SAXSdb — 8zuk

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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 heterocomplex Heteromer Protein × 42 PDB declaration: 42-meric（42） Consistent with protein copy count	Chain A； UniProt 267–568 Chain B； UniProt 267–568 Chain C； UniProt 267–568 Chain G； UniProt 267–568 Chain H； UniProt 267–568 Chain I； UniProt 267–568 Chain M； UniProt 267–568 Chain N； UniProt 267–568 Chain O； UniProt 267–568 Chain S； UniProt 267–568 Chain T； UniProt 267–568 Chain U； UniProt 267–568 Chain Y； UniProt 267–568 Chain Z； UniProt 267–568 Chain a； UniProt 267–568 Chain e； UniProt 267–568 Chain f； UniProt 267–568 Chain g； UniProt 267–568 Chain k； UniProt 267–568 Chain l； UniProt 267–568 Chain m； UniProt 267–568	Not recorded	Tumor necrosis factor receptor superfamily member 13C × 21 （Q96RJ3）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.83 Å

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 8ZUK	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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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
2ECY Solution structure of the Zinc finger, C3HC4 type (RING finger)" domain of TNF receptor-associated factor 3 Deposited 2007-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–101（59 aa） Fragment：RING-type, residues 8-66	Not recorded	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
2GKW Key contacts promote recongnito of BAFF-R by TRAF3 Deposited 2006-04-03	Different construct Different mutation/modification Different oligomeric state 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 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 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

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 2–303； UniProt 267–568 Author chain B； PDBConstruct 2–303； UniProt 267–568 Author chain C； PDBConstruct 2–303； UniProt 267–568 Author chain G； PDBConstruct 2–303； UniProt 267–568 Author chain H； PDBConstruct 2–303； UniProt 267–568 Author chain I； PDBConstruct 2–303； UniProt 267–568 Author chain M； PDBConstruct 2–303； UniProt 267–568 Author chain N； PDBConstruct 2–303； UniProt 267–568 Author chain O； PDBConstruct 2–303； UniProt 267–568 Author chain S； PDBConstruct 2–303； UniProt 267–568 Author chain T； PDBConstruct 2–303； UniProt 267–568 Author chain U； PDBConstruct 2–303； UniProt 267–568 Author chain Y； PDBConstruct 2–303； UniProt 267–568 Author chain Z； PDBConstruct 2–303； UniProt 267–568 Author chain a； PDBConstruct 2–303； UniProt 267–568 Author chain e； PDBConstruct 2–303； UniProt 267–568 Author chain f； PDBConstruct 2–303； UniProt 267–568 Author chain g； PDBConstruct 2–303； UniProt 267–568 Author chain k； PDBConstruct 2–303； UniProt 267–568 Author chain l； PDBConstruct 2–303； UniProt 267–568 Author chain m； PDBConstruct 2–303； UniProt 267–568

Tumor necrosis factor receptor superfamily member 13C

Homo sapiens

UniProt Q96RJ3

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 × 42 PDB declaration: 42-meric（42） Consistent with protein copy count	Chain D； UniProt 1–184 Chain E； UniProt 1–184 Chain F； UniProt 1–184 Chain J； UniProt 1–184 Chain K； UniProt 1–184 Chain L； UniProt 1–184 Chain P； UniProt 1–184 Chain Q； UniProt 1–184 Chain R； UniProt 1–184 Chain V； UniProt 1–184 Chain W； UniProt 1–184 Chain X； UniProt 1–184 Chain b； UniProt 1–184 Chain c； UniProt 1–184 Chain d； UniProt 1–184 Chain h； UniProt 1–184 Chain i； UniProt 1–184 Chain j； UniProt 1–184 Chain n； UniProt 1–184 Chain o； UniProt 1–184 Chain p； UniProt 1–184	Not recorded	TNF receptor-associated factor 3 × 21 （Q13114）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.83 Å

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 8ZUK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1MPV Structure of bhpBR3, the BAFF-binding loop of BR3 embedded in a beta-hairpin peptide Deposited 2002-09-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–31（6 aa） Fragment：BR3 loop (residues 26-31)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；293 K；Ionic strength (raw mmCIF value) no added salt；Pressure ambient NMR sample composition 2.9 mM bhpBR3 peptide \| 92% H2O, 8% D2O, 0.1 mM DSS, pH 4.5 NMR sample composition 2.9 mM bhpBR3 peptide \| 100% D2O, 0.1 mM DSS, pH 4.5	Resolution not provided
1OQE Crystal structure of sTALL-1 with BAFF-R Deposited 2003-03-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 108 PDB declaration: 108-meric	Chain K 16–46（31 aa） Fragment：extracellular domain Chain L 16–46（31 aa） Fragment：extracellular domain Chain M 16–46（31 aa） Fragment：extracellular domain Chain N 16–46（31 aa） Fragment：extracellular domain Chain O 16–46（31 aa） Fragment：extracellular domain Chain P 16–46（31 aa） Fragment：extracellular domain Chain Q 16–46（31 aa） Fragment：extracellular domain Chain R 16–46（31 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 2.50 Å R-free 0.259
1OSX Solution Structure of the Extracellular Domain of BLyS Receptor 3 (BR3) Deposited 2003-03-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–61（61 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；293 K；Ionic strength (raw mmCIF value) 50 mM NaCl, 25 mM Na2PO4；Pressure ambient NMR sample composition 1.5 mM BR3 U-15N,25 mM Na2PO4, 50 mM NaCl, 0.1 mM NaN3, 0.1 mM DSS-d10 \| 92%H2O/8%D2O NMR sample composition 1.5 mM BR3 U-15N,13C,25 mM Na2PO4, 50 mM NaCl, 0.1 mM NaN3, 0.1 mM DSS-d10 \| 92%H2O/8%D2O NMR sample composition 1.5 mM BR3 U-15N,13C,25 mM Na2PO4, 50 mM NaCl, 0.1 mM NaN3, 0.1 mM DSS-d10 \| 100% D2O	Resolution not provided
2HFG Crystal structure of hBR3 bound to CB3s-Fab Deposited 2006-06-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 7–54（48 aa） Fragment：cysteine rich domain (residues 7-54)	Mutation：V20N, L27P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions Drops contained 2.1 microliters protein solution (pH 6.5) and 2.9 microliters of (0.1M citric acid pH 3.0, 24% PEG 3350, and 0.1 M Praseodymium (III) acetate) over a reservoir of 24% PEG 3350. pH of final drop ~4.5.	Resolution 2.61 Å R-free 0.252
4V46 Crystal structure of the BAFF-BAFF-R complex Deposited 2003-03-23	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 × 120 PDB declaration: 120-meric	Chain B0 1–63（63 aa） Fragment：residues 1-63 Chain B1 1–63（63 aa） Fragment：residues 1-63 Chain B2 1–63（63 aa） Fragment：residues 1-63 Chain B3 1–63（63 aa） Fragment：residues 1-63 Chain B4 1–63（63 aa） Fragment：residues 1-63 Chain B5 1–63（63 aa） Fragment：residues 1-63 Chain B6 1–63（63 aa） Fragment：residues 1-63 Chain B7 1–63（63 aa） Fragment：residues 1-63 Chain B8 1–63（63 aa） Fragment：residues 1-63 Chain B9 1–63（63 aa） Fragment：residues 1-63 Chain BA 1–63（63 aa） Fragment：residues 1-63 Chain BB 1–63（63 aa） Fragment：residues 1-63 Chain BC 1–63（63 aa） Fragment：residues 1-63 Chain BD 1–63（63 aa） Fragment：residues 1-63 Chain BE 1–63（63 aa） Fragment：residues 1-63 Chain BF 1–63（63 aa） Fragment：residues 1-63 Chain BG 1–63（63 aa） Fragment：residues 1-63 Chain BH 1–63（63 aa） Fragment：residues 1-63 Chain BI 1–63（63 aa） Fragment：residues 1-63 Chain BJ 1–63（63 aa） Fragment：residues 1-63 Chain BK 1–63（63 aa） Fragment：residues 1-63 Chain BL 1–63（63 aa） Fragment：residues 1-63 Chain BM 1–63（63 aa） Fragment：residues 1-63 Chain BN 1–63（63 aa） Fragment：residues 1-63 Chain BO 1–63（63 aa） Fragment：residues 1-63 Chain BP 1–63（63 aa） Fragment：residues 1-63 Chain BQ 1–63（63 aa） Fragment：residues 1-63 Chain BR 1–63（63 aa） Fragment：residues 1-63 Chain BS 1–63（63 aa） Fragment：residues 1-63 Chain BT 1–63（63 aa） Fragment：residues 1-63 Chain BU 1–63（63 aa） Fragment：residues 1-63 Chain BV 1–63（63 aa） Fragment：residues 1-63 Chain BW 1–63（63 aa） Fragment：residues 1-63 Chain BX 1–63（63 aa） Fragment：residues 1-63 Chain BY 1–63（63 aa） Fragment：residues 1-63 Chain BZ 1–63（63 aa） Fragment：residues 1-63 Chain Ba 1–63（63 aa） Fragment：residues 1-63 Chain Bb 1–63（63 aa） Fragment：residues 1-63 Chain Bc 1–63（63 aa） Fragment：residues 1-63 Chain Bd 1–63（63 aa） Fragment：residues 1-63 Chain Be 1–63（63 aa） Fragment：residues 1-63 Chain Bf 1–63（63 aa） Fragment：residues 1-63 Chain Bg 1–63（63 aa） Fragment：residues 1-63 Chain Bh 1–63（63 aa） Fragment：residues 1-63 Chain Bi 1–63（63 aa） Fragment：residues 1-63 Chain Bj 1–63（63 aa） Fragment：residues 1-63 Chain Bk 1–63（63 aa） Fragment：residues 1-63 Chain Bl 1–63（63 aa） Fragment：residues 1-63 Chain Bm 1–63（63 aa） Fragment：residues 1-63 Chain Bn 1–63（63 aa） Fragment：residues 1-63 Chain Bo 1–63（63 aa） Fragment：residues 1-63 Chain Bp 1–63（63 aa） Fragment：residues 1-63 Chain Bq 1–63（63 aa） Fragment：residues 1-63 Chain Br 1–63（63 aa） Fragment：residues 1-63 Chain Bs 1–63（63 aa） Fragment：residues 1-63 Chain Bt 1–63（63 aa） Fragment：residues 1-63 Chain Bu 1–63（63 aa） Fragment：residues 1-63 Chain Bv 1–63（63 aa） Fragment：residues 1-63 Chain Bw 1–63（63 aa） Fragment：residues 1-63 Chain Bx 1–63（63 aa） Fragment：residues 1-63	Not recorded	MG MAGNESIUM ION × 40	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；sodium formate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.30 Å R-free 0.226
8ZUJ Pentagonal cluster of BAFF-BAFFR ectodomain complex Deposited 2024-06-09	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain A 2–78（77 aa） Chain B 2–78（77 aa） Chain C 2–78（77 aa） Chain G 2–78（77 aa） Chain H 2–78（77 aa） Chain I 2–78（77 aa） Chain M 2–78（77 aa） Chain N 2–78（77 aa） Chain O 2–78（77 aa） Chain S 2–78（77 aa） Chain T 2–78（77 aa） Chain U 2–78（77 aa） Chain Y 2–78（77 aa） Chain Z 2–78（77 aa） Chain a 2–78（77 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.58 Å

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

View Construct and Data Evidence

UniProt name	TR13C_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–184； UniProt 1–184 Author chain E； PDBConstruct 1–184； UniProt 1–184 Author chain F； PDBConstruct 1–184； UniProt 1–184 Author chain J； PDBConstruct 1–184； UniProt 1–184 Author chain K； PDBConstruct 1–184； UniProt 1–184 Author chain L； PDBConstruct 1–184； UniProt 1–184 Author chain P； PDBConstruct 1–184； UniProt 1–184 Author chain Q； PDBConstruct 1–184； UniProt 1–184 Author chain R； PDBConstruct 1–184； UniProt 1–184 Author chain V； PDBConstruct 1–184； UniProt 1–184 Author chain W； PDBConstruct 1–184； UniProt 1–184 Author chain X； PDBConstruct 1–184； UniProt 1–184 Author chain b； PDBConstruct 1–184； UniProt 1–184 Author chain c； PDBConstruct 1–184； UniProt 1–184 Author chain d； PDBConstruct 1–184； UniProt 1–184 Author chain h； PDBConstruct 1–184； UniProt 1–184 Author chain i； PDBConstruct 1–184； UniProt 1–184 Author chain j； PDBConstruct 1–184； UniProt 1–184 Author chain n； PDBConstruct 1–184； UniProt 1–184 Author chain o； PDBConstruct 1–184； UniProt 1–184 Author chain p； PDBConstruct 1–184； UniProt 1–184

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	8zuk
Deposition date deposition_date	2024-06-09
Structure title title	Cluster structure of the BAFF-BAFFR-TRAF3 complex
Keywords keywords	Receptor cluster, Signal complex, membrane receptor, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	71.87 Å
Radius of gyration Rg (electron density) rg_electron	71.76 Å
Forward intensity I(0) i0	2842240000.00
Molecular weight molecular_weight	463310.0 kDa
Excluded volume excluded_volume	584640 Å³
Envelope volume envelope_volume	924550 Å³
Hydration-shell volume shell_volume	108570 Å³
Envelope diameter envelope_diameter	219.2 Å
Shell Rg shell_rg	66.52 Å
Envelope Rg envelope_rg	69.52 Å
Shape Rg shape_rg	71.74 Å
Total Rg total_rg	71.77 Å
Total atoms total_atoms	32550
Residues n_residues	4116
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	213.9 Å
Rg (real space) rg_real	71.82 Å
Rg uncertainty (real space) rg_real_error	1.63 Å
I(0) (real space) i0_real	2.8420e+09
I(0) uncertainty (real space) i0_real_error	6.0830e+07
Rg (reciprocal space) rg_reciprocal	71.80 Å
I(0) (reciprocal space) i0_reciprocal	2842000000.0000
Solution quality estimate total_estimate	0.8443
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	87.5 Å
Skewness Skewness skewness	0.150
Kurtosis Kurtosis kurtosis	-0.743
Angular range angular_range	— – 0.1100 Å⁻¹
Current regularization parameter α current_alpha	0.0023
Highest regularization parameter α highest_alpha	81340000.0000
Real-space data points n_real_points	23
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.996; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; 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)

Entity 1 Entity 1 polymer

Description description	TNF receptor-associated factor 3
Molecular weight formula_weight	35444.4 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	21

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,G,H,I,M,N,O,S,T,U,Y,Z,a,e,f,g,k,l,m
Atom count atom_count	32550

MSNSLEKKVSLLQNESVEKNKSIQSLHNQICSFEIEIERQKEMLRNNESKILHLQRVIDSQAEKLKELDKEIRPFRQNWEEADSMKSSVESLQNRVTELESVDKSAGQVARNTGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVDTSDLPDPGGSLVPR

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Tumor necrosis factor receptor superfamily member 13C
Molecular weight formula_weight	19902.8 kDa
Source method src_method	man
Copy count entity_count	21

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F,J,K,L,P,Q,R,V,W,X,b,c,d,h,i,j,n,o,p

MRRGPRSLRGRDAPAPTPCVPAECFDLLVRHCVACGLLRTPRPKPAGASSPAPRTALQPQESVGAGAGEAALPLPGLLFGAPALLGLALVLALVLVGLVSWRRRQRRLRGASSAEAPDGDKDAPEPLDKVIILSPGISDATAPAWPPPGEDPGTTPPGHSVPVPATELGSTELVTTKTAGPEQQSNSLEVLFQ

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	Homo sapiens

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	2.83 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	205165

fit	/app/data/saxs_computation/zu/8zuk/8zuk.fit
pddf	/app/data/pr_computation/zu/8zuk/8zuk.pr.out
profile	/app/data/saxs_computation/zu/8zuk/8zuk.dat

Cluster structure of the BAFF-BAFFR-TRAF3 complex

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

Tumor necrosis factor receptor superfamily member 13C

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)