular_range— – 0.4850 Å−1
Current regularization parameter α current_alpha2.6630
Highest regularization parameter α highest_alpha181400.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.022; Oscil: 0.891; Stabil: 0.989; Sysdev: 0.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1weqa1
Class classg — Small proteins
Fold Fold foldg.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamilyg.50.1 — FYVE/PHD zinc finger
Family Family familyg.50.1.2 — PHD domain
Domain ID domain_idd1weqa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1weqa3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1weqA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
▶

8. Citations (1)

▶

9. Files and Curves (10)