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- PDB-1vg1: GDP-Bound Rab7 -

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Basic information

Entry
Database: PDB / ID: 1vg1
TitleGDP-Bound Rab7
ComponentsRas-related protein Rab-7
KeywordsPROTEIN TRANSPORT / GTP-binding protein
Function / homology
Function and homology information


RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / TBC/RABGAPs / RAC2 GTPase cycle / RHOH GTPase cycle / RAC3 GTPase cycle / phagosome acidification / lipophagy / protein to membrane docking / RHOG GTPase cycle ...RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / TBC/RABGAPs / RAC2 GTPase cycle / RHOH GTPase cycle / RAC3 GTPase cycle / phagosome acidification / lipophagy / protein to membrane docking / RHOG GTPase cycle / RAB geranylgeranylation / RHOQ GTPase cycle / positive regulation of viral process / epidermal growth factor catabolic process / synaptic vesicle recycling via endosome / RAC1 GTPase cycle / alveolar lamellar body / sterol sensor activity / phagosome-lysosome fusion / negative regulation of exosomal secretion / MHC class II antigen presentation / lysosome to ER cholesterol transport / retromer complex binding / presynaptic endosome / retromer complex / exocytic vesicle / endosome to plasma membrane protein transport / protein localization to lysosome / early endosome to late endosome transport / positive regulation of exosomal secretion / melanosome membrane / phagophore assembly site membrane / bone resorption / protein targeting to lysosome / retrograde transport, endosome to Golgi / Neutrophil degranulation / endosome to lysosome transport / autophagosome membrane / viral release from host cell / response to bacterium / autophagosome assembly / lipid catabolic process / cholesterol homeostasis / phagocytic vesicle / lipid droplet / small monomeric GTPase / small GTPase binding / phagocytic vesicle membrane / mitochondrial membrane / positive regulation of protein catabolic process / terminal bouton / GDP binding / late endosome / synaptic vesicle membrane / late endosome membrane / G protein activity / lysosome / endosome membrane / lysosomal membrane / GTPase activity / GTP binding / protein-containing complex / mitochondrion / metal ion binding / 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'-DIPHOSPHATE / Ras-related protein Rab-7a
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRak, A. / Pylypenko, O. / Niculae, A. / Pyatkov, K. / Goody, R.S. / Alexandrov, K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structure of the Rab7:REP-1 complex: insights into the mechanism of Rab prenylation and choroideremia disease
Authors: Rak, A. / Pylypenko, O. / Niculae, A. / Pyatkov, K. / Goody, R.S. / Alexandrov, K.
History
DepositionApr 22, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 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 / pdbx_struct_conn_angle / struct_conn / 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_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-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5893
Polymers21,1211
Non-polymers4682
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.500, 103.200, 51.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1144-

HOH

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Components

#1: Protein Ras-related protein Rab-7 / RAS-related protein P23 / RAS-related protein BRL-RAS


Mass: 21120.998 Da / Num. of mol.: 1 / Fragment: Gtpase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09527
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 25% PEG 3350, 0.25M Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 2, 2002
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→18.8 Å / Num. all: 13877 / Num. obs: 13877 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 27.7 Å2 / Rsym value: 0.057 / Net I/σ(I): 20.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 1929 / Rsym value: 0.322 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1refinement
ProDCdata collection
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rab7 from REP1:Rab7 complex (PDB code 1VG0)

1vg0


Resolution: 1.9→18.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2358514.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 694 5 %RANDOM
Rwork0.187 ---
obs0.187 13858 99.4 %-
all-13858 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5484 Å2 / ksol: 0.380535 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→18.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 29 144 1506
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.091.5
X-RAY DIFFRACTIONc_mcangle_it3.772
X-RAY DIFFRACTIONc_scbond_it4.532
X-RAY DIFFRACTIONc_scangle_it5.862.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 113 5 %
Rwork0.227 2140 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PG4_XPLOR_PARAM.TXT
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5GDP_XPLOR_PARAM.TXT

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