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- PDB-1wms: High resolution crystal structure of human Rab9 GTPase: a novel a... -

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Basic information

Entry
Database: PDB / ID: 1wms
TitleHigh resolution crystal structure of human Rab9 GTPase: a novel antiviral drug target
ComponentsRas-related protein Rab-9A
KeywordsPROTEIN TRANSPORT / GTPase
Function / homology
Function and homology information


negative regulation by host of symbiont catalytic activity / Rab protein signal transduction / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / RHOBTB3 ATPase cycle / RAB GEFs exchange GTP for GDP on RABs / retrograde transport, endosome to Golgi / positive regulation of exocytosis / phagocytic vesicle / transport vesicle ...negative regulation by host of symbiont catalytic activity / Rab protein signal transduction / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / RHOBTB3 ATPase cycle / RAB GEFs exchange GTP for GDP on RABs / retrograde transport, endosome to Golgi / positive regulation of exocytosis / phagocytic vesicle / transport vesicle / trans-Golgi network membrane / phagocytic vesicle membrane / GDP binding / melanosome / protein transport / late endosome / regulation of protein localization / lysosome / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Rab9 / 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 ...Rab9 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-9A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsChen, L. / DiGiammarino, E. / Zhou, X.E. / Wang, Y. / Toh, D. / Hodge, T.W. / Meehan, E.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: High resolution crystal structure of human Rab9 GTPase: A novel antiviral drug target
Authors: Chen, L. / DiGiammarino, E. / Zhou, X.E. / Wang, Y. / Toh, D. / Hodge, T.W. / Meehan, E.J.
History
DepositionJul 16, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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-9A
B: Ras-related protein Rab-9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1934
Polymers40,3072
Non-polymers8862
Water9,152508
1
A: Ras-related protein Rab-9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5972
Polymers20,1531
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5972
Polymers20,1531
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.400, 45.620, 51.220
Angle α, β, γ (deg.)99.75, 107.17, 101.84
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ras-related protein Rab-9A / Rab-9 / Rab9


Mass: 20153.473 Da / Num. of mol.: 2 / Fragment: C-terminal truncated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Rab9 / Plasmid: pET28-Rab9(1-177) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51151
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG4000, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 73993 / Num. obs: 73993 / % possible obs: 84.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 25.5
Reflection shellResolution: 1.25→1.29 Å / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.392 / % possible all: 39.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
SHELXLrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OIV

1oiv


Resolution: 1.25→10 Å / Num. parameters: 29064 / Num. restraintsaints: 34491 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The structure was refined also with CNS 1.0
RfactorNum. reflection% reflectionSelection details
Rfree0.196 3697 5 %Random
Rwork0.139 ---
all0.141 73767 --
obs0.139 73767 84.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2552 / Occupancy sum non hydrogen: 3229
Refinement stepCycle: LAST / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 56 508 3226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.05
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps0.086

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