8T5Q: SARS-CoV-2 ORF3a peptide

SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain. Determined by X-ray diffraction at 1.9 Å resolution. Released 29 Nov 2023.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 9
Atoms: 8,505
Mol. weight: 129.91 kDa
Released: 29 Nov 2023

Explore 8T5Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T5Q contains 58 α-helices and 72 β-strands across 9 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: 10 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	376-377	2	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	419-421	3
β-strand	430-434	5	1
α-helix	435-436	2
β-strand	443-447	5	1
α-helix	454-456	3
α-helix	458-459	2
β-strand	463	1	2
α-helix	464-466	3
β-strand	467-474	8	2
α-helix	475-479	5
β-strand	486	1	1
β-strand	489-496	8	1

Chain B: 9 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	376-377	2	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	454-456	3
α-helix	458-459	2
β-strand	463	1	4
α-helix	464-466	3
β-strand	467-474	8	4
α-helix	475-478	4
β-strand	486	1	5
β-strand	489	1	5
β-strand	490-496	7	3

Chain C: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	335-347	13
β-strand	353-359	7	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	406-414	9	7
α-helix	419-421	3
β-strand	430-434	5	6
β-strand	443-447	5	6
α-helix	454-456	3
α-helix	458-459	2
β-strand	463	1	7
α-helix	464-466	3
β-strand	467-474	8	7
α-helix	475-477	3
β-strand	486	1	6
β-strand	489-496	8	6

Chain D: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	335-347	13
β-strand	353-359	7	8
α-helix	361-370	10
β-strand	376-377	2	9
α-helix	378-380	3
β-strand	381-382	2	9
β-strand	389-395	7	9
α-helix	400-402	3
β-strand	406-414	9	9
α-helix	419-421	3
β-strand	430-434	5	8
β-strand	443-447	5	8
α-helix	454-456	3
α-helix	458-459	2
β-strand	463	1	9
α-helix	464-466	3
β-strand	467-474	8	9
α-helix	475-478	4
β-strand	486	1	8
β-strand	489-496	8	8

Chain E: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	335-347	13
β-strand	353-358	6	10
α-helix	361-369	9
β-strand	376-377	2	11
α-helix	378-380	3
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	415	1
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
α-helix	464-466	3
β-strand	467-474	8	11
α-helix	475-478	4
β-strand	486	1	12
β-strand	489	1	12
β-strand	490-496	7	10

Chain F: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	335-347	13
β-strand	353-358	6	13
α-helix	361-370	10
β-strand	375-377	3	14
α-helix	378-380	3
β-strand	381-382	2	14
β-strand	389-395	7	14
α-helix	400-402	3
β-strand	406-414	9	14
α-helix	419-421	3
β-strand	430-434	5	13
α-helix	435-436	2
β-strand	443-447	5	13
α-helix	454-456	3
α-helix	458-459	2
β-strand	463	1	14
α-helix	464-466	3
β-strand	467-474	8	14
α-helix	475-478	4
β-strand	486	1	15
β-strand	489	1	15
β-strand	490-496	7	13

Chain G: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	205-206	2	2
α-helix	207	1

Chains H and I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	205-206	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TNF receptor-associated factor 2	A, B, C, D, E, F	protein	188	Homo sapiens	Q12933 (AlphaFold model)
ORF3a protein	G, H, I	protein	5	Severe acute respiratory syndrome coronavirus 2	P0DTC3 (AlphaFold model)

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

>8T5Q_1 TNF receptor-associated factor 2 (chains A, B, C, D, E, F)
SEALSSKVQQLERSIGLKDLAMADLEQKVLEMEASTYDGVFIWKISDFARKRQEAVAGRI
PAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMKGPNDALLRWPFNQKVTLM
LLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEAKNSYVRDDAIFIK
AIVDLTGL

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

>8T5Q_2 ORF3a protein (chains G, H, I)
PIQAS

Primary citation

SARS-CoV-2 ORF3a-Mediated NF-kappa B Activation Is Not Dependent on TRAF-Binding Sequence. Busscher, B.M., Befekadu, H.B., Liu, Z. et al. Viruses (2023) 15. DOI 10.3390/v15112229 · 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
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…
1D0J 2.5 Å, Structure of tnf receptor associated factor 2 in complex with a M4-1BB peptide
3M0A 2.61 Å, Crystal structure of TRAF2:cIAP2 complex
3M06 2.67 Å, Crystal Structure of TRAF2

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