7BWT: SopD-Rab8 complex structure

SopD-Rab8 complex structure. Determined by X-ray diffraction at 2.3 Å resolution. Released 24 Feb 2021.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Salmonella typhimurium, Homo sapiens
Chains: 2
Atoms: 3,932
Mol. weight: 60.61 kDa
Ligands: MG, GDP
Released: 24 Feb 2021

Explore 7BWT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BWT contains 25 α-helices and 19 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: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	37-40	4
α-helix	41-43	3
α-helix	46-48	3
α-helix	49-60	12
β-strand	73	1	1
α-helix	76-89	14
α-helix	96-98	3
β-strand	99-103	5	2
β-strand	109-114	6	2
β-strand	117-123	7	2
α-helix	124-127	4
α-helix	141-160	20
α-helix	162-167	6
α-helix	169-177	9
α-helix	180-190	11
α-helix	198-200	3
β-strand	201-202	2	3
α-helix	209-215	7
α-helix	216-219	4
β-strand	232-237	6	4
β-strand	240-245	6	4
α-helix	248-255	8
β-strand	260	1	1
α-helix	261-263	3
α-helix	264-283	20
α-helix	285-298	14
β-strand	305-306	2	3
β-strand	307	1	5
β-strand	310	1	5

Chain B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	6
α-helix	21-30	10
β-strand	45-52	8	6
β-strand	55-62	8	6
α-helix	75-78	4
β-strand	83-89	7	6
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	6
α-helix	133-143	11
β-strand	146-149	4	6
β-strand	151	1	7
β-strand	156	1	7
α-helix	158-176	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SPI-1 type III secretion system effector SopD	A	protein	336	Salmonella typhimurium	P40722 (AlphaFold model)
Ras-related protein Rab-8A	B	protein	182	Homo sapiens	P61006 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7BWT_1 SPI-1 type III secretion system effector SopD (chains A)
MGSSHHHHHHSSGLVPRGSHPVTLSFGNHQNYTLNESRLAHLLSADKEKAIHMGGWDKVQ
DHFRAEKKDHALEVLHSIIHGQGRGEPGEMEVNVEDINKIYAFKRLQHLACPAHQDLFTI
KMDASQTQFLLMVGDTVISQSNIKDILNISDDAVIESMSREERQLFLQICEVIGSKMTWH
PELLQESISTLRKEVTGNAQIKTAVYEMMRPAEAPDHPLVEWQDSLTADEKSMLACINAG
NFEPTTQFCKIGYQEVQGEVAFSMMHPCISYLLHSYSPFSEFKPTNSGFLKKLNQDYNDY
HAKKMFIDVILEKLYLTHERSLHIGKDGCSRNILLT

Sequence of entity 2 (B), FASTA

>7BWT_2 Ras-related protein Rab-8A (chains B)
AKTYDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQI
WDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGN
KCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKKLEGNS
PQ

Ligands and cofactors

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

Water and common crystallization additives (PEG, GOL) are not listed.

Primary citation

The Salmonella effector protein SopD targets Rab8 to positively and negatively modulate the inflammatory response. Lian, H., Jiang, K., Tong, M. et al. Nat Microbiol (2021) 6:658-671. DOI 10.1038/s41564-021-00866-3 · PubMed

Other PDB entries of the same protein (UniProt P40722 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5CPC 2.15 Å, Crystal structure of SopD, a type III secreted virulence effector from Salmonella enterica

Browse structure collections

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