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- PDB-1t91: crystal structure of human small GTPase Rab7(GTP) -

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Basic information

Entry
Database: PDB / ID: 1t91
Titlecrystal structure of human small GTPase Rab7(GTP)
ComponentsRas-related protein Rab-7
KeywordsPROTEIN TRANSPORT / small GTPase
Function / homology
Function and homology information


synaptic vesicle recycling via endosome / lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / neurotransmitter receptor transport, postsynaptic endosome to lysosome / epidermal growth factor catabolic process / alveolar lamellar body / negative regulation of intralumenal vesicle formation / Suppression of autophagy ...synaptic vesicle recycling via endosome / lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / neurotransmitter receptor transport, postsynaptic endosome to lysosome / epidermal growth factor catabolic process / alveolar lamellar body / negative regulation of intralumenal vesicle formation / Suppression of autophagy / phagosome-lysosome fusion / negative regulation of exosomal secretion / establishment of vesicle localization / retromer complex binding / phagosome maturation / presynaptic endosome / protein localization to lysosome / endosome to plasma membrane protein transport / early endosome to late endosome transport / phagophore assembly site membrane / positive regulation of exosomal secretion / RAB geranylgeranylation / protein targeting to lysosome / melanosome membrane / RAB GEFs exchange GTP for GDP on RABs / RHOD GTPase cycle / RHOF GTPase cycle / retrograde transport, endosome to Golgi / TBC/RABGAPs / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / autophagosome membrane / viral release from host cell / RHOH GTPase cycle / RHOG GTPase cycle / autophagosome assembly / RAC2 GTPase cycle / RAC3 GTPase cycle / bone resorption / intracellular transport / lipid catabolic process / phagocytic vesicle / lipid droplet / RAC1 GTPase cycle / Prevention of phagosomal-lysosomal fusion / MHC class II antigen presentation / secretory granule membrane / small monomeric GTPase / response to bacterium / small GTPase binding / mitochondrial membrane / phagocytic vesicle membrane / endocytosis / positive regulation of protein catabolic process / GDP binding / synaptic vesicle membrane / late endosome membrane / late endosome / protein transport / G protein activity / lysosome / endosome membrane / lysosomal membrane / intracellular membrane-bounded organelle / GTPase activity / Neutrophil degranulation / GTP binding / glutamatergic synapse / Golgi apparatus / mitochondrion / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Small GTPase Rab domain 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 ...Small GTPase Rab domain 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'-TRIPHOSPHATE / Ras-related protein Rab-7a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSong, H. / Hong, W. / Wu, M. / Wang, T.
CitationJournal: Embo J. / Year: 2005
Title: Structural basis for recruitment of RILP by small GTPase Rab7.
Authors: Wu, M. / Wang, T. / Loh, E. / Hong, W. / Song, H.
History
DepositionMay 14, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-7
B: Ras-related protein Rab-7
C: Ras-related protein Rab-7
D: Ras-related protein Rab-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,19712
Polymers94,0074
Non-polymers2,1908
Water9,062503
1
A: Ras-related protein Rab-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0493
Polymers23,5021
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0493
Polymers23,5021
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ras-related protein Rab-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0493
Polymers23,5021
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ras-related protein Rab-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0493
Polymers23,5021
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.695, 56.777, 74.510
Angle α, β, γ (deg.)71.51, 71.72, 77.75
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ras-related protein Rab-7


Mass: 23501.748 Da / Num. of mol.: 4 / Mutation: Q67L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Rab7 / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Star / References: UniProt: P51149
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.23 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: polyethylene glycol monomethyl ether 2000, ammonium sulfate, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9722 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 2, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9722 Å / Relative weight: 1
ReflectionResolution: 1.9→33.049 Å / Num. all: 63332 / Num. obs: 61851 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.059 / Net I/σ(I): 5.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.8 % / % possible all: 92.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: mouse rab5c, 1HUQ

1huq


Resolution: 1.9→20 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 1920 3.04 %random
Rwork0.2433 ---
all0.2522 61851 --
obs0.2493 59931 94.5 %-
Solvent computationSolvent model: MAXIMUM LIKELIHOOD
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5616 0 132 503 6251
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_bond_other_d0
X-RAY DIFFRACTIONr_angle_refined_deg1.712
X-RAY DIFFRACTIONr_angle_other_deg3.549

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