8T5P: SARS-CoV-2 ORF3a peptide

SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain. Determined by X-ray diffraction at 2.5 Å resolution. Released 29 Nov 2023.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 9
Atoms: 9,228
Mol. weight: 132.54 kDa
Released: 29 Nov 2023

Explore 8T5P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T5P contains 57 α-helices and 70 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	378-409	32
β-strand	416-422	7	1
α-helix	424-432	9
β-strand	439-440	2	2
α-helix	441-443	3
β-strand	444-445	2	2
β-strand	452-458	7	2
α-helix	463-465	3
β-strand	469-477	9	2
α-helix	478-479	2
α-helix	482-484	3
β-strand	493-497	5	1
β-strand	507-511	5	1
α-helix	518-520	3
α-helix	522-523	2
β-strand	527	1	2
α-helix	528-530	3
β-strand	531-538	8	2
α-helix	539-544	6
β-strand	549	1	1
β-strand	552-559	8	1

Chain B: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	378-409	32
β-strand	416-422	7	3
α-helix	424-432	9
β-strand	439-440	2	4
α-helix	441-443	3
β-strand	444-445	2	4
β-strand	452-458	7	4
α-helix	463-465	3
β-strand	469-477	9	4
α-helix	482-484	3
β-strand	493-497	5	3
β-strand	507-511	5	3
α-helix	518-520	3
α-helix	522-523	2
β-strand	527	1	4
β-strand	531-538	8	4
α-helix	539-544	6
β-strand	549	1	3
β-strand	552-559	8	3

Chain C: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	378-409	32
β-strand	416-422	7	5
α-helix	424-432	9
β-strand	439-440	2	6
α-helix	441-443	3
β-strand	444-445	2	6
β-strand	452-458	7	6
α-helix	463-465	3
β-strand	469-477	9	6
α-helix	482-484	3
β-strand	493-497	5	5
β-strand	507-511	5	5
α-helix	512-514	3
α-helix	522-523	2
β-strand	527	1	6
α-helix	528-530	3
β-strand	531-538	8	6
α-helix	539-544	6
β-strand	549	1	5
β-strand	552-559	8	5

Chain D: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	378-409	32
β-strand	416-422	7	7
α-helix	424-432	9
β-strand	438-440	3	8
α-helix	441-443	3
β-strand	444-445	2	8
β-strand	452-458	7	8
α-helix	463-465	3
β-strand	469-477	9	8
α-helix	478	1
α-helix	482-484	3
β-strand	493-497	5	7
β-strand	507-511	5	7
α-helix	518-520	3
α-helix	522-523	2
β-strand	527	1	8
α-helix	528-530	3
β-strand	531-538	8	8
α-helix	539-543	5
β-strand	549	1	7
β-strand	552-559	8	7

Chain E: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	378-409	32
β-strand	416-422	7	9
α-helix	424-432	9
β-strand	439-440	2	10
α-helix	441-443	3
β-strand	444-445	2	10
β-strand	452-458	7	10
α-helix	463-465	3
β-strand	469-477	9	10
α-helix	482-484	3
β-strand	493-497	5	9
β-strand	507-511	5	9
α-helix	512-514	3
α-helix	518-520	3
α-helix	522-523	2
β-strand	527	1	10
α-helix	528-530	3
β-strand	531-538	8	10
α-helix	539-544	6
β-strand	549	1	9
β-strand	552-559	8	9

Chain F: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	378-410	33
β-strand	416-421	6	11
α-helix	424-432	9
β-strand	439-440	2	12
α-helix	441-443	3
β-strand	444-445	2	12
β-strand	452-458	7	12
α-helix	463-465	3
β-strand	469-477	9	12
α-helix	482-484	3
β-strand	493-497	5	11
β-strand	507-511	5	11
α-helix	518-520	3
α-helix	522-523	2
β-strand	527	1	12
α-helix	528-530	3
β-strand	531-538	8	12
α-helix	539-544	6
β-strand	549	1	13
β-strand	552	1	13
β-strand	553-559	7	11

Chain G: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	37-38	2	2
α-helix	39	1

Chains H and I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	37-38	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TNF receptor-associated factor 3	A, B, C, D, E, F	protein	192	Homo sapiens	Q13114 (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

>8T5P_1 TNF receptor-associated factor 3 (chains A, B, C, D, E, F)
NTGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGK
TLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTL
MLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLENGTYIKDDTIFI
KVIVDTSDLPDP

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

>8T5P_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 Q13114 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2GKW 2.7 Å, Key contacts promote recongnito of BAFF-R by TRAF3
1FLK 2.8 Å, Molecular basis for CD40 signaling mediated by TRAF3
1ZMS 2.8 Å, LMP1 Protein binds to TRAF3 as a structural CD40
8ZUK 2.83 Å, Cluster structure of the BAFF-BAFFR-TRAF3 complex
1L0A 2.9 Å, Downstream regulator tank binds to the CD40 recognition site on TRAF3
1FLL 3.5 Å, Molecular basis for CD40 signaling mediated by TRAF3
1KZZ 3.5 Å, Downstream regulator tank binds to the CD40 recognition site on TRAF3
1RF3 3.5 Å, Structurally Distinct Recognition Motifs in Lymphotoxin-B Receptor and CD40 for…
2ECY Solution structure of the Zinc finger, C3HC4 type (RING finger)" domain of TNF…

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