4DID: Salmonella effector N-terminal domain SopB

Crystal structure of Salmonella effector N-terminal domain SopB in complex with Cdc42. Determined by X-ray diffraction at 2.35 Å resolution. Released 29 Feb 2012.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Homo sapiens, Salmonella enterica subsp. enterica serovar Typhimurium
Chains: 2
Atoms: 2,491
Mol. weight: 38.76 kDa
Ligands: MG, GDP
Released: 29 Feb 2012

Explore 4DID in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DID contains 18 α-helices and 9 β-strands across 2 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, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	1
α-helix	16-25	10
β-strand	41-46	6	1
β-strand	49-56	8	1
α-helix	62-64	3
α-helix	68-71	4
β-strand	77-83	7	1
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	1
α-helix	123-130	8
α-helix	136-138	3
α-helix	139-148	10
β-strand	154-156	3	1
α-helix	165-176	12

Chain B: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	49-52	4	1
α-helix	59-62	4
α-helix	66-68	3
β-strand	72	1	2
α-helix	73-90	18
α-helix	96-107	12
α-helix	108-110	3
α-helix	112-113	2
β-strand	115	1	2
α-helix	118-142	25
α-helix	147-166	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell division control protein 42 homolog	A	protein	193	Homo sapiens	P60953 (AlphaFold model)
Inositol phosphate phosphatase sopB	B	protein	152	Salmonella enterica subsp. enterica serovar Typhimurium	O30916 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DID_1 Cell division control protein 42 homolog (chains A)
MGSSHHHHHHMQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEP
YTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPF
LLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFD
EAILAALEPPEPK

Sequence of entity 2 (B), FASTA

>4DID_2 Inositol phosphate phosphatase sopB (chains B)
QILSGQGKAPAKAPDARPEIIVLREPGATWGNYLQHQKASNHSLHNLYNLQRDLLTVAAT
VLGKQDPVLTSMANQMELAKVKADRPATKQEEAAAKALKKNLIELIAARTQQQDGLPAKE
AHRFAAVAFRDAQVKQLNNQPWQTIKNTLTHN

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Primary citation

Structure of Salmonella Effector Protein SopB N-terminal Domain in Complex with Host Rho GTPase Cdc42. Burkinshaw, B.J., Prehna, G., Worrall, L.J. et al. J Biol Chem (2012) 287:13348-13355. DOI 10.1074/jbc.M111.331330 · PubMed

Other PDB entries of the same protein (UniProt P60953 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2NGR 1.9 Å, Transition state complex for GTP hydrolysis by CDC42: comparisons of the high resolution…
4JS0 1.9 Å, Complex of Cdc42 with the CRIB-PR domain of IRSp53
6SUP 2.0 Å, Crystal Structure of TcdB2-TccC3-Cdc42
3VHL 2.08 Å, Crystal structure of the DHR-2 domain of DOCK8 in complex with Cdc42 (T17N mutant)
1GRN 2.1 Å, Crystal structure of the CDC42/CDC42GAP/ALF3 complex.
1NF3 2.1 Å, Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity…
2DFK 2.15 Å, Crystal structure of the CDC42-Collybistin II complex
2WM9 2.2 Å, Structure of the complex between DOCK9 and Cdc42.
2WMO 2.2 Å, Structure of the complex between DOCK9 and Cdc42.
1GZS 2.3 Å, Crystal structure of the complex between the gef domain of the salmonella typhimurium…
1KI1 2.3 Å, Guanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42
3GCG 2.3 Å, crystal structure of MAP and CDC42 complex

Browse structure collections

About this viewer

MolViewer shows 4DID directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.