3NB3: Outer membrane protein A

Name: PDB 3NB3: The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components
Published: 2011-02-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components. Determined by electron microscopy at 19.0 Å resolution. Released 16 Feb 2011.

Method: Electron microscopy
Resolution: 19.0 Å
Organism: Escherichia coli
Chains: 4
Atoms: 5,945
Mol. weight: 150.15 kDa
Released: 16 Feb 2011

Explore 3NB3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3NB3 contains 13 α-helices and 50 β-strands across 4 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.

Chains A, B and C: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	6-16	11	1
β-strand	34-46	13	1
β-strand	49-60	12	1
α-helix	61-62	2
β-strand	72-86	15	1
β-strand	91-107	17	1
β-strand	113-132	20	1
β-strand	135-144	10	1
β-strand	161-169	9	1

Chain D: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	9-23	15	4
β-strand	31-32	2	4
β-strand	35-45	11	4
β-strand	50-61	12	4
β-strand	71-82	12	4
β-strand	86-94	9	4
α-helix	98-101	4
α-helix	102-104	3
β-strand	124-134	11	4
α-helix	135-138	4
β-strand	143-150	8	4
β-strand	153	1	5
β-strand	155	1	6
α-helix	156	1
β-strand	165	1	6
α-helix	172-174	3
β-strand	176	1	5
β-strand	179-188	10	4
β-strand	191-201	11	4
α-helix	202-203	2
β-strand	212	1	7
β-strand	217-229	13	4
β-strand	232-242	11	4
β-strand	246	1	8
β-strand	251	1	7
β-strand	252	1	8
β-strand	255-265	11	4
β-strand	271-283	13	4
β-strand	292-305	14	4
β-strand	310-319	10	4
α-helix	325-330	6
β-strand	337-345	9	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein A	A, B, C	protein	346	Escherichia coli	P0A910 (AlphaFold model)
Outer membrane protein C	D	protein	346	Escherichia coli	P06996 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>3NB3_1 Outer membrane protein A (chains A, B, C)
MKKTAIAIAVALAGFATVAQAAPKDNTWYTGAKLGWSQYHDTGFINNNGPTHENKLGAGA
FGGYQVNPYVGFEMGYDWLGRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGG
MVWRADTYSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTNNIGDAHTIGTRPDN
GMLSLGVSYRFGQGEAAPVVAPAPAPAPEVQTKHFTLKSDVLFNFNKATLKPEGQAALDQ
LYSQLSNLDPKDGSVVVLGYTDRIGSDAYNQGLSERRAQSVVDYLISKGIPADKISARGM
GESNPVTGNTCDNVKQRAALIDCLAPDRRVEIEVKGIKDVVTQPQA

Sequence of entity 2 (D), FASTA

>3NB3_2 Outer membrane protein C (chains D)
AEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQI
QGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNF
MQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGNPSGEGFTSGVTNNGRDALRQNGDGV
GGSITYDYEGFGIGGAISSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQ
TYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSLAYLQSKGKNLGRGYDDEDILKYVDV
GATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF

Primary citation

The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion. Zhao, H., Sequeira, R.D., Galeva, N.A. et al. Virology (2011) 409:319-327. DOI 10.1016/j.virol.2010.10.030 · PubMed

Other PDB entries of the same protein (UniProt P0A910 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1QJP 1.65 Å, High resolution structure of the outer membrane protein A (OMPA) transmembrane domain
5M2Q 1.7 Å, Structure of cobinamide-bound BtuF mutant W66F, the periplasmic vitamin B12 binding…
9FZC 2.27 Å, Structure of OmpA-short in complex with nanobody Nb01
1BXW 2.5 Å, Outer membrane protein A (OMPA) transmembrane domain
6LYR 3.28 Å, Structure of the BAM complex
6ITC 3.45 Å, Structure of a substrate engaged SecA-SecY protein translocation machine
3JBU 3.64 Å, Mechanisms of Ribosome Stalling by SecM at Multiple Elongation Steps
1G90 NMR Solution Structure of Outer Membrane Protein A Transmembrane Domain: 10 conformers
2GE4 High-resolution solution structure of outer membrane protein A transmembrane domain
2JMM NMR solution structure of a minimal transmembrane beta-barrel platform protein
2MQE Solution structure of Escherichia coli Outer membrane protein A C-terminal domain
9A2M Model of E. coli OmpA by in-cell photo-crosslinking MS and deep learning

Browse structure collections

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