1d0j

STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE

Method: X-RAY DIFFRACTION D_max: 127.7 Å Quality: GOOD

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

TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 334–501 Chain B； UniProt 334–501 Chain C； UniProt 334–501	Fragment：TRAF DOMAIN	4-1BB LIGAND RECEPTOR × 2 （P20334）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.50 Å R-free 0.270
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain D； UniProt 334–501 Chain E； UniProt 334–501 Chain F； UniProt 334–501	Fragment：TRAF DOMAIN	4-1BB LIGAND RECEPTOR × 3 （P20334）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.50 Å R-free 0.270
3	Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count	Chain A； UniProt 334–501 Chain B； UniProt 334–501 Chain C； UniProt 334–501 Chain D； UniProt 334–501 Chain E； UniProt 334–501 Chain F； UniProt 334–501	Fragment：TRAF DOMAIN	4-1BB LIGAND RECEPTOR × 5 （P20334）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.50 Å R-free 0.270
4	Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count	Chain A； UniProt 334–501 Chain B； UniProt 334–501 Chain C； UniProt 334–501 Chain D； UniProt 334–501 Chain E； UniProt 334–501 Chain F； UniProt 334–501	Fragment：TRAF DOMAIN	4-1BB LIGAND RECEPTOR × 5 （P20334）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.50 Å R-free 0.270

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 1D0J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CA4 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) Deposited 1999-02-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.20 Å R-free 0.251
1CA4 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) Deposited 1999-02-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.20 Å R-free 0.251
1CA9 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A PEPTIDE FROM TNF-R2 Deposited 1999-02-25	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 310–501（192 aa） Fragment：TRAF DOMAIN Chain B 310–501（192 aa） Fragment：TRAF DOMAIN Chain C 310–501（192 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.30 Å R-free 0.289
1CA9 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A PEPTIDE FROM TNF-R2 Deposited 1999-02-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 310–501（192 aa） Fragment：TRAF DOMAIN Chain E 310–501（192 aa） Fragment：TRAF DOMAIN Chain F 310–501（192 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.30 Å R-free 0.289
1CA9 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A PEPTIDE FROM TNF-R2 Deposited 1999-02-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 310–501（192 aa） Fragment：TRAF DOMAIN Chain B 310–501（192 aa） Fragment：TRAF DOMAIN Chain C 310–501（192 aa） Fragment：TRAF DOMAIN Chain D 310–501（192 aa） Fragment：TRAF DOMAIN Chain E 310–501（192 aa） Fragment：TRAF DOMAIN Chain F 310–501（192 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.30 Å R-free 0.289
1CZY CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE TRAF DOMAIN OF HUMAN TRAF2 AND AN LMP1 BINDING PEPTIDE Deposited 1999-09-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES BUFFER, pH 6.00, VAPOR DIFFUSION, temperature 20K	Resolution 2.00 Å R-free 0.245
1CZZ STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 17-RESIDUE CD40 PEPTIDE Deposited 1999-09-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 315–501（187 aa） Fragment：TRAF DOMAIN Chain B 315–501（187 aa） Fragment：TRAF DOMAIN Chain C 315–501（187 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；293 K；PEG4K, MES, PH 5.6, VAPOR DIFFUSION, temperature 293K	Resolution 2.70 Å R-free 0.267
1D01 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A HUMAN CD30 PEPTIDE Deposited 1999-09-07	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 20K	Resolution 2.00 Å R-free 0.244
1D01 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A HUMAN CD30 PEPTIDE Deposited 1999-09-07	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 20K	Resolution 2.00 Å R-free 0.244
1D0A STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE Deposited 1999-09-09	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.251
1D0A STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE Deposited 1999-09-09	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.251
1D0A STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE Deposited 1999-09-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.251
1D0A STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE Deposited 1999-09-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.251
1F3V Crystal structure of the complex between the N-terminal domain of TRADD and the TRAF domain of TRAF2 Deposited 2000-06-06	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 B 331–501（171 aa） Fragment：TRAF DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.261
1QSC CRYSTAL STRUCTURE OF THE TRAF DOMAIN OF TRAF2 IN A COMPLEX WITH A PEPTIDE FROM THE CD40 RECEPTOR Deposited 1999-06-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 311–501（191 aa） Fragment：TRAF DOMAIN Chain B 311–501（191 aa） Fragment：TRAF DOMAIN Chain C 311–501（191 aa） Fragment：TRAF DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；MME-PEG 2000, MAGNESIUM CHLORIDE, BISTRIS PROPANE, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K	Resolution 2.40 Å R-free 0.257
3KNV Crystal structure of the RING and first zinc finger domains of TRAF2 Deposited 2009-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–133（133 aa） Fragment：RING and the first zinc finger domains: UNP residues 1-133	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 8000, 0.1 M HEPES pH 7.5, 8% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.239
3M06 Crystal Structure of TRAF2 Deposited 2010-03-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 266–329（64 aa） Fragment：Residues 266-329 Chain B 266–329（64 aa） Fragment：Residues 266-329 Chain C 266–329（64 aa） Fragment：Residues 266-329	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；8% PEG3350, 6% Tacsimate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.67 Å R-free 0.233
3M06 Crystal Structure of TRAF2 Deposited 2010-03-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 266–329（64 aa） Fragment：Residues 266-329 Chain E 266–329（64 aa） Fragment：Residues 266-329 Chain F 266–329（64 aa） Fragment：Residues 266-329	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；8% PEG3350, 6% Tacsimate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.67 Å R-free 0.233
3M0A Crystal structure of TRAF2:cIAP2 complex Deposited 2010-03-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 266–329（64 aa） Fragment：Residues 266-329 Chain B 266–329（64 aa） Fragment：Residues 266-329 Chain C 266–329（64 aa） Fragment：Residues 266-329	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；8% PEG 3350, 6% Tacsimate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.61 Å R-free 0.268
3M0D Crystal structure of the TRAF1:TRAF2:cIAP2 complex Deposited 2010-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 266–329（64 aa） Fragment：Residues 266-329 Chain B 266–329（64 aa） Fragment：Residues 266-329	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.15M AmSO4, 0.1M MES, 15% PEG 4000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.247
3M0D Crystal structure of the TRAF1:TRAF2:cIAP2 complex Deposited 2010-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 266–329（64 aa） Fragment：Residues 266-329 Chain B 266–329（64 aa） Fragment：Residues 266-329	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.15M AmSO4, 0.1M MES, 15% PEG 4000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.247
8T5Q SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain Deposited 2023-06-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 315–501（187 aa） Fragment：TRAF domain (UNP residues 315-501) Chain B 315–501（187 aa） Fragment：TRAF domain (UNP residues 315-501) Chain C 315–501（187 aa） Fragment：TRAF domain (UNP residues 315-501)	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277.15 K；0.1 M sodium citrate, pH 5.0, 20% w/v PEG8000	Resolution 1.90 Å R-free 0.240
8T5Q SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain Deposited 2023-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 315–501（187 aa） Fragment：TRAF domain (UNP residues 315-501) Chain E 315–501（187 aa） Fragment：TRAF domain (UNP residues 315-501) Chain F 315–501（187 aa） Fragment：TRAF domain (UNP residues 315-501)	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277.15 K；0.1 M sodium citrate, pH 5.0, 20% w/v PEG8000	Resolution 1.90 Å R-free 0.240

13 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRAF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–168； UniProt 334–501 Author chain B； PDBConstruct 1–168； UniProt 334–501 Author chain C； PDBConstruct 1–168； UniProt 334–501 Author chain D； PDBConstruct 1–168； UniProt 334–501 Author chain E； PDBConstruct 1–168； UniProt 334–501 Author chain F； PDBConstruct 1–168； UniProt 334–501

4-1BB LIGAND RECEPTOR

OrganismNot specified

UniProt P20334

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain G； UniProt 231–236 Chain H； UniProt 231–236	Fragment：TRAF2-BINDING SEQUENCE Non-standard monomer：Yes (specific site not provided by mmCIF)	TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2 × 3 （Q12933）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.50 Å R-free 0.270
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain I； UniProt 231–236 Chain J； UniProt 231–236 Chain K； UniProt 231–236	Fragment：TRAF2-BINDING SEQUENCE Non-standard monomer：Yes (specific site not provided by mmCIF)	TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2 × 3 （Q12933）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.50 Å R-free 0.270
3	Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count	Chain G； UniProt 231–236 Chain H； UniProt 231–236 Chain I； UniProt 231–236 Chain J； UniProt 231–236 Chain K； UniProt 231–236	Fragment：TRAF2-BINDING SEQUENCE Non-standard monomer：Yes (specific site not provided by mmCIF)	TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2 × 6 （Q12933）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.50 Å R-free 0.270
4	Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count	Chain G； UniProt 231–236 Chain H； UniProt 231–236 Chain I； UniProt 231–236 Chain J； UniProt 231–236 Chain K； UniProt 231–236	Fragment：TRAF2-BINDING SEQUENCE Non-standard monomer：Yes (specific site not provided by mmCIF)	TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2 × 6 （Q12933）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.50 Å R-free 0.270

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1D0J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5WI8 Crystal structure of murine 4-1BB from HEK293T cells in P21 space group Deposited 2017-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–160（137 aa）	Not recorded	GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295.15 K；0.1 M sodium acetate pH 4.5, 30% w/V polyethylene glycol (PEG) 8000, and 0.2 M lithium sulfate	Resolution 2.95 Å R-free 0.279
5WI8 Crystal structure of murine 4-1BB from HEK293T cells in P21 space group Deposited 2017-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 24–160（137 aa）	Not recorded	GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295.15 K；0.1 M sodium acetate pH 4.5, 30% w/V polyethylene glycol (PEG) 8000, and 0.2 M lithium sulfate	Resolution 2.95 Å R-free 0.279
5WI8 Crystal structure of murine 4-1BB from HEK293T cells in P21 space group Deposited 2017-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain C 24–160（137 aa）	Not recorded	GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295.15 K；0.1 M sodium acetate pH 4.5, 30% w/V polyethylene glycol (PEG) 8000, and 0.2 M lithium sulfate	Resolution 2.95 Å R-free 0.279
5WI8 Crystal structure of murine 4-1BB from HEK293T cells in P21 space group Deposited 2017-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain D 24–160（137 aa）	Not recorded	GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295.15 K；0.1 M sodium acetate pH 4.5, 30% w/V polyethylene glycol (PEG) 8000, and 0.2 M lithium sulfate	Resolution 2.95 Å R-free 0.279
5WIW Crystal structure of murine 4-1BB N128A mutant from HEK293T cells in P43 space group Deposited 2017-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–160（137 aa）	Mutation：N128A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1 M sodium acetate pH 4.5, 30% w/V PEG 8000, 0.2M lithium sulfate	Resolution 2.30 Å R-free 0.228
5WIW Crystal structure of murine 4-1BB N128A mutant from HEK293T cells in P43 space group Deposited 2017-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 24–160（137 aa）	Mutation：N128A	GOL GLYCEROL × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1 M sodium acetate pH 4.5, 30% w/V PEG 8000, 0.2M lithium sulfate	Resolution 2.30 Å R-free 0.228
5WJF Crystal structure of murine 4-1BB from HEK293T cells in P21212 space group Deposited 2017-07-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–160（137 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1 M bicine and 30% W/V PEG 6000	Resolution 2.60 Å R-free 0.288
5WJF Crystal structure of murine 4-1BB from HEK293T cells in P21212 space group Deposited 2017-07-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 24–160（137 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1 M bicine and 30% W/V PEG 6000	Resolution 2.60 Å R-free 0.288
6MKZ Crystal structure of murine 4-1BB/4-1BBL complex Deposited 2018-09-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 24–160（137 aa） Fragment：residues 24-160 Chain D 24–160（137 aa） Fragment：residues 24-160	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；20% PEG 4000, 0.2M ammonium chloride	Resolution 2.65 Å R-free 0.238

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

View Construct and Data Evidence

UniProt name	TNR9_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 2–7； UniProt 231–236 Author chain H； PDBConstruct 2–7； UniProt 231–236 Author chain I； PDBConstruct 2–7； UniProt 231–236 Author chain J； PDBConstruct 2–7； UniProt 231–236 Author chain K； PDBConstruct 2–7； UniProt 231–236

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d0j
Deposition date deposition_date	1999-09-10
Structure title title	STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE
Keywords keywords	B-SANDWICH, PROTEIN-PEPTIDE COMPLEX, APOPTOSIS; APOPTOSIS
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	41.18 Å
Radius of gyration Rg (electron density) rg_electron	40.43 Å
Forward intensity I(0) i0	182048000.00
Molecular weight molecular_weight	111860.0 kDa
Excluded volume excluded_volume	140690 Å³
Envelope volume envelope_volume	203760 Å³
Hydration-shell volume shell_volume	41928 Å³
Envelope diameter envelope_diameter	128.3 Å
Shell Rg shell_rg	47.21 Å
Envelope Rg envelope_rg	38.07 Å
Shape Rg shape_rg	40.42 Å
Total Rg total_rg	40.85 Å
Total atoms total_atoms	7873
Residues n_residues	1035
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	127.7 Å
Rg (real space) rg_real	41.09 Å
Rg uncertainty (real space) rg_real_error	1.22 Å
I(0) (real space) i0_real	1.8200e+08
I(0) uncertainty (real space) i0_real_error	3.1150e+06
Rg (reciprocal space) rg_reciprocal	41.18 Å
I(0) (reciprocal space) i0_reciprocal	182100000.0000
Solution quality estimate total_estimate	0.8888
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	60.5 Å
Skewness Skewness skewness	0.050
Kurtosis Kurtosis kurtosis	-0.805
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17050000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.786

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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	TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
Molecular weight formula_weight	19006.9 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	8112

AMADLEQKVLEMEASTYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEAKNSYVRDDAIFIKAIVDLTGL

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	4-1BB LIGAND RECEPTOR
Molecular weight formula_weight	629.6 kDa
Source method src_method	syn
Copy count entity_count	5

Polymer Polymer

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

XGAAQEE

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	239

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7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1d0ja1
Class class	b — All beta proteins
Fold Fold fold	b.8 — TRAF domain-like
Superfamily Superfamily superfamily	b.8.1 — TRAF domain-like
Family Family family	b.8.1.1 — MATH domain

Domain ID domain_id	d1d0ja2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.2 — Trimerization domain of TRAF
Family Family family	h.1.2.1 — Trimerization domain of TRAF

Domain ID domain_id	d1d0jb1
Class class	b — All beta proteins
Fold Fold fold	b.8 — TRAF domain-like
Superfamily Superfamily superfamily	b.8.1 — TRAF domain-like
Family Family family	b.8.1.1 — MATH domain

Domain ID domain_id	d1d0jb2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.2 — Trimerization domain of TRAF
Family Family family	h.1.2.1 — Trimerization domain of TRAF

Domain ID domain_id	d1d0jc1
Class class	b — All beta proteins
Fold Fold fold	b.8 — TRAF domain-like
Superfamily Superfamily superfamily	b.8.1 — TRAF domain-like
Family Family family	b.8.1.1 — MATH domain

Domain ID domain_id	d1d0jc2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.2 — Trimerization domain of TRAF
Family Family family	h.1.2.1 — Trimerization domain of TRAF

Domain ID domain_id	d1d0jd1
Class class	b — All beta proteins
Fold Fold fold	b.8 — TRAF domain-like
Superfamily Superfamily superfamily	b.8.1 — TRAF domain-like
Family Family family	b.8.1.1 — MATH domain

Domain ID domain_id	d1d0jd2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.2 — Trimerization domain of TRAF
Family Family family	h.1.2.1 — Trimerization domain of TRAF

Domain ID domain_id	d1d0je1
Class class	b — All beta proteins
Fold Fold fold	b.8 — TRAF domain-like
Superfamily Superfamily superfamily	b.8.1 — TRAF domain-like
Family Family family	b.8.1.1 — MATH domain

Domain ID domain_id	d1d0je2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.2 — Trimerization domain of TRAF
Family Family family	h.1.2.1 — Trimerization domain of TRAF

Domain ID domain_id	d1d0jf1
Class class	b — All beta proteins
Fold Fold fold	b.8 — TRAF domain-like
Superfamily Superfamily superfamily	b.8.1 — TRAF domain-like
Family Family family	b.8.1.1 — MATH domain

Domain ID domain_id	d1d0jf2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.2 — Trimerization domain of TRAF
Family Family family	h.1.2.1 — Trimerization domain of TRAF

CATH v4.4 (6 domains)

Domain ID domain_id	1d0jA00
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	1d0jB00
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	1d0jC00
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	1d0jD00
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	1d0jE00
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	1d0jF00
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 (2)

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Unit-cell length a length_a	135.900 Å
Unit-cell length b length_b	85.600 Å
Unit-cell length c length_c	124.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.2700

fit	/app/data/saxs_computation/d0/1d0j/1d0j.fit
pddf	/app/data/pr_computation/d0/1d0j/1d0j.pr.out
profile	/app/data/saxs_computation/d0/1d0j/1d0j.dat

STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE

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

TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2

State in the Current Structure

Other States of the Same Protein in the Database

4-1BB LIGAND RECEPTOR

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) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)