7EQ2: GDP-bound Rab1a-T75D

Crystal structure of GDP-bound Rab1a-T75D. Determined by X-ray diffraction at 1.55 Å resolution. Released 2 Nov 2022.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,366
Mol. weight: 44.32 kDa
Ligands: CAC, NCO, MG, GDP
Released: 2 Nov 2022

Explore 7EQ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7EQ2 contains 16 α-helices and 14 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	1
α-helix	24-33	10
β-strand	48-55	8	1
β-strand	58-65	8	1
α-helix	70-73	4
α-helix	78-82	5
β-strand	86-92	7	1
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	1
α-helix	129-131	3
α-helix	136-145	10
β-strand	150-152	3	1
β-strand	154	1	2
β-strand	159	1	2
α-helix	161-177	17

Chain B: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	3
α-helix	24-33	10
β-strand	48-55	8	3
β-strand	58-65	8	3
α-helix	70-73	4
α-helix	78-82	5
β-strand	86-92	7	3
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	3
α-helix	129-131	3
α-helix	136-146	11
β-strand	150-152	3	3
α-helix	161-177	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-1A	A, B	protein	184	Homo sapiens	P62820 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7EQ2_1 Ras-related protein Rab-1A (chains A, B)
MSSMNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTI
KLQIWDTAGQERFRDITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKL
LVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRMLEHH
HHHH

Ligands and cofactors

ID	Name	Formula	Copies
CAC	Cacodylate ion	C2 H6 As O2	2
NCO	Cobalt hexammine(iii)	Co H18 N6	4
MG	Magnesium ion	Mg	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

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

Primary citation

Aurora kinase A-mediated phosphorylation triggers structural alteration of Rab1A to enhance ER complexity during mitosis. Zhang, W., Zhang, Z., Xiang, Y. et al. Nat Struct Mol Biol (2024). DOI 10.1038/s41594-023-01165-7

Other PDB entries of the same protein (UniProt P62820 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WWX 1.5 Å, Crystal structure of the SidM/DrrA(GEF/GDF domain)-Rab1(GTPase domain) complex
3SFV 1.73 Å, Crystal structure of the GDP-bound Rab1a S25N mutant in complex with the coiled-coil…
3TKL 2.18 Å, Crystal structure of the GTP-bound Rab1a in complex with the coiled-coil domain of LidA…
2FOL 2.63 Å, Crystal structure of human RAB1A in complex with GDP
9MHF 2.73 Å, Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L)
4JVS 2.78 Å, Crystal structure of LepB GAP domain from Legionella drancourtii in complex with…
4FMC 2.8 Å, EspG-Rab1 complex
3L0I 2.85 Å, Complex structure of SidM/DrrA with the wild type Rab1
4FMD 3.05 Å, EspG-Rab1 complex structure at 3.05 A
4FMB 3.2 Å, VirA-Rab1 complex structure
4IRU 3.2 Å, Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and…
9MHG 3.2 Å, Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase…

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