SAXSdb — 2ecy

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

TNF receptor-associated factor 3

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 43–101	Fragment：RING-type, residues 8-66	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions：pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.10mM Protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 50uM Zncl2+1mM IDA; 10% D2O, 90% H2O \| 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 2ECY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FLK MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 Deposited 2000-08-14	Different construct 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 341–568（228 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.80 Å R-free 0.286
1FLK MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 Deposited 2000-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 341–568（228 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.80 Å R-free 0.286
1FLL MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 Deposited 2000-08-14	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 341–568（228 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å R-free 0.312
1FLL MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 Deposited 2000-08-14	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 B 341–568（228 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å R-free 0.312
1FLL MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 Deposited 2000-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 341–568（228 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å R-free 0.312
1KZZ DOWNSTREAM REGULATOR TANK BINDS TO THE CD40 RECOGNITION SITE ON TRAF3 Deposited 2002-02-08	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 377–568（192 aa） Fragment：Residues 377-568	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；298 K；100mM MES, 15% PEG1000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.50 Å R-free 0.307
1KZZ DOWNSTREAM REGULATOR TANK BINDS TO THE CD40 RECOGNITION SITE ON TRAF3 Deposited 2002-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 377–568（192 aa） Fragment：Residues 377-568	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；298 K；100mM MES, 15% PEG1000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.50 Å R-free 0.307
1L0A DOWNSTREAM REGULATOR TANK BINDS TO THE CD40 RECOGNITION SITE ON TRAF3 Deposited 2002-02-08	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 × 2 PDB declaration: dimeric	Chain A 377–568（192 aa） Fragment：Residues 377-568	Mutation：T195K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；100mM MES, 15% PEG1000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.295
1L0A DOWNSTREAM REGULATOR TANK BINDS TO THE CD40 RECOGNITION SITE ON TRAF3 Deposited 2002-02-08	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 × 6 PDB declaration: hexameric	Chain A 377–568（192 aa） Fragment：Residues 377-568	Mutation：T195K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；100mM MES, 15% PEG1000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.295
1RF3 Structurally Distinct Recognition Motifs in Lymphotoxin-B Receptor and CD40 for TRAF-mediated Signaling Deposited 2003-11-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 377–568（192 aa） Fragment：Recognition motif (residues 377-568)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；15% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å R-free 0.315
1ZMS LMP1 Protein binds to TRAF3 as a structural CD40 Deposited 2005-05-10	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 377–568（192 aa） Fragment：Sequence database residues 377-568	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；15% PEG 4000, 0.1 M MES, pH 6.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.80 Å R-free 0.255
1ZMS LMP1 Protein binds to TRAF3 as a structural CD40 Deposited 2005-05-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 377–568（192 aa） Fragment：Sequence database residues 377-568	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；15% PEG 4000, 0.1 M MES, pH 6.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.80 Å R-free 0.255
2GKW Key contacts promote recongnito of BAFF-R by TRAF3 Deposited 2006-04-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 377–568（192 aa） Fragment：TRAF domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；15% PEG 4000, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.260
8T5P SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain Deposited 2023-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 377–568（192 aa） Fragment：TRAF domain (UNP residues 377-568) Chain B 377–568（192 aa） Fragment：TRAF domain (UNP residues 377-568) Chain C 377–568（192 aa） Fragment：TRAF domain (UNP residues 377-568)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；13% PEG3350, 0.1 M Tris, pH 8.0, 0.25 M ammonium sulfate	Resolution 2.50 Å R-free 0.242
8T5P SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain Deposited 2023-06-14	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 × 4 PDB declaration: tetrameric	Chain D 377–568（192 aa） Fragment：TRAF domain (UNP residues 377-568) Chain E 377–568（192 aa） Fragment：TRAF domain (UNP residues 377-568) Chain F 377–568（192 aa） Fragment：TRAF domain (UNP residues 377-568)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；13% PEG3350, 0.1 M Tris, pH 8.0, 0.25 M ammonium sulfate	Resolution 2.50 Å R-free 0.242
8ZUK Cluster structure of the BAFF-BAFFR-TRAF3 complex Deposited 2024-06-09	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 × 42 PDB declaration: 42-meric	Chain A 267–568（302 aa） Chain B 267–568（302 aa） Chain C 267–568（302 aa） Chain G 267–568（302 aa） Chain H 267–568（302 aa） Chain I 267–568（302 aa） Chain M 267–568（302 aa） Chain N 267–568（302 aa） Chain O 267–568（302 aa） Chain S 267–568（302 aa） Chain T 267–568（302 aa） Chain U 267–568（302 aa） Chain Y 267–568（302 aa） Chain Z 267–568（302 aa） Chain a 267–568（302 aa） Chain e 267–568（302 aa） Chain f 267–568（302 aa） Chain g 267–568（302 aa） Chain k 267–568（302 aa） Chain l 267–568（302 aa） Chain m 267–568（302 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å

9 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRAF3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–66； UniProt 43–101

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	2ecy
Deposition date deposition_date	2007-02-14
Structure title title	Solution structure of the Zinc finger, C3HC4 type (RING finger)" domain of TNF receptor-associated factor 3
Keywords keywords	;Metal Binding Protein, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, APOPTOSIS ;; APOPTOSIS
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.67 Å
Radius of gyration Rg (electron density) rg_electron	15.90 Å
Forward intensity I(0) i0	350002000.00
Molecular weight molecular_weight	144820.0 kDa
Excluded volume excluded_volume	175990 Å³
Envelope volume envelope_volume	40744 Å³
Hydration-shell volume shell_volume	15069 Å³
Envelope diameter envelope_diameter	75.1 Å
Shell Rg shell_rg	29.50 Å
Envelope Rg envelope_rg	27.66 Å
Shape Rg shape_rg	16.02 Å
Total Rg total_rg	15.95 Å
Total atoms total_atoms	17640
Residues n_residues	1320
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	70.1 Å
Rg (real space) rg_real	16.46 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	3.5000e+08
I(0) uncertainty (real space) i0_real_error	4.6700e+06
Rg (reciprocal space) rg_reciprocal	16.37 Å
I(0) (reciprocal space) i0_reciprocal	350000000.0000
Solution quality estimate total_estimate	0.6158
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	13.3 Å
Skewness Skewness skewness	1.107
Kurtosis Kurtosis kurtosis	0.610
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	145600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.001; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.999

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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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8. Citations (1)

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Description description	TNF receptor-associated factor 3
Molecular weight formula_weight	7136.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	17640

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

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

fit	/app/data/saxs_computation/ec/2ecy/2ecy.fit
pddf	/app/data/pr_computation/ec/2ecy/2ecy.pr.out
profile	/app/data/saxs_computation/ec/2ecy/2ecy.dat

Solution structure of the Zinc finger, C3HC4 type (RING finger)" domain of TNF receptor-associated factor 3

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

TNF receptor-associated factor 3

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)