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2yuc

Solution structure of the TRAF-type zinc finger domains (102-164) from human TNF receptor associated factor 4

Method: SOLUTION NMR Dmax: 74.5 Å Quality: SUSPICIOUS
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TNF receptor-associated factor 4

Homo sapiens

UniProt Q9BUZ4

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 102–164 Fragment：TRAF-type zinc finger domains ZN ZINC ION × 2 SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.24mM U-15N, 13C-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM DTT; 0.02% NaN3; 0.05mM ZnCl2; 1mM IDA, 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 2YUC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2EOD Solution structure of TRAF-type zinc finger domains (190- 248) from human TNF receptor-associated factor 4 Deposited 2007-03-29 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 190–248（59 aa） Fragment：zf-TRAF, UNP residues 190-248
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.13mM uniformly 13C,15N-labeled protein; 20mM TrisHCl; 100mM NaCl; 1mM DTT; 0.02% NaN3; 0.05mM ZnCl2; 1mM IDA; 10% D2O, 90% H2O | 10% D2O, 90% H2O
Resolution not provided
3ZJB The structure of the TRAF domain of human TRAF4 Deposited 2013-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 283–470（188 aa） Fragment：MATH DOMAIN, RESIDUES 283-470
Chain B 283–470（188 aa） Fragment：MATH DOMAIN, RESIDUES 283-470
Chain C 283–470（188 aa） Fragment：MATH DOMAIN, RESIDUES 283-470
Not recorded CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；15% PEG 4000, 0.1M HEPES PH 7.0
Resolution 1.84 Å R-free 0.200
4K8U Crystal structure of TRAF4 TRAF domain Deposited 2013-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 281–470（190 aa） Fragment：UNP residues 281-470
Chain B 281–470（190 aa） Fragment：UNP residues 281-470
Chain C 281–470（190 aa） Fragment：UNP residues 281-470
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；13% PEG 3350, 0.14M Magnessium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.281
4M4E TRAF domain of human TRAF4 Deposited 2013-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 292–466（175 aa）
Chain B 292–466（175 aa）
Chain C 292–466（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；289 K；0.2M Ammonium fluoride, 20%(w/v) Polyethylene glycol 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.60 Å R-free 0.277
5YC1 TRAF4_GPIb complex Deposited 2017-09-06 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 × 4 PDB declaration: tetrameric
Chain A 290–470（181 aa） Fragment：UNP residues 290-470
Chain B 290–470（181 aa） Fragment：UNP residues 290-470
Chain C 290–470（181 aa） Fragment：UNP residues 290-470
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；magnesium formate dehydrate, polyethylene glycol 3350
Resolution 2.51 Å R-free 0.265
5YC1 TRAF4_GPIb complex Deposited 2017-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 290–470（181 aa） Fragment：UNP residues 290-470
Chain E 290–470（181 aa） Fragment：UNP residues 290-470
Chain F 290–470（181 aa） Fragment：UNP residues 290-470
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；magnesium formate dehydrate, polyethylene glycol 3350
Resolution 2.51 Å R-free 0.265
9OGV Identification of ligands for E3 ligases using fragment-based methods Deposited 2025-05-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 292–466（175 aa）
Chain B 292–466（175 aa）
Chain C 292–466（175 aa）
Not recorded A1CA9 N-(1,3-thiazol-2-yl)quinoxaline-6-carboxamide × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；10-15% PEG 3350, 0.1 M Bis-TRIS pH 6.5
Resolution 2.80 Å R-free 0.295
9OLB Identification of ligands for E3 ligases using fragment-based methods Deposited 2025-05-12 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 292–466（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10-15% PEG 3350, 0.1 M Bis-TRIS pH 6.5
Resolution 2.62 Å R-free 0.276
9OLB Identification of ligands for E3 ligases using fragment-based methods Deposited 2025-05-12 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 292–466（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10-15% PEG 3350, 0.1 M Bis-TRIS pH 6.5
Resolution 2.62 Å R-free 0.276
9OLB Identification of ligands for E3 ligases using fragment-based methods Deposited 2025-05-12 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 292–466（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10-15% PEG 3350, 0.1 M Bis-TRIS pH 6.5
Resolution 2.62 Å R-free 0.276

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRAF4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–70； UniProt 102–164

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 2yuc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2yuc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2yuc
Deposition date deposition_date2007-04-06
Structure title titleSolution structure of the TRAF-type zinc finger domains (102-164) from human TNF receptor associated factor 4
Keywords keywords;zf-TRAF, Cysteine-rich domain associated with RING and Traf domains protein 1, Malignant 62, RING finger protein 83, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.53 Å
Radius of gyration Rg (electron density) rg_electron16.40 Å
Forward intensity I(0) i0538450000.00
Molecular weight molecular_weight166600.0 kDa
Excluded volume excluded_volume196710 ų
Envelope volume envelope_volume52980 ų
Hydration-shell volume shell_volume20779 ų
Envelope diameter envelope_diameter74.0 Å
Shell Rg shell_rg28.20 Å
Envelope Rg envelope_rg22.07 Å
Shape Rg shape_rg16.46 Å
Total Rg total_rg16.64 Å
Total atoms total_atoms21800
Residues n_residues1520
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 dmax74.5 Å
Rg (real space) rg_real16.75 Å
Rg uncertainty (real space) rg_real_error0.89 Å
I(0) (real space) i0_real5.3850e+08
I(0) uncertainty (real space) i0_real_error7.2150e+06
Rg (reciprocal space) rg_reciprocal16.73 Å
I(0) (reciprocal space) i0_reciprocal538400000.0000
Solution quality estimate total_estimate0.4594
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.5 Å
Skewness Skewness skewness0.559
Kurtosis Kurtosis kurtosis-0.097
Angular range angular_range— – 0.4800 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha345600.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.298; Stabil: 1.000; Sysdev: 0.338; Positv: 1.000; Valcen: 0.061; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2yucA01
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)
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8. Citations (1)

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9. Files and Curves (10)