2YMS: Outer membrane protein assembly factor bamb

Structure and assembly of a b-propeller with nine blades and a new conserved repetitive sequence motif. Determined by X-ray diffraction at 2.1 Å resolution. Released 30 Oct 2013.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: ESCHERICHIA COLI
Chains: 4
Atoms: 2,689
Mol. weight: 37.62 kDa
Released: 30 Oct 2013

Explore 2YMS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YMS contains 1 α-helix and 38 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.

Chain A: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	66-68	3	1
β-strand	71-75	5	1
β-strand	80-85	6	1
β-strand	91-96	6	1
β-strand	111-118	8	2
β-strand	121-126	6	2
β-strand	130-135	6	2
β-strand	141-146	6	2
α-helix	154-155	2
β-strand	156-158	3	3
β-strand	161-165	5	3
β-strand	170-175	6	3
β-strand	181-186	6	3

Chain B: 0 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	115-118	4	4
β-strand	121-125	5	4
β-strand	130-135	6	4
β-strand	141-146	6	4
β-strand	151	1	5
β-strand	156-158	3	6
β-strand	161-165	5	6
β-strand	166	1	5
β-strand	171-175	5	6
β-strand	181-185	5	6

Chain C: 0 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	233-235	3	7
β-strand	238-242	5	7
β-strand	247-271	6	7
β-strand	277-282	6	7
β-strand	286-292	7	8
β-strand	295-300	6	8
β-strand	305-309	5	8
β-strand	315-319	5	8

Chain D: 0 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	252-254	3	9
β-strand	257-261	5	9
β-strand	267-271	5	9
β-strand	277-281	5	9
β-strand	286-291	6	10
β-strand	295-300	6	10
β-strand	305-309	5	10
β-strand	315-319	5	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor bamb	A	protein	130	ESCHERICHIA COLI	P77774 (AlphaFold model)
Outer membrane protein assembly factor bamb	B	protein	74	ESCHERICHIA COLI	P77774 (AlphaFold model)
Outer membrane protein assembly factor bamb	C	protein	75	ESCHERICHIA COLI	P77774 (AlphaFold model)
Outer membrane protein assembly factor bamb	D	protein	74	ESCHERICHIA COLI	P77774 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2YMS_1 OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB (chains A)
NLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGGH
VYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAV
KWTVNLDMPS

Sequence of entity 2 (B), FASTA

>2YMS_2 OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB (chains B)
GGVTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQ
ALNEADGAVKWTVN

Sequence of entity 3 (C), FASTA

>2YMS_3 OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB (chains C)
DTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMA
LTIDGGVTLWTQSDL

Sequence of entity 4 (D), FASTA

>2YMS_4 OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB (chains D)
VDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVM
ALTIDGGVTLWTQS

Primary citation

Structure and Assembly of a B-Propeller with Nine Blades and a New Conserved Repetitive Sequence Motif. Albrecht, R., Zeth, K. To be published.

Other PDB entries of the same protein (UniProt P77774 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3Q7M 1.65 Å, The crystal structure of BamB from the BAM complex in spacegroup I222
3Q7N 1.77 Å, The crystal structure of BamB from the BAM complex in spacegroup P212121
3PRW 1.8 Å, Crystal structure of the lipoprotein BamB
3Q7O 2.09 Å, The crystal structure of BamB from the BAM complex in spacegroup P213
4XGA 2.15 Å, Crystal structure of BamB and BamA P3-5 complex from E.coli
2YH3 2.6 Å, The structure of BamB from E. coli
3P1L 2.6 Å, Crystal structure of Escherichia coli BamB, a lipoprotein component of the beta-barrel…
9CNW 2.6 Å, CryoEM structure of the APO-BAM complex in DDM detergent
9HG6 2.73 Å, BAM-SurA complex in the swing-in state
9HG5 2.82 Å, BAM-SurA complex in the swing-in state with full length BamC resolved
9HG7 2.83 Å, BAM-SurA complex in the swing-out state
9HG9 2.88 Å, BAM-SurA-darobactin complex in the swing-in state

Browse structure collections

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