SAXSdb — 5yc1

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

TNF receptor-associated factor 4

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 290–470 Chain B； UniProt 290–470 Chain C； UniProt 290–470	Fragment：UNP residues 290-470	GPIb peptide × 1	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
2	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain D； UniProt 290–470 Chain E； UniProt 290–470 Chain F； UniProt 290–470	Fragment：UNP residues 290-470	GPIb peptide × 2	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

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 5YC1	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 mutation/modification Different oligomeric state 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 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
2YUC Solution structure of the TRAF-type zinc finger domains (102-164) from human TNF receptor associated factor 4 Deposited 2007-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 102–164（63 aa） Fragment：TRAF-type zinc finger domains	Not recorded	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
3ZJB The structure of the TRAF domain of human TRAF4 Deposited 2013-01-17	Different construct Different oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state 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
9OGV Identification of ligands for E3 ligases using fragment-based methods Deposited 2025-05-02	Different construct Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 9 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 1–181； UniProt 290–470 Author chain B； PDBConstruct 1–181； UniProt 290–470 Author chain C； PDBConstruct 1–181； UniProt 290–470 Author chain D； PDBConstruct 1–181； UniProt 290–470 Author chain E； PDBConstruct 1–181； UniProt 290–470 Author chain F； PDBConstruct 1–181； UniProt 290–470

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	5yc1
Deposition date deposition_date	2017-09-06
Structure title title	TRAF4_GPIb complex
Keywords keywords	Complex, Platelet receptor, TRAF4, interaction, SIGNALING PROTEIN-PEPTIDE complex; SIGNALING PROTEIN/PEPTIDE
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	42.02 Å
Radius of gyration Rg (electron density) rg_electron	41.82 Å
Forward intensity I(0) i0	173523000.00
Molecular weight molecular_weight	109880.0 kDa
Excluded volume excluded_volume	138600 Å³
Envelope volume envelope_volume	198790 Å³
Hydration-shell volume shell_volume	41745 Å³
Envelope diameter envelope_diameter	140.9 Å
Shell Rg shell_rg	44.13 Å
Envelope Rg envelope_rg	40.76 Å
Shape Rg shape_rg	41.80 Å
Total Rg total_rg	42.03 Å
Total atoms total_atoms	7805
Residues n_residues	964
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	139.3 Å
Rg (real space) rg_real	42.27 Å
Rg uncertainty (real space) rg_real_error	1.40 Å
I(0) (real space) i0_real	1.7350e+08
I(0) uncertainty (real space) i0_real_error	3.4320e+06
Rg (reciprocal space) rg_reciprocal	42.02 Å
I(0) (reciprocal space) i0_reciprocal	173500000.0000
Solution quality estimate total_estimate	0.8419
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.7 Å
Skewness Skewness skewness	0.436
Kurtosis Kurtosis kurtosis	-0.474
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12920000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.428

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	TNF receptor-associated factor 4
Molecular weight formula_weight	20712.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7834

QELQELRRELEELSVGSDGVLIWKIGSYGRRLQEAKAKPNLECFSPAFYTHKYGYKLQVSAFLNGNGSGEGTHLSLYIRVLPGAFDNLLEWPFARRVTFSLLDQSDPGLAKPQHVTETFHPDPNWKNFQKPGTWRGSLDESSLGFGYPKFISHQDIRKRNYVRDDAVFIRAAVELPRKILS

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 2 Entity 2 polymer

Description description	GPIb peptide
Molecular weight formula_weight	673.8 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,I,K

RLRAR

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5yc1A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

Domain ID domain_id	5yc1B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

Domain ID domain_id	5yc1C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

Domain ID domain_id	5yc1D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

Domain ID domain_id	5yc1E00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

Domain ID domain_id	5yc1F00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

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8. Citations (1)

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Unit-cell length a length_a	56.716 Å
Unit-cell length b length_b	88.594 Å
Unit-cell length c length_c	120.757 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.506 Å
Low-resolution limit resolution_low	33.781 Å
R factor r_factor	0.2141
R_work r_work	0.2114
R_free r_free	0.2649

fit	/app/data/saxs_computation/yc/5yc1/5yc1.fit
pddf	/app/data/pr_computation/yc/5yc1/5yc1.pr.out
profile	/app/data/saxs_computation/yc/5yc1/5yc1.dat

TRAF4_GPIb complex

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

TNF receptor-associated factor 4

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)