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- PDB-2y8e: Crystal structure of D. melanogaster Rab6 GTPase bound to GMPPNP -

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Basic information

Entry
Database: PDB / ID: 2y8e
TitleCrystal structure of D. melanogaster Rab6 GTPase bound to GMPPNP
ComponentsRAB-PROTEIN 6
KeywordsHYDROLASE / NUCLEOTIDE BINDING / GTP BINDING
Function / homology
Function and homology information


Intra-Golgi traffic / Retrograde transport at the Trans-Golgi-Network / TBC/RABGAPs / protein targeting to Golgi apparatus / RAB geranylgeranylation / germarium-derived egg chamber formation / R7 cell development / oocyte microtubule cytoskeleton polarization / RAB GEFs exchange GTP for GDP on RABs / compound eye morphogenesis ...Intra-Golgi traffic / Retrograde transport at the Trans-Golgi-Network / TBC/RABGAPs / protein targeting to Golgi apparatus / RAB geranylgeranylation / germarium-derived egg chamber formation / R7 cell development / oocyte microtubule cytoskeleton polarization / RAB GEFs exchange GTP for GDP on RABs / compound eye morphogenesis / pole plasm oskar mRNA localization / COPI-independent Golgi-to-ER retrograde traffic / Rab protein signal transduction / receptor recycling / Neutrophil degranulation / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / regulation of postsynaptic membrane potential / exocytosis / phototransduction / vesicle-mediated transport / endomembrane system / autophagosome / axon guidance / intracellular protein transport / actin binding / cytoplasmic vesicle / perikaryon / lysosome / Golgi membrane / neuronal cell body / GTPase activity / synapse / GTP binding / Golgi apparatus / cytosol
Similarity search - Function
: / 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 ...: / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab6
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsWalden, M. / Edwards, T.A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of the Drosophila Melanogaster Rab6 Gtpase at 1.4 A Resolution
Authors: Walden, M. / Jenkins, H.T. / Edwards, T.A.
History
DepositionFeb 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: RAB-PROTEIN 6
B: RAB-PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0679
Polymers40,6862
Non-polymers1,3817
Water4,071226
1
A: RAB-PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9864
Polymers20,3431
Non-polymers6433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RAB-PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0825
Polymers20,3431
Non-polymers7394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-59 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.520, 42.710, 86.860
Angle α, β, γ (deg.)90.00, 133.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2088-

HOH

21B-2090-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.97427, 0.11653, 0.19292), (0.07756, -0.63033, 0.77244), (0.21162, 0.76753, 0.60507)
Vector: -84.32848, -12.78898, 16.55235)

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Components

#1: Protein RAB-PROTEIN 6 / GH09086P / RAB6


Mass: 20343.035 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O18334
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.92 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growpH: 8
Details: 2.4 M AMMONIUM SULPHATE, 0.1 M IMIDAZOLE PH 8.0, 2.5% PEG 400, 2.5% DMSO AND 3% TRIMETHYLAMINE N-OXIDE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.39→31.7 Å / Num. obs: 61395 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 12.326 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.7
Reflection shellResolution: 1.39→1.47 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.4 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YZQ

1yzq


Resolution: 1.39→63.4 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.7 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.17296 3121 5.1 %RANDOM
Rwork0.14458 ---
obs0.14607 58225 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.573 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.29 Å2
2---0.15 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.39→63.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2682 0 81 226 2989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222853
X-RAY DIFFRACTIONr_bond_other_d0.0010.021936
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9843880
X-RAY DIFFRACTIONr_angle_other_deg0.92834699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2423.308133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00615517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0561526
X-RAY DIFFRACTIONr_chiral_restr0.0990.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02605
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4781.51669
X-RAY DIFFRACTIONr_mcbond_other0.4171.5683
X-RAY DIFFRACTIONr_mcangle_it2.4422720
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.50331184
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2364.51152
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.34634789
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 207 -
Rwork0.212 4196 -
obs--94.53 %

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