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- PDB-4lhx: Crystal structure of nucleotide-free Rab8:Rabin8 -

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Basic information

Entry
Database: PDB / ID: 4lhx
TitleCrystal structure of nucleotide-free Rab8:Rabin8
Components
  • Rab-3A-interacting protein
  • Ras-related protein Rab-8A
KeywordsPROTEIN TRANSPORT / Small GTPase / Guanine Nucleotide Exchange Factor
Function / homology
Function and homology information


ciliary basal body-plasma membrane docking / neurotransmitter receptor transport to postsynaptic membrane / negative regulation of filopodium assembly / Golgi vesicle fusion to target membrane / protein localization to organelle / regulation of protein transport / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / BBSome-mediated cargo-targeting to cilium ...ciliary basal body-plasma membrane docking / neurotransmitter receptor transport to postsynaptic membrane / negative regulation of filopodium assembly / Golgi vesicle fusion to target membrane / protein localization to organelle / regulation of protein transport / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / BBSome-mediated cargo-targeting to cilium / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / proximal dendrite / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / non-motile cilium / vesicle docking involved in exocytosis / TBC/RABGAPs / protein targeting to membrane / 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 / guanyl-nucleotide exchange factor activity / 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 / protein transport / lamellipodium / actin cytoskeleton / GTPase binding / midbody / vesicle / lysosome / endosome / endosome membrane / regulation of autophagy / cilium / ciliary basal body / Golgi membrane / neuronal cell body / GTPase activity / dendrite / centrosome / GTP binding / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / Golgi apparatus / extracellular exosome / nucleoplasm / identical protein binding / nucleus / 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 Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Rho (Ras homology) subfamily of Ras-like small GTPases ...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 Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ras-related protein Rab-8A / Rab-3A-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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: Rab-3A-interacting protein
D: Rab-3A-interacting protein
E: Rab-3A-interacting protein
F: Rab-3A-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7369
Polymers78,4486
Non-polymers2883
Water00
1
A: Ras-related protein Rab-8A
E: Rab-3A-interacting protein
F: Rab-3A-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3204
Polymers39,2243
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-58 kcal/mol
Surface area18080 Å2
MethodPISA
2
B: Ras-related protein Rab-8A
C: Rab-3A-interacting protein
D: Rab-3A-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4165
Polymers39,2243
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-75 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.645, 165.301, 166.404
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
Rab-3A-interacting protein / Rab3A-interacting protein / Rabin-3 / SSX2-interacting protein


Mass: 8982.210 Da / Num. of mol.: 4 / Fragment: unp residues 157-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3IP, RABIN8 / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL)DE3 / References: UniProt: Q96QF0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES. cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES), pH 6.6, 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: 3.05→19.9 Å / Num. all: 21895 / Num. obs: 21696 / % possible obs: 99.1 % / Observed criterion σ(F): 6.5 / Observed criterion σ(I): 18.07

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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: 3.05→19.94 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.882 / SU B: 0.005 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.449 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29996 1076 5 %RANDOM
Rwork0.26357 ---
obs0.26537 20544 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.485 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å20 Å20 Å2
2--4.24 Å20 Å2
3----7.49 Å2
Refinement stepCycle: LAST / Resolution: 3.05→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4735 0 15 0 4750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214820
X-RAY DIFFRACTIONr_bond_other_d00.023152
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.9586490
X-RAY DIFFRACTIONr_angle_other_deg4.40737708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7955640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71925.024205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.80615826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.381527
X-RAY DIFFRACTIONr_chiral_restr0.080.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025489
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02958
X-RAY DIFFRACTIONr_nbd_refined0.2710.21555
X-RAY DIFFRACTIONr_nbd_other0.2380.23510
X-RAY DIFFRACTIONr_nbtor_refined0.2050.22454
X-RAY DIFFRACTIONr_nbtor_other0.1150.22601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2206
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0190.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3180.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5050.23
X-RAY DIFFRACTIONr_symmetry_hbond_other0.3160.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5211.53190
X-RAY DIFFRACTIONr_mcbond_other2.0931.51320
X-RAY DIFFRACTIONr_mcangle_it2.66624970
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.71131630
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4084.51520
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: 3.05→3.127 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 76 -
Rwork0.353 1471 -
obs--98.91 %

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