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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count | Chain A; UniProt 377–568 | Fragment:Recognition motif (residues 377-568) | 24-residue peptide from Lymphotoxin-B Receptor × 3 (P36941) | 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 |
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 1RF3 | 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 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 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 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 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 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 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 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 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 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 |
| 1ZMS LMP1 Protein binds to TRAF3 as a structural CD40 Deposited 2005-05-10 | Different construct Different oligomeric state 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 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 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 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 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 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 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 1–192; UniProt 377–568 |