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- PDB-1vg9: The crystal structures of the REP-1 protein in complex with C-ter... -

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Basic information

Entry
Database: PDB / ID: 1vg9
TitleThe crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein
Components
  • Rab proteins geranylgeranyltransferase component A 1
  • Ras-related protein Rab-7
KeywordsPROTEIN BINDING/PROTEIN TRANSPORT / RAB PRENYLATION / POST-TRANSLATIONAL MODIFICATION / PROTEIN BINDING-PROTEIN TRANSPORT COMPLEX
Function / homology
Function and homology information


RAB GEFs exchange GTP for GDP on RABs / TBC/RABGAPs / RHOF GTPase cycle / RHOD GTPase cycle / synaptic vesicle recycling via endosome / positive regulation of viral process / lipophagy / phagosome acidification / RAC2 GTPase cycle / RHOH GTPase cycle ...RAB GEFs exchange GTP for GDP on RABs / TBC/RABGAPs / RHOF GTPase cycle / RHOD GTPase cycle / synaptic vesicle recycling via endosome / positive regulation of viral process / lipophagy / phagosome acidification / RAC2 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / protein to membrane docking / RAB geranylgeranylation / Rab-protein geranylgeranyltransferase complex / RHOQ GTPase cycle / epidermal growth factor catabolic process / alveolar lamellar body / RAC1 GTPase cycle / negative regulation of exosomal secretion / phagosome-lysosome fusion / establishment of vesicle localization / presynaptic endosome / MHC class II antigen presentation / protein geranylgeranylation / retromer complex binding / vesicle-mediated transport in synapse / retromer complex / neurotransmitter receptor transport, postsynaptic endosome to lysosome / endosome to plasma membrane protein transport / phagophore assembly site membrane / protein targeting to lysosome / positive regulation of exosomal secretion / melanosome membrane / early endosome to late endosome transport / retrograde transport, endosome to Golgi / protein targeting to membrane / GDP-dissociation inhibitor activity / Neutrophil degranulation / small GTPase-mediated signal transduction / endosome to lysosome transport / blood vessel development / viral release from host cell / autophagosome membrane / autophagosome assembly / intracellular transport / bone resorption / lipid catabolic process / phagocytic vesicle / vesicle-mediated transport / lipid droplet / GTPase activator activity / small monomeric GTPase / intracellular protein transport / response to bacterium / mitochondrial membrane / terminal bouton / small GTPase binding / synaptic vesicle membrane / phagocytic vesicle membrane / positive regulation of protein catabolic process / GDP binding / late endosome membrane / late endosome / G protein activity / lysosome / endosome / endosome membrane / lysosomal membrane / GTPase activity / protein-containing complex binding / GTP binding / glutamatergic synapse / Golgi apparatus / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
Rab protein geranylgeranyltransferase component A / : / RAE1/2 domain I, C-terminal region / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / small GTPase Rab1 family profile. ...Rab protein geranylgeranyltransferase component A / : / RAE1/2 domain I, C-terminal region / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / Ras-related protein Rab-7a / Rab proteins geranylgeranyltransferase component A 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 23, 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 1.4Nov 10, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 1.5Oct 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: Rab proteins geranylgeranyltransferase component A 1
B: Ras-related protein Rab-7
C: Rab proteins geranylgeranyltransferase component A 1
D: Ras-related protein Rab-7
E: Rab proteins geranylgeranyltransferase component A 1
F: Ras-related protein Rab-7
G: Rab proteins geranylgeranyltransferase component A 1
H: Ras-related protein Rab-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,30524
Polymers374,9738
Non-polymers3,33216
Water18,7721042
1
A: Rab proteins geranylgeranyltransferase component A 1
B: Ras-related protein Rab-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5766
Polymers93,7432
Non-polymers8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Rab proteins geranylgeranyltransferase component A 1
D: Ras-related protein Rab-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5766
Polymers93,7432
Non-polymers8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Rab proteins geranylgeranyltransferase component A 1
F: Ras-related protein Rab-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5766
Polymers93,7432
Non-polymers8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Rab proteins geranylgeranyltransferase component A 1
H: Ras-related protein Rab-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5766
Polymers93,7432
Non-polymers8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.392, 144.691, 200.086
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Rab proteins geranylgeranyltransferase component A 1 / Rab escort protein 1 / REP-1


Mass: 72622.234 Da / Num. of mol.: 4 / Mutation: K231Q, K462R, T473A, A483G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P37727
#2: Protein
Ras-related protein Rab-7 / RAS-related protein P23 / RAS-related protein BRL-RAS


Mass: 21120.998 Da / Num. of mol.: 4 / 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

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Non-polymers , 5 types, 1058 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical
ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1042 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91847 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91847 Å / Relative weight: 1
ReflectionResolution: 2.5→19.4 Å / Num. all: 129867 / Num. obs: 129867 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 39.7 Å2 / Rsym value: 0.051 / Net I/σ(I): 17.99
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 6.06 / Num. unique all: 14368 / Rsym value: 0.219 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1refinement
ProDCdata collection
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VG0

1vg0


Resolution: 2.5→19.42 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3957873.88 / 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
Rfree0.25 6493 5 %RANDOM
Rwork0.206 ---
obs0.206 129845 99.7 %-
all-129845 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.1999 Å2 / ksol: 0.299375 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21354 0 208 1042 22604
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 1082 5 %
Rwork0.251 20550 -
obs--99.7 %
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-PEG.PARAM

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