1D0J: Tnf receptor associated factor 2

Structure of tnf receptor associated factor 2 in complex with a M4-1BB peptide. Determined by X-ray diffraction at 2.5 Å resolution. Released 8 Mar 2000.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 11
Atoms: 8,112
Mol. weight: 117.19 kDa
Released: 8 Mar 2000

Explore 1D0J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1D0J contains 45 α-helices and 75 β-strands across 11 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	335-347	13
β-strand	353-359	7	1
α-helix	361-369	9
β-strand	375-377	3	2
α-helix	378-380	3
β-strand	381-382	2	2
β-strand	389-395	7	2
α-helix	400-402	3
β-strand	406-414	9	2
α-helix	415-416	2
α-helix	419-421	3
β-strand	430-434	5	1
β-strand	443-447	5	1
α-helix	458-459	2
β-strand	463	1	2
β-strand	467-474	8	2
α-helix	475-477	3
β-strand	486	1	1
β-strand	489-496	8	1

Chain B: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	335-347	13
β-strand	353-358	6	3
α-helix	361-369	9
β-strand	375-377	3	4
α-helix	378-380	3
β-strand	381-382	2	4
β-strand	389-395	7	4
α-helix	400-402	3
β-strand	406-414	9	4
α-helix	419-421	3
β-strand	430-434	5	3
β-strand	443-447	5	3
α-helix	458-459	2
β-strand	463	1	4
β-strand	467-474	8	4
β-strand	486	1	5
β-strand	489	1	5
β-strand	490-496	7	3

Chain C: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	335-347	13
β-strand	353-358	6	6
α-helix	361-369	9
β-strand	376-377	2	7
α-helix	378-380	3
β-strand	381-382	2	7
β-strand	389-395	7	7
α-helix	400-402	3
β-strand	406-413	8	7
β-strand	414	1	8
α-helix	419-421	3
β-strand	430-435	6	6
β-strand	443-447	5	6
α-helix	458-459	2
β-strand	463	1	8
β-strand	467-474	8	7
α-helix	475-477	3
β-strand	486	1	9
β-strand	489	1	9
β-strand	490-496	7	6

Chain D: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	335-347	13
β-strand	353-359	7	10
α-helix	361-369	9
β-strand	376-377	2	11
β-strand	381-382	2	11
β-strand	389-395	7	11
α-helix	400-402	3
β-strand	406-414	9	11
α-helix	419-421	3
β-strand	430-434	5	10
β-strand	443-447	5	10
α-helix	454-456	3
α-helix	458-459	2
β-strand	463	1	11
β-strand	467-474	8	11
α-helix	475-477	3
β-strand	486	1	10
β-strand	489-496	8	10

Chain E: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	335-347	13
β-strand	353-359	7	12
α-helix	361-369	9
β-strand	375-377	3	13
α-helix	378-380	3
β-strand	381-382	2	13
β-strand	389-395	7	13
α-helix	400-402	3
β-strand	406-414	9	13
α-helix	419-421	3
β-strand	430-434	5	12
β-strand	443-447	5	12
α-helix	458-459	2
β-strand	463	1	13
β-strand	467-474	8	13
α-helix	475-477	3
β-strand	486	1	12
β-strand	489-496	8	12

Chain F: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	335-347	13
β-strand	353-359	7	14
α-helix	361-369	9
β-strand	376-377	2	15
α-helix	378-380	3
β-strand	381-382	2	15
β-strand	389-395	7	15
α-helix	400-402	3
β-strand	406-413	8	15
β-strand	414	1	16
α-helix	415-416	2
α-helix	419-421	3
β-strand	430-434	5	14
β-strand	443-447	5	14
α-helix	458-459	2
β-strand	463	1	16
β-strand	467-474	8	15
α-helix	475-477	3
β-strand	486	1	14
β-strand	489-496	8	14

Chains G, H, I and K: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	233-234	2	2

Chain J: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	232	1
β-strand	233-234	2	13
α-helix	235	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor receptor associated protein 2	A, B, C, D, E, F	protein	168	Homo sapiens	Q12933 (AlphaFold model)
4-1BB ligand receptor	G, H, I, J, K	protein	7		P20334 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>1D0J_1 TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2 (chains A, B, C, D, E, F)
AMADLEQKVLEMEASTYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLR
IYLNGDGTGRGTHLSLFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTS
SSFQRPVNDMNIASGCPLFCPVSKMEAKNSYVRDDAIFIKAIVDLTGL

Sequence of entity 2 (G, H, I, J, K), FASTA

>1D0J_2 4-1BB LIGAND RECEPTOR (chains G, H, I, J, K)
XGAAQEE

Primary citation

The structural basis for the recognition of diverse receptor sequences by TRAF2. Ye, H., Park, Y.C., Kreishman, M. et al. Mol Cell (1999) 4:321-330. DOI 10.1016/S1097-2765(00)80334-2 · PubMed

Other PDB entries of the same protein (UniProt Q12933 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KNV 1.9 Å, Crystal structure of the RING and first zinc finger domains of TRAF2
8T5Q 1.9 Å, SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain
1CZY 2.0 Å, Crystal structure of the complex between the traf domain of human TRAF2 and an LMP1…
1D00 2.0 Å, Structure of tnf receptor associated factor 2 in complex with a 5-residue CD40 peptide
1D01 2.0 Å, Structure of tnf receptor associated factor 2 in complex with a human CD30 peptide
1D0A 2.0 Å, Structure of tnf receptor associated factor 2 (TRAF2) in complex with a human OX40 peptide
1F3V 2.0 Å, Crystal structure of the complex between the N-terminal domain of TRADD and the TRAF…
1CA4 2.2 Å, Structure of tnf receptor associated factor 2 (TRAF2)
1CA9 2.3 Å, Structure of tnf receptor associated factor 2 in complex with a peptide from tnf-R2
1QSC 2.4 Å, Crystal structure of the traf domain of TRAF2 in a complex with a peptide from the CD40…
3M0A 2.61 Å, Crystal structure of TRAF2:cIAP2 complex
3M06 2.67 Å, Crystal Structure of TRAF2

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