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- PDB-2gil: Structure of the extremely slow GTPase Rab6A in the GTP bound for... -

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Basic information

Entry
Database: PDB / ID: 2gil
TitleStructure of the extremely slow GTPase Rab6A in the GTP bound form at 1.8 resolution
ComponentsRas-related protein Rab-6A
KeywordsPROTEIN TRANSPORT / protein-nucleotide complex / GTPase-fold
Function / homology
Function and homology information


peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / endosome to plasma membrane transport vesicle / protein localization to Golgi membrane / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / acrosomal membrane / protein localization to Golgi apparatus / Pre-NOTCH Processing in Golgi / myosin V binding ...peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / endosome to plasma membrane transport vesicle / protein localization to Golgi membrane / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / acrosomal membrane / protein localization to Golgi apparatus / Pre-NOTCH Processing in Golgi / myosin V binding / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / COPI-independent Golgi-to-ER retrograde traffic / TBC/RABGAPs / antigen processing and presentation / endomembrane system / secretory granule membrane / trans-Golgi network membrane / small monomeric GTPase / intracellular protein transport / trans-Golgi network / neuron projection development / cytoplasmic vesicle / ciliary basal body / Golgi membrane / protein domain specific binding / GTPase activity / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / 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 ...: / 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-6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsBergbrede, T. / Pylypenko, O. / Rak, A. / Alexandrov, K.
CitationJournal: J.STRUCT.BIOL. / Year: 2005
Title: Structure of the extremely slow GTPase Rab6A in the GTP bound form at 1.8 resolution
Authors: Bergbrede, T. / Pylypenko, O. / Rak, A. / Alexandrov, A.
History
DepositionMar 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 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-6A
B: Ras-related protein Rab-6A
C: Ras-related protein Rab-6A
D: Ras-related protein Rab-6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,66712
Polymers74,4774
Non-polymers2,1908
Water13,313739
1
A: Ras-related protein Rab-6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1673
Polymers18,6191
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1673
Polymers18,6191
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ras-related protein Rab-6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1673
Polymers18,6191
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ras-related protein Rab-6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1673
Polymers18,6191
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.008, 124.853, 66.162
Angle α, β, γ (deg.)90.00, 107.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ras-related protein Rab-6A / Rab-6


Mass: 18619.230 Da / Num. of mol.: 4 / Fragment: Rab6aNd12Cd33 (residues 12-173)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20340
#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.: 739 / 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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM TrisHCl, 1M LiCl, 32% (w/v) polyethylene glycol 1000, 3.3mM Nonyl-D-glucoside, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0398 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0398 Å / Relative weight: 1
ReflectionResolution: 1.82→19.05 Å / Num. all: 48538 / Num. obs: 48538 / % possible obs: 87.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 25.99 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.032 / Net I/σ(I): 17.44
Reflection shellResolution: 1.82→1.9 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3482 / Rsym value: 0.146 / % possible all: 52.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ProDCdata collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1D5C

1d5c


Resolution: 1.82→19.05 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.878 / SU B: 3.892 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.187 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27735 2428 5 %RANDOM
Rwork0.20484 ---
all0.20849 46121 --
obs0.20849 46121 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.728 Å2
Refinement stepCycle: LAST / Resolution: 1.82→19.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5194 0 132 739 6065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225413
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9817336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99723.636253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83115979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4781547
X-RAY DIFFRACTIONr_chiral_restr0.0880.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023955
X-RAY DIFFRACTIONr_nbd_refined0.2070.22800
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23709
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2605
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.246
X-RAY DIFFRACTIONr_mcbond_it0.8141.53310
X-RAY DIFFRACTIONr_mcangle_it1.34325196
X-RAY DIFFRACTIONr_scbond_it1.89432444
X-RAY DIFFRACTIONr_scangle_it2.8354.52140
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 79 -
Rwork0.211 1492 -
obs--52 %

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