4FMB: VirA-Rab1 complex structure

VirA-Rab1 complex structure. Determined by X-ray diffraction at 3.2 Å resolution. Released 5 Sept 2012.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Shigella flexneri, Homo sapiens
Chains: 6
Atoms: 12,435
Mol. weight: 180.23 kDa
Ligands: MG, GDP, AF3
Released: 5 Sept 2012

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

Secondary structure: helices and β-sheets

4FMB contains 69 α-helices and 78 β-strands across 6 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: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	48-55	8
α-helix	58-63	6
β-strand	66-67	2	1
β-strand	77-83	7	1
β-strand	86-93	8	1
β-strand	96-103	8	1
β-strand	106-111	6	1
α-helix	112-113	2
α-helix	114-122	9
β-strand	128-129	2	2
β-strand	136-142	7	2
α-helix	152-160	9
β-strand	163-165	3	2
β-strand	171	1	3
α-helix	172-174	3
α-helix	182-191	10
α-helix	192-195	4
β-strand	199-202	4	2
β-strand	206	1	2
α-helix	209-218	10
β-strand	230	1	4
α-helix	236-246	11
α-helix	255-264	10
α-helix	268-276	9
β-strand	286	1	3
α-helix	287-307	21
β-strand	316-325	10	2
β-strand	342-353	12	2
β-strand	358-369	12	2
β-strand	376	1	4
α-helix	377-383	7
α-helix	386-388	3
β-strand	390-399	10	2

Chains B, D and F: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	5
α-helix	24-32	9
β-strand	47-53	7	5
β-strand	60-66	7	5
α-helix	71-73	3
α-helix	74-78	5
β-strand	86-92	7	5
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	5
α-helix	136-144	9
β-strand	150-153	4	5
β-strand	154	1	6
β-strand	159	1	6
α-helix	161-173	13

Chain C: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	48-55	8
α-helix	58-63	6
β-strand	66-67	2	7
β-strand	77-83	7	7
β-strand	86-93	8	7
β-strand	96-103	8	7
β-strand	106-111	6	7
α-helix	112-113	2
α-helix	114-122	9
β-strand	128-129	2	8
β-strand	136-142	7	8
α-helix	152-160	9
β-strand	163-165	3	8
β-strand	171	1	9
α-helix	172-174	3
α-helix	182-191	10
α-helix	192-195	4
β-strand	199-202	4	8
β-strand	206	1	8
α-helix	207-208	2
α-helix	209-218	10
β-strand	230	1	10
α-helix	236-246	11
α-helix	255-264	10
α-helix	268-276	9
β-strand	286	1	9
α-helix	287-307	21
β-strand	316-325	10	8
α-helix	326-327	2
β-strand	342-353	12	8
β-strand	358-369	12	8
β-strand	376	1	10
α-helix	377-383	7
α-helix	386-388	3
β-strand	390-399	10	8

Chain E: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	48-55	8
α-helix	58-63	6
β-strand	65-67	3	13
β-strand	77-83	7	13
β-strand	86-93	8	13
β-strand	96-103	8	13
β-strand	106-111	6	13
α-helix	112-113	2
α-helix	114-122	9
β-strand	128-129	2	14
β-strand	136-142	7	14
α-helix	152-160	9
β-strand	163-165	3	14
β-strand	171	1	15
α-helix	172-174	3
α-helix	182-191	10
α-helix	192-195	4
β-strand	199-202	4	14
β-strand	206	1	14
α-helix	209-218	10
β-strand	230	1	16
α-helix	236-246	11
α-helix	255-264	10
α-helix	268-276	9
β-strand	286	1	15
α-helix	287-307	21
β-strand	316-325	10	14
α-helix	326-327	2
β-strand	342-353	12	14
β-strand	358-369	12	14
β-strand	376	1	16
α-helix	377-383	7
α-helix	386-388	3
β-strand	390-399	10	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cysteine protease-like virA	A, C, E	protein	361	Shigella flexneri	Q7BU69 (AlphaFold model)
Ras-related protein Rab-1A	B, D, F	protein	171	Homo sapiens	P62820 (AlphaFold model)

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

>4FMB_1 Cysteine protease-like virA (chains A, C, E)
GPLGSIYSPHETLAEKHSEKKLMDSFSPSLSQDKMDGEFAHANIDGISIRLCLNKGICSV
FYLDGDKIQSTQLSSKEYNNLLSSLPPKQFNLGKVHTITAPVSGNFKTHKPAPEVIETAI
NCCTSIIPNDDYFHVKDTDFNSVWHDIYRDIRASDSNSTKIYFNNIEIPLKLIADLINEL
GINEFIDSKKELQMLSYNQVNKIINSNFPQQDLCFQTEKLLFTSLFQDPAFISALTSAFW
QSLHITSSSVEHIYAQIMSENIENRLNFMPEQRVINNCGHIIKINAVVPKNDTAISASGG
RAYEVSSSILPSHITCNGVGINKIETSYLVHAGTLPSSEGLRNAIPPESRQVSFAIISPD
V

Sequence of entity 2 (B, D, F), FASTA

>4FMB_2 Ras-related protein Rab-1A (chains B, D, F)
PEYDALFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIW
DTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNK
CDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	3
AF3	Aluminum fluoride	Al F3	3

Primary citation

Structurally Distinct Bacterial TBC-like GAPs Link Arf GTPase to Rab1 Inactivation to Counteract Host Defenses. Dong, N., Zhu, Y., Lu, Q. et al. Cell (2012) 150:1029-1041. DOI 10.1016/j.cell.2012.06.050 · PubMed

Other PDB entries of the same protein (UniProt Q7BU69 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3EB8 2.4 Å, VirA
3EE1 3.01 Å, Novel fold of VirA, a type III secretion system effector protein from Shigella flexneri

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