4FMC: EspG-Rab1 complex

EspG-Rab1 complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 5 Sept 2012.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Escherichia coli, Homo sapiens
Chains: 6
Atoms: 11,470
Mol. weight: 170.79 kDa
Ligands: MG, GDP, AF3
Released: 5 Sept 2012

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

Secondary structure: helices and β-sheets

4FMC contains 68 α-helices and 65 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: 16 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	50-60	11
α-helix	70-79	10
β-strand	83-85	3	1
β-strand	91-98	8	1
β-strand	104-110	7	1
β-strand	115-120	6	1
β-strand	126-131	6	1
α-helix	140-142	3
β-strand	146-147	2	2
β-strand	151	1	3
β-strand	153-156	4	2
α-helix	166-176	11
β-strand	181-183	3	2
β-strand	186	1	4
α-helix	202-209	8
β-strand	214-217	4	2
β-strand	220-221	2	2
α-helix	224-233	10
α-helix	241-244	4
α-helix	245-250	6
α-helix	254-262	9
β-strand	265	1	2
α-helix	268-278	11
α-helix	281-289	9
α-helix	293-296	4
α-helix	297-301	5
α-helix	304-315	12
β-strand	325-332	8	2
β-strand	338-349	12	2
α-helix	350-351	2
β-strand	358-369	12	2
α-helix	377-383	7
β-strand	387-394	8	2

Chain B: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	5
α-helix	24-33	10
α-helix	41-43	3
β-strand	46-55	10	5
β-strand	58-67	10	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	129-131	3
α-helix	136-146	11
β-strand	150-152	3	5
α-helix	161-175	15

Chain C: 15 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	50-60	11
α-helix	71-79	9
β-strand	83-85	3	6
β-strand	91-98	8	6
β-strand	104-110	7	6
β-strand	115-120	6	6
β-strand	126-131	6	6
α-helix	140-142	3
β-strand	146-147	2	7
β-strand	151	1	4
β-strand	153-156	4	7
α-helix	166-176	11
β-strand	181-183	3	7
β-strand	186	1	3
α-helix	202-209	8
β-strand	214-217	4	7
β-strand	220-222	3	7
α-helix	224-233	10
α-helix	241-244	4
α-helix	245-250	6
α-helix	254-262	9
β-strand	265	1	7
α-helix	268-278	11
α-helix	281-289	9
α-helix	293-296	4
α-helix	297-315	19
β-strand	325-332	8	7
β-strand	338-349	12	7
α-helix	350-351	2
β-strand	358-369	12	7
α-helix	377-383	7
β-strand	387-394	8	7

Chain D: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	8
α-helix	24-33	10
α-helix	41-43	3
β-strand	46-55	10	8
β-strand	58-67	10	8
α-helix	71-73	3
α-helix	74-78	5
β-strand	86-92	7	8
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	8
α-helix	136-146	11
β-strand	150-152	3	8
β-strand	154	1	9
β-strand	159	1	9
α-helix	161-175	15

Chain E: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	50-60	11
α-helix	72-79	8
β-strand	83-85	3	10
β-strand	91-98	8	10
β-strand	104-110	7	10
β-strand	115-120	6	10
β-strand	126-131	6	10
α-helix	140-142	3
β-strand	146-147	2	11
β-strand	153-156	4	11
α-helix	166-176	11
β-strand	181-183	3	11
α-helix	202-209	8
β-strand	214-217	4	11
β-strand	220-221	2	11
α-helix	224-233	10
α-helix	242-244	3
α-helix	245-250	6
α-helix	254-263	10
β-strand	265	1	11
α-helix	268-278	11
α-helix	281-290	10
α-helix	293-296	4
α-helix	297-301	5
α-helix	304-315	12
β-strand	325-332	8	11
β-strand	338-349	12	11
α-helix	350-351	2
β-strand	358-369	12	11
α-helix	378-381	4
β-strand	387-394	8	11

Chain F: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	25-31	7
β-strand	46-47	2	12
β-strand	66-67	2	12
α-helix	71-73	3
α-helix	100-102	3
α-helix	109-112	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ROrf2	A, C, E	protein	351	Escherichia coli	Q7DB50 (AlphaFold model)
Ras-related protein Rab-1A	B, D	protein	171	Homo sapiens	P62820 (AlphaFold model)
Ras-related protein Rab-1A	F	protein	117	Homo sapiens	P62820 (AlphaFold model)

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

>4FMC_1 ROrf2 (chains A, C, E)
EMSCAEKLLKVLSFGLWNPTYSRSERQSFQELLTVLEPVYPLPNELGRVSARFSDGSSLR
ISVTNSESIEAEIRTPNNEKITVLLESNEQNRLLQSLPIDRHMPYIQVHRALSEMDLTDT
TSMRNLLGFTSKLSTTLIPHNAQTDPLSGPTPFSSIFMDTCRGLGNAKLSLNGVDIPANA
QMLLRDALGLKDTHSSPTRNVIDHGISRHDAEQIARESSGSDKQKAEVVEFLCHPEAATA
ICSAFYQSFNVPALTLTHERISKASEYNAERSLDTPNACINISISQSSDGNIYVTSHTGV
LIMAPEDRPNEMGMLTNRTSYEVPQGVKCIIDEMVRALQPRYAASETYLQN

Sequence of entity 2 (B, D), FASTA

>4FMC_2 Ras-related protein Rab-1A (chains B, D)
PEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIW
DTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNK
CDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM

Sequence of entity 3 (F), FASTA

>4FMC_3 Ras-related protein Rab-1A (chains F)
LLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERF
RTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTT

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

Water and common crystallization additives (PGE) are not listed.

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 Q7DB50 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3PCR 2.5 Å, Structure of EspG-Arf6 complex
3PCS 2.86 Å, Structure of EspG-PAK2 autoinhibitory Ialpha3 helix complex
4FMD 3.05 Å, EspG-Rab1 complex structure at 3.05 A
4FME 4.1 Å, EspG-Rab1-Arf6 complex

Browse structure collections

About this viewer

MolViewer shows 4FMC 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.