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- PDB-6ff8: Crystal structure of uncomplexed Rab32 in the active GTP-bound st... -

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Basic information

Entry
Database: PDB / ID: 6ff8
TitleCrystal structure of uncomplexed Rab32 in the active GTP-bound state at 2.13 Angstrom resolution
ComponentsRas-related protein Rab-32
KeywordsSIGNALING PROTEIN / small GTPase / Rab / GTP / vesicle trafficking / cell dynamics
Function / homology
Function and homology information


BLOC-2 complex binding / AP-3 adaptor complex binding / AP-1 adaptor complex binding / endosome to melanosome transport / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / melanosome assembly / melanosome organization / melanosome membrane / GTP-dependent protein binding ...BLOC-2 complex binding / AP-3 adaptor complex binding / AP-1 adaptor complex binding / endosome to melanosome transport / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / melanosome assembly / melanosome organization / melanosome membrane / GTP-dependent protein binding / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / protein localization to membrane / antigen processing and presentation / endomembrane system / phagocytic vesicle / vesicle-mediated transport / mitochondrion organization / intracellular protein transport / trans-Golgi network / phagocytic vesicle membrane / melanosome / mitochondrial outer membrane / early endosome / GTPase activity / GTP binding / endoplasmic reticulum / mitochondrion / membrane / cytosol
Similarity search - Function
Ras-related protein Rab29/Rab38/Rab32 / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...Ras-related protein Rab29/Rab38/Rab32 / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-32
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsKhan, A.R. / Kecman, T.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/1A/1239 Ireland
CitationJournal: Small GTPases / Year: 2019
Title: LRRK2 binds to the Rab32 subfamily in a GTP-dependent mannerviaits armadillo domain.
Authors: McGrath, E. / Waschbusch, D. / Baker, B.M. / Khan, A.R.
History
DepositionJan 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-32
B: Ras-related protein Rab-32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2726
Polymers41,1772
Non-polymers1,0954
Water90150
1
A: Ras-related protein Rab-32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1363
Polymers20,5881
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1363
Polymers20,5881
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.658, 53.658, 129.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Ras-related protein Rab-32


Mass: 20588.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB32 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13637
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: O.2M sodium potassium tartrate, 0.1M Bis-Tris propane pH 8.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.13→41.36 Å / Num. obs: 20447 / % possible obs: 99.3 % / Redundancy: 4.2 % / Net I/σ(I): 12.4
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1646 / CC1/2: 0.588 / Rpim(I) all: 0.488 / Rrim(I) all: 1.02 / Rsym value: 0 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4cym

4cym


Resolution: 2.13→41.352 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.49
RfactorNum. reflection% reflection
Rfree0.2232 1015 4.96 %
Rwork0.1907 --
obs0.1923 20447 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.13→41.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 66 50 2891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182905
X-RAY DIFFRACTIONf_angle_d1.9223942
X-RAY DIFFRACTIONf_dihedral_angle_d21.4661048
X-RAY DIFFRACTIONf_chiral_restr0.137435
X-RAY DIFFRACTIONf_plane_restr0.011486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.24230.19561470.16842770X-RAY DIFFRACTION100
2.2423-2.38280.19191410.16472750X-RAY DIFFRACTION100
2.3828-2.56680.19031450.1892784X-RAY DIFFRACTION100
2.5668-2.8250.26731350.22112782X-RAY DIFFRACTION100
2.825-3.23370.29811520.23082771X-RAY DIFFRACTION100
3.2337-4.07350.24281490.1992789X-RAY DIFFRACTION100
4.0735-41.35990.17971460.16592786X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4314-0.18-0.04152.1939-0.62633.5481-0.0680.004-0.1076-0.080.04940.23190.083-0.24470.02320.2008-0.0139-0.04940.202-0.01110.2271-25.1357-21.1088.0906
22.68590.23020.13023.10160.13923.275-0.00260.04880.1559-0.04950.0874-0.3217-0.16190.236-0.06830.219-0.0062-0.01160.2025-0.04940.2642-5.9007-0.738718.5322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 19:198)
2X-RAY DIFFRACTION2(chain B and resseq 20:196)

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