4FMD: EspG-Rab1 complex structure

EspG-Rab1 complex structure at 3.05 A. Determined by X-ray diffraction at 3.05 Å resolution. Released 5 Sept 2012.

Method: X-ray diffraction
Resolution: 3.05 Å
Organisms: Escherichia coli, Homo sapiens
Chains: 6
Atoms: 12,146
Mol. weight: 176.12 kDa
Ligands: AF3, GDP, MG
Released: 5 Sept 2012

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

Secondary structure: helices and β-sheets

4FMD contains 69 α-helices and 72 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, 17 β-strands

Element	Residues	Length	Sheet
α-helix	50-60	11
α-helix	69-79	11
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	139-142	4
β-strand	146-147	2	2
β-strand	151	1	3
β-strand	153-157	5	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	220-222	3	2
α-helix	224-233	10
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	304-316	13
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	387-395	9	2

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	5
α-helix	24-33	10
β-strand	46-55	10	5
β-strand	58-67	10	5
α-helix	71-73	3
α-helix	74-78	5
α-helix	81-83	3
β-strand	86-92	7	5
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	5
α-helix	136-145	10
β-strand	150-152	3	5
β-strand	154	1	6
β-strand	159	1	6
α-helix	161-175	15

Chain C: 16 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	50-60	11
α-helix	69-79	11
β-strand	83-85	3	7
β-strand	91-98	8	7
β-strand	104-110	7	7
β-strand	115-120	6	7
β-strand	126-131	6	7
α-helix	139-142	4
β-strand	146-147	2	8
β-strand	151	1	4
α-helix	152	1
β-strand	153-156	4	8
α-helix	166-176	11
β-strand	181-183	3	8
β-strand	186	1	3
α-helix	202-209	8
β-strand	214-217	4	8
β-strand	220-222	3	8
α-helix	223	1
α-helix	224-233	10
α-helix	245-250	6
α-helix	254-262	9
β-strand	265	1	8
α-helix	268-278	11
α-helix	281-289	9
α-helix	293-296	4
α-helix	297-316	20
β-strand	324-332	9	8
β-strand	338-349	12	8
α-helix	350-351	2
β-strand	358-369	12	8
α-helix	377-383	7
β-strand	387-394	8	8

Chain D: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	9
β-strand	13-18	6	9
α-helix	24-33	10
α-helix	41-43	3
β-strand	46-55	10	9
β-strand	58-67	10	9
α-helix	71-73	3
α-helix	74-78	5
β-strand	86-92	7	9
α-helix	96-112	17
β-strand	118-124	7	9
α-helix	136-146	11
β-strand	150-152	3	9
α-helix	161-175	15

Chain E: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	50-60	11
α-helix	69-79	11
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	126-130	5	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	220-222	3	11
α-helix	224-232	9
α-helix	245-250	6
α-helix	254-263	10
β-strand	265	1	11
α-helix	268-278	11
α-helix	281-289	9
α-helix	293-296	4
α-helix	297-316	20
β-strand	324-332	9	11
β-strand	338-349	12	11
α-helix	350-351	2
β-strand	358-369	12	11
α-helix	377-383	7
β-strand	387-394	8	11

Chain F: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	15-18	4	12
α-helix	24-33	10
β-strand	46-48	3	12
β-strand	65-67	3	12
α-helix	71-73	3
α-helix	74-78	5
α-helix	81-83	3
β-strand	86-92	7	12
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	12
α-helix	136-143	8
α-helix	144-146	3
β-strand	150-152	3	12
β-strand	154	1	13
β-strand	159	1	13
α-helix	161-173	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
EspG protein	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	164	Homo sapiens	P62820 (AlphaFold model)

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

>4FMD_1 EspG protein (chains A, C, E)
EMSCAEKLLKVLSFGLWNPTYSRSERQSFQELLTVLEPVYPLPNELGRVSARFSDGSSLR
ISVTNSESIEAEIRTPNNEKITVLLESNEQNRLLQSLPIDRHMPYIQVHRALSEMDLTDT
TSMRNLLGFTSKLSTTLIPHNAQTDPLSGPTPFSSIFMDTCRGLGNAKLSLNGVDIPANA
QMLLRDALGLKDTHSSPTRNVIDHGISRHDAEQIARESSGSDKQKAEVVEFLCHPEAATA
ICSAFYQSFNVPALTLTHERISKASEYNAERSLDTPNACINISISQSSDGNIYVTSHTGV
LIMAPEDRPNEMGMLTNRTSYEVPQGVKCTIDEMVRALQPRYAASETYLQN

Sequence of entity 2 (B, D), FASTA

>4FMD_2 Ras-related protein Rab-1A (chains B, D)
PEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIW
DTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNK
CDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM

Sequence of entity 3 (F), FASTA

>4FMD_3 Ras-related protein Rab-1A (chains F)
KLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQER
FRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKK
VVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM

Ligands and cofactors

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

Water and common crystallization additives (PGE, PEG) 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
4FMC 2.8 Å, EspG-Rab1 complex
3PCS 2.86 Å, Structure of EspG-PAK2 autoinhibitory Ialpha3 helix complex
4FME 4.1 Å, EspG-Rab1-Arf6 complex

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