3QBT: OCRL1 540-678

Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp. Determined by X-ray diffraction at 2.0 Å resolution. Released 23 Mar 2011.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 8
Atoms: 10,400
Mol. weight: 148.64 kDa
Ligands: GNP, MG
Released: 23 Mar 2011

Explore 3QBT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QBT contains 47 α-helices and 83 β-strands across 8 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: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	1
α-helix	21-30	10
α-helix	37-39	3
β-strand	42-43	2	2
β-strand	44-52	9	1
β-strand	55-63	9	1
α-helix	68-70	3
α-helix	71-74	4
α-helix	75-77	3
β-strand	83-89	7	1
α-helix	93-97	5
α-helix	99-109	11
β-strand	111	1	3
β-strand	115-121	7	1
α-helix	126-128	3
α-helix	133-142	10
β-strand	146-149	4	1
β-strand	151	1	4
β-strand	156	1	4
α-helix	158-175	18

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	553-560	8
β-strand	565-567	3	13
β-strand	571-577	7	2
β-strand	579	1	14
β-strand	583-591	9	13
β-strand	597-602	6	2
β-strand	615-618	4	13
β-strand	621-624	4	2
β-strand	629-636	8	13
β-strand	638	1	14
α-helix	640-648	9
β-strand	655-661	7	2
β-strand	666-675	10	2

Chain C: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	5
α-helix	21-30	10
α-helix	37-39	3
β-strand	42-43	2	6
β-strand	44-52	9	5
β-strand	55-63	9	5
α-helix	68-70	3
α-helix	71-74	4
α-helix	75-77	3
β-strand	83-89	7	5
α-helix	93-97	5
α-helix	99-109	11
β-strand	111	1	7
β-strand	115-121	7	5
α-helix	126-128	3
α-helix	133-143	11
β-strand	146-149	4	5
β-strand	151	1	8
β-strand	156	1	8
α-helix	158-175	18

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	553-560	8
β-strand	565-567	3	15
β-strand	571-578	8	6
β-strand	579	1	16
β-strand	583-591	9	15
β-strand	597-602	6	6
β-strand	615-618	4	15
β-strand	621-624	4	6
β-strand	629-636	8	15
β-strand	638	1	16
α-helix	640-648	9
β-strand	655-661	7	6
β-strand	666-676	11	6

Chain E: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	9
α-helix	21-30	10
α-helix	37-40	4
β-strand	42-52	11	9
β-strand	55-64	10	9
α-helix	68-70	3
α-helix	71-75	5
β-strand	83-89	7	9
α-helix	93-97	5
α-helix	99-109	11
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	158-174	17

Chain F: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	541-560	20
β-strand	565-567	3	17
β-strand	571-578	8	9
β-strand	581	1	9
β-strand	583-591	9	17
β-strand	597-602	6	9
β-strand	615-618	4	17
β-strand	621-624	4	9
β-strand	629-636	8	17
α-helix	643-646	4
β-strand	648	1	3
β-strand	652-661	10	9
β-strand	666-676	11	9

Chain G: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	11
α-helix	21-30	10
α-helix	37-40	4
β-strand	42-52	11	11
β-strand	55-64	10	11
α-helix	68-70	3
α-helix	71-74	4
α-helix	75-77	3
β-strand	83-89	7	11
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	11
α-helix	126-128	3
α-helix	133-143	11
β-strand	146-149	4	11
β-strand	151	1	12
β-strand	156	1	12
α-helix	158-173	16

Chain H: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	541-560	20
β-strand	565-567	3	18
β-strand	571-577	7	11
β-strand	578	1	19
β-strand	579	1	20
β-strand	581	1	19
β-strand	583-591	9	18
β-strand	597-601	5	11
β-strand	615-618	4	18
β-strand	621-624	4	11
β-strand	629-636	8	18
β-strand	638	1	20
α-helix	640-646	7
β-strand	648	1	7
β-strand	652-661	10	11
β-strand	666-675	10	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-8A	A, C, E, G	protein	174	Homo sapiens	P61006 (AlphaFold model)
Inositol polyphosphate 5-phosphatase OCRL-1	B, D, F, H	protein	140	Homo sapiens	Q01968 (AlphaFold model)

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

>3QBT_1 Ras-related protein Rab-8A (chains A, C, E, G)
GHMDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIW
DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNK
CDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK

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

>3QBT_2 Inositol polyphosphate 5-phosphatase OCRL-1 (chains B, D, F, H)
GERRYRKVFEDSVRIMDRMENDFLPSLELSRREFVFENVKFRQLQKEKFQISNNGQVPCH
FSFIPKLNDSQYCKPWLRAEPFEGYLEPNETVDISLDVYVSKDSVTILNSGEDKIEDILV
LHLDRGKDYFLTISGNYLPS

Ligands and cofactors

ID	Name	Formula	Copies
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	4
MG	Magnesium ion	Mg	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

A structural basis for Lowe syndrome caused by mutations in the Rab-binding domain of OCRL1. Hou, X., Hagemann, N., Schoebel, S. et al. EMBO J (2011) 30:1659-1670. DOI 10.1038/emboj.2011.60 · 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)
4LHV 1.95 Å, Crystal structure of Rab8 in its inactive GDP-bound form
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

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