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4bkw

Crystal structure of the C-terminal region of human ZFYVE9

Method: X-RAY DIFFRACTION Dmax: 78.4 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 9

HOMO SAPIENS

UniProt O95405

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 895–1425 Fragment：PROTEIN INTERACTING DOMAIN, RESIDUES 895-1425 EDO 1,2-ETHANEDIOL × 5 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；0.1M BIS-TRIS PH 6.5, 0.15M MAGNESIUM CHLORIDE, 30% PEG 3350 Resolution 2.53 Å R-free 0.247

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 4BKW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DEV CRYSTAL STRUCTURE OF SMAD2 MH2 DOMAIN BOUND TO THE SMAD-BINDING DOMAIN OF SARA Deposited 1999-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 669–709（41 aa） Fragment：SARA SMAD2-BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；TRIS, DIOXANE, AMMONIUM SULFATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Resolution 2.20 Å R-free 0.276
1DEV CRYSTAL STRUCTURE OF SMAD2 MH2 DOMAIN BOUND TO THE SMAD-BINDING DOMAIN OF SARA Deposited 1999-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 669–709（41 aa） Fragment：SARA SMAD2-BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；TRIS, DIOXANE, AMMONIUM SULFATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Resolution 2.20 Å R-free 0.276
1MK2 SMAD3 SBD complex Deposited 2002-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 773–810（38 aa） Fragment：SARA SBD domain, residues 773-810
Not recorded ACY ACETIC ACID × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.74 Å R-free 0.271
1MK2 SMAD3 SBD complex Deposited 2002-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 773–810（38 aa） Fragment：SARA SBD domain, residues 773-810
Not recorded ACY ACETIC ACID × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.74 Å R-free 0.271
5MJY Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (SARA complex structure) Deposited 2016-12-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–22（22 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.1 M MMT buffer pH 9.0, 25% PEG1500
Resolution 2.25 Å R-free 0.235
5MJY Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (SARA complex structure) Deposited 2016-12-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–22（22 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.1 M MMT buffer pH 9.0, 25% PEG1500
Resolution 2.25 Å R-free 0.235

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ZFYV9_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–531； UniProt 895–1425

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 4bkw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4bkw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4bkw
Deposition date deposition_date2013-04-30
Structure title titleCrystal structure of the C-terminal region of human ZFYVE9
Keywords keywordsRECEPTOR, PROTEIN INTERACTION DOMAIN, TGF-BETA AND EGFR SIGNALLING, SGC; RECEPTOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.94 Å
Radius of gyration Rg (electron density) rg_electron24.82 Å
Forward intensity I(0) i043839200.00
Molecular weight molecular_weight52937.0 kDa
Excluded volume excluded_volume67084 ų
Envelope volume envelope_volume83903 ų
Hydration-shell volume shell_volume28173 ų
Envelope diameter envelope_diameter80.4 Å
Shell Rg shell_rg32.02 Å
Envelope Rg envelope_rg24.80 Å
Shape Rg shape_rg24.80 Å
Total Rg total_rg25.77 Å
Total atoms total_atoms3721
Residues n_residues479
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax78.4 Å
Rg (real space) rg_real25.86 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real4.3840e+07
I(0) uncertainty (real space) i0_real_error5.9070e+05
Rg (reciprocal space) rg_reciprocal25.89 Å
I(0) (reciprocal space) i0_reciprocal43840000.0000
Solution quality estimate total_estimate0.9125
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.6 Å
Skewness Skewness skewness0.222
Kurtosis Kurtosis kurtosis-0.553
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11760000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.940
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4bkwA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily220 — Domain of unknown function (DUF3480), N-terminal subdomain
Domain ID domain_id4bkwA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily40 —
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8. Citations (1)

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9. Files and Curves (10)