4LHV: Rab8 in its inactive GDP-bound form

Crystal structure of Rab8 in its inactive GDP-bound form. Determined by X-ray diffraction at 1.95 Å resolution. Released 9 Oct 2013.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,901
Mol. weight: 102.18 kDa
Ligands: GDP, MG
Released: 9 Oct 2013

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

Secondary structure: helices and β-sheets

4LHV contains 29 α-helices and 42 β-strands across 5 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	1
α-helix	21-30	10
β-strand	45-52	8	1
β-strand	55-62	8	1
α-helix	75-77	3
β-strand	83-89	7	1
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	1
α-helix	126-128	3
α-helix	133-143	11
β-strand	146-149	4	1
β-strand	151	1	2
β-strand	156	1	2
α-helix	158-175	18

Chain B: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	3
α-helix	21-30	10
β-strand	33	1	4
β-strand	45-52	8	3
β-strand	55-63	9	3
β-strand	83-89	7	3
α-helix	93-109	17
β-strand	115-121	7	3
α-helix	126-128	3
α-helix	133-142	10
β-strand	146-149	4	3
β-strand	151	1	5
β-strand	156	1	5
α-helix	158-173	16

Chain C: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	6
α-helix	21-30	10
β-strand	45-52	8	6
β-strand	55-63	9	6
β-strand	81-89	9	6
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	6
α-helix	126-128	3
α-helix	133-143	11
β-strand	146-149	4	6
β-strand	151	1	4
β-strand	156	1	4
α-helix	158-173	16

Chain D: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	7
α-helix	21-30	10
β-strand	33	1	2
β-strand	45-52	8	7
β-strand	55-63	9	7
β-strand	83-89	7	7
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	7
α-helix	126-128	3
α-helix	133-143	11
β-strand	146-149	4	7
β-strand	151	1	8
β-strand	156	1	8
α-helix	158-175	18

Chain E: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	9
α-helix	21-30	10
β-strand	45-52	8	9
β-strand	55-63	9	9
β-strand	83-89	7	9
α-helix	93-109	17
β-strand	115-121	7	9
α-helix	126-128	3
α-helix	133-142	10
β-strand	146-149	4	9
β-strand	151	1	10
β-strand	156	1	10
α-helix	158-173	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-8A	A, B, C, D, E	protein	174	Homo sapiens	P61006 (AlphaFold model)

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

>4LHV_1 Ras-related protein Rab-8A (chains A, B, C, D, E)
GSHDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIW
DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNK
CDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK

Ligands and cofactors

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

Primary citation

Intermediates in the Guanine Nucleotide Exchange Reaction of Rab8 Protein Catalyzed by Guanine Nucleotide Exchange Factors Rabin8 and GRAB. Guo, Z., Hou, X., Goody, R.S. et al. J Biol Chem (2013) 288:32466-32474. DOI 10.1074/jbc.M113.498329 · PubMed

Other PDB entries of the same protein (UniProt P61006 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LHW 1.55 Å, Crystal structure of Rab8 in its active GppNHp-bound form
6SQ2 1.68 Å, Structure of a phosphomimetic switch 2 variant of Rab8a in complex with the phospho-Rab…
6WHE 1.73 Å, Structure of phosphomimetic Rab8a GTPase (T72E) in the GTP-bound state
6RIR 1.77 Å, Crystal structure of phosphorylated Rab8a in complex with the Rab-binding domain of RILPL2
9M0O 1.83 Å, Crystal structure of OPTN 138-170 in complex with GTP-bound RAB8A1-176 (Q67L)
7LWB 1.9 Å, Crystal Structure of phospho-Rab8a with the RH2 domain (117-165) of RILPL2
6ZSI 1.91 Å, The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members.
9IKQ 1.93 Å, Crystal structure of OPTN LZD in complex with GTP-bound Rab8a(Q67L)
3QBT 2.0 Å, Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp
6ZSJ 2.0 Å, The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members.
6YX5 2.14 Å, Structure of DrrA from Legionella pneumophilia in complex with human Rab8a
7BWT 2.3 Å, SopD-Rab8 complex structure

Browse structure collections

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