9FZC: OmpA-short

Structure of OmpA-short in complex with nanobody Nb01. Determined by X-ray diffraction at 2.27 Å resolution. Released 17 Jul 2024.

Method: X-ray diffraction
Resolution: 2.27 Å
Organisms: Escherichia coli K-12, Vicugna pacos
Chains: 4
Atoms: 4,898
Mol. weight: 66.92 kDa
Ligands: CA, OCT
Released: 17 Jul 2024

Explore 9FZC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FZC contains 8 α-helices and 46 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 and B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	6-19	14	1
β-strand	30	1	1
β-strand	33-46	14	1
β-strand	49-63	15	1
β-strand	70-86	17	1
β-strand	91-108	18	1
β-strand	112-130	19	1
β-strand	135-144	10	1
β-strand	149	1	2
β-strand	155	1	2
β-strand	158-169	12	1

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	5
β-strand	14	1	6
β-strand	21-28	8	5
α-helix	34-36	3
β-strand	39-44	6	7
β-strand	51-56	6	7
β-strand	62-64	3	7
β-strand	72-77	6	5
β-strand	82-87	6	5
α-helix	92-94	3
β-strand	96-102	7	7
α-helix	103-104	2
β-strand	111	1	7
β-strand	117-119	3	7
β-strand	120	1	6

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	8
β-strand	14	1	9
β-strand	21-28	8	8
α-helix	34-36	3
β-strand	39-44	6	10
β-strand	51-56	6	10
β-strand	62-64	3	10
β-strand	72-77	6	8
β-strand	82-87	6	8
α-helix	92-94	3
β-strand	96-103	8	10
α-helix	104	1
β-strand	110-111	2	10
β-strand	117-119	3	10
β-strand	120	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein A	A, B	protein	173	Escherichia coli K-12	P0A910 (AlphaFold model)
Nanobody 01	C, D	protein	123	Vicugna pacos

Sequence of entity 1 (A, B), FASTA

>9FZC_1 Outer membrane protein A (chains A, B)
MSAPKDNTWYTGAKLGWSQYHDTGFINNNGPTHENQLGAGAFGGYQVNPYVGFEMGYDWL
GRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTKSNVYGKNHDTG
VSPVFAGGVEYAITPEIATRLEYQWTNNIGDAHTIGTRPDNGMLSLGVSYRFA

Sequence of entity 2 (C, D), FASTA

>9FZC_2 Nanobody 01 (chains C, D)
GPSQVQLVESGGGLVQPGGSLRLSCVVSGTGFTFSKSPMSWARQAPGKEREWVSAIFADS
STYYSDSVRGRFTISRDNAKNTVYLQMNNVKPEDTAVYYCGHRRLGKTTYDYRGKGTRVT
VSA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
OCT	N-octane	C8 H18	17

Primary citation

Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies. Sorgenfrei, M., Hurlimann, L.M., Printz, A. et al. Commun Biol (2025) 8:1047-1047. DOI 10.1038/s42003-025-08345-9 · 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…
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
3NB3 19.0 Å, The host outer membrane proteins OmpA and OmpC are packed at specific sites in the…
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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