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- PDB-4li0: Crystal structure of GDP-bound Rab8:GRAB -

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Basic information

Entry
Database: PDB / ID: 4li0
TitleCrystal structure of GDP-bound Rab8:GRAB
Components
  • Guanine nucleotide exchange factor for Rab-3A
  • Ras-related protein Rab-8A
KeywordsPROTEIN TRANSPORT / Small GTPase / Guanine Nucleotide Exchange Factor
Function / homology
Function and homology information


guanyl-nucleotide exchange factor activity => GO:0005085 / Golgi to plasma membrane transport vesicle / 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 ...guanyl-nucleotide exchange factor activity => GO:0005085 / Golgi to plasma membrane transport vesicle / 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 / vesicle docking involved in exocytosis / trans-Golgi network transport vesicle / regulation of exocytosis / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / non-motile cilium / endocytic recycling / TBC/RABGAPs / ciliary membrane / ciliary base / Golgi organization / exocytosis / cilium assembly / protein secretion / phagocytic vesicle / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / centriole / axonogenesis / small monomeric GTPase / trans-Golgi network membrane / ciliary basal body / regulation of autophagy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / regulation of long-term neuronal synaptic plasticity / cilium / small GTPase binding / autophagy / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / protein transport / midbody / dendritic spine / postsynaptic density / endosome membrane / endosome / Golgi membrane / GTPase activity / centrosome / neuronal cell body / glutamatergic synapse / GTP binding / extracellular exosome / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4880 / GDP/GTP exchange factor Sec2, N-terminal / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4880 / GDP/GTP exchange factor Sec2, N-terminal / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-8A / Guanine nucleotide exchange factor for Rab-3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 / 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 / _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: Guanine nucleotide exchange factor for Rab-3A
D: Guanine nucleotide exchange factor for Rab-3A
E: Guanine nucleotide exchange factor for Rab-3A
F: Guanine nucleotide exchange factor for Rab-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6068
Polymers81,7196
Non-polymers8862
Water0
1
A: Ras-related protein Rab-8A
E: Guanine nucleotide exchange factor for Rab-3A
F: Guanine nucleotide exchange factor for Rab-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3034
Polymers40,8603
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-49 kcal/mol
Surface area18060 Å2
MethodPISA
2
B: Ras-related protein Rab-8A
C: Guanine nucleotide exchange factor for Rab-3A
D: Guanine nucleotide exchange factor for Rab-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3034
Polymers40,8603
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-64 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.930, 160.380, 166.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 21259.371 Da / Num. of mol.: 2 / Fragment: unp residues 1-184
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: Protein
Guanine nucleotide exchange factor for Rab-3A / Rab-3A-interacting-like protein 1 / Rab3A-interacting-like protein 1 / Rabin3-like 1


Mass: 9800.137 Da / Num. of mol.: 4 / Fragment: unp residues 73-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3IL1 / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL)DE3 / References: UniProt: Q8TBN0
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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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: 4.53 Å3/Da / Density % sol: 72.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 1.6 M ammonium sulphate and sodium acetate. cryo solution containing 20% glycerol in the reservoir solution, pH 5.3, 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 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: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→48.21 Å / Num. all: 19050 / Num. obs: 21124 / % possible obs: 99.6 % / Observed criterion σ(F): 7.6 / Observed criterion σ(I): 9.9

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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: 3.3→48.21 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.896 / SU B: 51.803 / SU ML: 0.391 / Cross valid method: THROUGHOUT / ESU R: 1.408 / ESU R Free: 0.47 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28962 1140 5.1 %RANDOM
Rwork0.24419 ---
obs0.24643 21124 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.488 Å2
Baniso -1Baniso -2Baniso -3
1-15.72 Å20 Å20 Å2
2---5.55 Å2-0 Å2
3----10.17 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4807 0 56 0 4863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194916
X-RAY DIFFRACTIONr_bond_other_d0.0020.024681
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.986596
X-RAY DIFFRACTIONr_angle_other_deg0.823310762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.62525.356239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.69315949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3151530
X-RAY DIFFRACTIONr_chiral_restr0.0720.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021067
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_refined0.199
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.25
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.168
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6685.6212446
X-RAY DIFFRACTIONr_mcbond_other3.6665.6172445
X-RAY DIFFRACTIONr_mcangle_it6.2748.3953047
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6945.9412470
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 97 -
Rwork0.376 1511 -
obs--96.52 %
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)
10.21470.29-0.64960.5873-0.15134.78130.0322-0.03770.05890.0885-0.15470.15640.2139-0.24680.12250.3145-0.0397-0.04660.1725-0.05010.113531.318333.801826.0627
21.559-3.41080.046319.1290.69450.1273-0.0969-0.05230.22490.15750.09870.27510.2213-0.096-0.00180.7936-0.1679-0.04610.76690.03890.386731.367430.2245-9.3037
38.6412-4.25171.05332.5867-0.42250.8513-0.01250.2511-0.2620.0185-0.00720.1422-0.26370.07560.01970.8681-0.26960.07330.6455-0.03740.358634.233836.610860.7653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 170
2X-RAY DIFFRACTION1B8 - 170
3X-RAY DIFFRACTION2C80 - 140
4X-RAY DIFFRACTION2D80 - 140
5X-RAY DIFFRACTION3E80 - 140
6X-RAY DIFFRACTION3F80 - 140

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