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- PDB-4lhw: Crystal structure of Rab8 in its active GppNHp-bound form -

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Basic information

Entry
Database: PDB / ID: 4lhw
TitleCrystal structure of Rab8 in its active GppNHp-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 / vesicle-mediated transport in synapse / regulation of protein transport / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / RAB geranylgeranylation / myosin V binding / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs ...neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / RAB geranylgeranylation / myosin V binding / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / protein localization to cilium / non-motile cilium / vesicle docking involved in exocytosis / TBC/RABGAPs / ciliary membrane / ciliary base / Golgi organization / exocytosis / protein secretion / cilium assembly / phagocytic vesicle / Anchoring of the basal body to the plasma membrane / centriole / protein tyrosine kinase binding / axonogenesis / small monomeric GTPase / ciliary basal body / trans-Golgi network membrane / regulation of autophagy / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of long-term neuronal synaptic plasticity / cellular response to insulin stimulus / cilium / small GTPase binding / autophagy / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / midbody / endosome / dendritic spine / endosome membrane / postsynaptic density / Golgi membrane / GTPase activity / centrosome / neuronal cell body / glutamatergic synapse / GTP binding / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
: / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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 ...: / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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 Rab-8A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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_auth_seq_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)102,69016
Polymers99,8405
Non-polymers2,85111
Water18,8981049
1
A: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6334
Polymers19,9681
Non-polymers6653
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)20,5143
Polymers19,9681
Non-polymers5472
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)20,5143
Polymers19,9681
Non-polymers5472
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)20,5143
Polymers19,9681
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5143
Polymers19,9681
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.381, 96.676, 105.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1049 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH ...Details: Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
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: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→19.9 Å / Num. obs: 132605 / % possible obs: 99.2 % / Observed criterion σ(I): 21.62

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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: 1.55→19.89 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.064 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.183 6688 5 %RANDOM
Rwork0.144 ---
obs0.146 125855 99.2 %-
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: 17.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2---0.73 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6913 0 173 1049 8135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227247
X-RAY DIFFRACTIONr_bond_other_d00.025004
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9819771
X-RAY DIFFRACTIONr_angle_other_deg4.147312171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0995875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2724.13339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.317151383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5731551
X-RAY DIFFRACTIONr_chiral_restr0.3340.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027861
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021508
X-RAY DIFFRACTIONr_nbd_refined0.2330.21586
X-RAY DIFFRACTIONr_nbd_other0.2490.25228
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23625
X-RAY DIFFRACTIONr_nbtor_other0.110.23547
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2845
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0240.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2990.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4821.54267
X-RAY DIFFRACTIONr_mcbond_other2.0771.51780
X-RAY DIFFRACTIONr_mcangle_it2.47726874
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.17832980
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7364.52886
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.183 443 -
Rwork0.135 9142 -
obs--98.28 %
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)
10.06440.01720.01510.1753-0.05580.2097-0.0061-0.0044-0.0066-0.0063-0.0077-0.01480.00660.02450.0138-0.01060.00450.00110.00250.0033-0.003130.9729-14.8494-5.3893
20.0790.05270.01510.1683-0.03590.2446-0.0064-0.002-0.0038-0.00840.00250.002-0.0320.02970.0040.0129-0.0073-0.0018-0.00690.0018-0.014527.774116.377.5781
30.0982-0.0380.13270.22410.05260.3831-0.01310.0294-0.0144-0.0143-0.0120.022-0.04610.03070.0251-0.0074-0.0024-0.00490.00060.0059-0.00685.13216.4024-18.4353
40.0182-0.00850.05540.2821-0.03370.38240.0116-0.0122-0.00960.0077-0.0236-0.0084-0.02640.00590.012-0.0058-0.00710.0062-0.0015-0.0026-0.009135.772211.746-30.6809
50.19860.1225-0.19640.488-0.38780.4460.04460.06210.04880.06780.08220.1015-0.0165-0.0442-0.1268-0.02410.00310.0141-0.00060.0270.02165.6292-0.73562.926
60.00320.00260.0050.0065-0.00280.0185-0.00210.00450.00350.00140.0006-0.0003-0.00380.0030.00150.0060.00010.0024-0.00330.00070.005130.71912.382-10.1315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 176
2X-RAY DIFFRACTION2B3 - 175
3X-RAY DIFFRACTION3C6 - 176
4X-RAY DIFFRACTION4D4 - 176
5X-RAY DIFFRACTION5E6 - 176
6X-RAY DIFFRACTION6A401 - 644
7X-RAY DIFFRACTION6B301 - 488
8X-RAY DIFFRACTION6C301 - 531
9X-RAY DIFFRACTION6D301 - 527
10X-RAY DIFFRACTION6E301 - 455

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