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- PDB-4lhv: Crystal structure of Rab8 in its inactive GDP-bound form -

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Basic information

Entry
Database: PDB / ID: 4lhv
TitleCrystal structure of Rab8 in its inactive GDP-bound form
ComponentsRas-related protein Rab-8A
KeywordsPROTEIN TRANSPORT / Small GTPase
Function / homology
Function and homology information


neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / protein localization to cilium ...neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / non-motile cilium / vesicle docking involved in exocytosis / TBC/RABGAPs / ciliary membrane / ciliary base / Golgi organization / exocytosis / cilium assembly / phagocytic vesicle / centriole / axonogenesis / Anchoring of the basal body to the plasma membrane / protein tyrosine kinase binding / trans-Golgi network membrane / small monomeric GTPase / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of long-term neuronal synaptic plasticity / small GTPase binding / autophagy / centriolar satellite / phagocytic vesicle membrane / recycling endosome membrane / cellular response to insulin stimulus / synaptic vesicle / GDP binding / Regulation of PLK1 Activity at G2/M Transition / actin cytoskeleton / midbody / lysosome / endosome membrane / endosome / regulation of autophagy / cilium / ciliary basal body / Golgi membrane / neuronal cell body / GTPase activity / dendrite / centrosome / GTP binding / nucleolus / glutamatergic synapse / Golgi apparatus / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
: / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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 ...: / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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-8A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGuo, Z. / Hou, X.M. / Goody, R.S. / Itzen, A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Intermediates in the Guanine Nucleotide Exchange Reaction of Rab8 Protein Catalyzed by Guanine Nucleotide Exchange Factors Rabin8 and GRAB.
Authors: Guo, Z. / Hou, X. / Goody, R.S. / Itzen, A.
History
DepositionJul 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Sep 20, 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _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-8A
B: Ras-related protein Rab-8A
C: Ras-related protein Rab-8A
D: Ras-related protein Rab-8A
E: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,17715
Polymers99,8405
Non-polymers2,33810
Water8,161453
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A: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4353
Polymers19,9681
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4353
Polymers19,9681
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4353
Polymers19,9681
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4353
Polymers19,9681
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4353
Polymers19,9681
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.836, 75.950, 106.618
Angle α, β, γ (deg.)90.00, 98.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-362-

HOH

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Components

#1: Protein
Ras-related protein Rab-8A / Oncogene c-mel


Mass: 19967.920 Da / Num. of mol.: 5 / Fragment: unp residues 6-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB8A, MEL, RAB8 / Plasmid: oPINE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL)DE3 / References: UniProt: P61006
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM ...Details: All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 67917 / Num. obs: 67378 / % possible obs: 99.2 % / Observed criterion σ(F): 3.8 / Observed criterion σ(I): 19.16

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASESphasing
REFMAC5.2.0019refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YZQ

1yzq


Resolution: 1.95→19.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.064 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.69 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24428 3388 5 %RANDOM
Rwork0.20229 ---
obs0.20441 63957 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.651 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å2-0.2 Å2
2--0.56 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6273 0 145 453 6871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226530
X-RAY DIFFRACTIONr_bond_other_d00.024410
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9798797
X-RAY DIFFRACTIONr_angle_other_deg4.199310754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1465790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6324.799298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.796151210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2371533
X-RAY DIFFRACTIONr_chiral_restr0.0820.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027102
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021345
X-RAY DIFFRACTIONr_nbd_refined0.2230.21422
X-RAY DIFFRACTIONr_nbd_other0.2410.24370
X-RAY DIFFRACTIONr_nbtor_refined0.1830.23203
X-RAY DIFFRACTIONr_nbtor_other0.1120.23138
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2452
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.228
X-RAY DIFFRACTIONr_mcbond_it1.9041.53914
X-RAY DIFFRACTIONr_mcbond_other4.3251.51633
X-RAY DIFFRACTIONr_mcangle_it2.96426254
X-RAY DIFFRACTIONr_scbond_it2.0832616
X-RAY DIFFRACTIONr_scangle_it3.2994.52538
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 227 -
Rwork0.237 4711 -
obs--99.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.03130.0197-0.00420.01410.00480.0332-0.00590.0004-0.0013-0.00330.0021-0.00110.0028-0.00110.0039-0.0031-0.00180.00310.0036-0.00090.0062-16.204638.534437.4141
20.05440.0414-0.00120.04070.0260.0795-0.00390.0004-0.0017-0.00150.0019-0.0040.0048-0.00050.002-0.0023-0.00170.00350.00270.00110.00538.402453.332612.2765
30.08760.0213-0.0030.0278-0.00430.0106-0.0021-0.01230.0017-0.00390.00040.00050.00110.00210.0017-0.0045-0.00090.00250.0047-0.00060.006113.94667.443540.992
40.0243-0.00590.01110.0784-0.02340.0130.0013-0.0001-0.0005-0.0029-0.00040.01240.00040-0.001-0.00430.00010.00080.0028-0.00040.009-22.108368.962227.7026
50.0926-0.0724-0.02140.26180.16540.1440.0184-0.0028-0.0003-0.02840.0046-0.0196-0.0160.0068-0.023-0.002900.00490.0009-0.00190.0086-19.156389.48977.6638
60.0003-0.0002-0.00040.0020.00080.0007-0.0006-0.00050.0001-0.0004-0.0004-0.00010.00040.00010.001-0.0028-0.00060.00220.00390.00030.0068-6.558358.977326.7469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 176
2X-RAY DIFFRACTION2B5 - 176
3X-RAY DIFFRACTION3C6 - 176
4X-RAY DIFFRACTION4D6 - 176
5X-RAY DIFFRACTION5E5 - 174
6X-RAY DIFFRACTION6A301 - 434
7X-RAY DIFFRACTION6B301 - 394
8X-RAY DIFFRACTION6C301 - 394
9X-RAY DIFFRACTION6D301 - 384
10X-RAY DIFFRACTION6E301 - 347

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