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- PDB-4lhz: Crystal structure of GTP-bound Rab8:Rabin8 -

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Basic information

Entry
Database: PDB / ID: 4lhz
TitleCrystal structure of GTP-bound 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 / Golgi to plasma membrane transport vesicle / neurotransmitter receptor transport to postsynaptic membrane / protein localization to motile cilium / Golgi vesicle fusion to target membrane / regulation of protein transport / protein localization to organelle / negative regulation of filopodium assembly / vesicle-mediated transport in synapse / VxPx cargo-targeting to cilium ...ciliary basal body-plasma membrane docking / Golgi to plasma membrane transport vesicle / neurotransmitter receptor transport to postsynaptic membrane / protein localization to motile cilium / Golgi vesicle fusion to target membrane / regulation of protein transport / protein localization to organelle / negative regulation of filopodium assembly / vesicle-mediated transport in synapse / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / BBSome-mediated cargo-targeting to cilium / proximal dendrite / Golgi to plasma membrane transport / myosin V binding / RAB geranylgeranylation / positive regulation of cilium assembly / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / protein localization to cilium / 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 / protein secretion / 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 / guanyl-nucleotide exchange factor activity / regulation of autophagy / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of long-term neuronal synaptic plasticity / cilium / cellular response to insulin stimulus / autophagy / small GTPase binding / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / Regulation of PLK1 Activity at G2/M Transition / protein transport / synaptic vesicle / lamellipodium / GTPase binding / midbody / dendritic spine / postsynaptic density / endosome membrane / endosome / Golgi membrane / GTPase activity / centrosome / neuronal cell body / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / extracellular exosome / 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 Rab1 family 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 Rab1 family 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
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-8A / Rab-3A-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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)79,4948
Polymers78,4486
Non-polymers1,0462
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)39,7474
Polymers39,2243
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-47 kcal/mol
Surface area17780 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)39,7474
Polymers39,2243
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-53 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.337, 165.561, 167.263
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 173-248
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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, 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: 3.59 Å3/Da / Density % sol: 65.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution ...Details: Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6). In order to produce nucleotide-bound forms of Rab8:Rabin8 complexes, the nucleotide-free Rab8:Rabin8 crystals were soaked with cryo solution containing 30 % (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6 and 1 mM respective nucleotide GDP/GTP for one hours at 278 K, 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→20 Å / Num. all: 19050 / Num. obs: 18932 / % possible obs: 99.4 % / Observed criterion σ(F): 9.9 / Observed criterion σ(I): 9.54

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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: PDB ENTRY 1YZQ

1yzq


Resolution: 3.2→19.99 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.857 / SU B: 0.005 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.469 / ESU R Free: 0.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30877 954 5.1 %RANDOM
Rwork0.27761 ---
obs0.27918 17905 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.122 Å2
Baniso -1Baniso -2Baniso -3
1-4.28 Å20 Å20 Å2
2--2.11 Å20 Å2
3----6.39 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4735 0 64 0 4799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214854
X-RAY DIFFRACTIONr_bond_other_d00.023132
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9716555
X-RAY DIFFRACTIONr_angle_other_deg4.43937664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.525641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70425.025201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.43615809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8531526
X-RAY DIFFRACTIONr_chiral_restr0.0760.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025503
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02955
X-RAY DIFFRACTIONr_nbd_refined0.2680.21551
X-RAY DIFFRACTIONr_nbd_other0.240.23529
X-RAY DIFFRACTIONr_nbtor_refined0.2030.22436
X-RAY DIFFRACTIONr_nbtor_other0.1140.22549
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2205
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1060.25
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0951.53194
X-RAY DIFFRACTIONr_mcbond_other1.0821.51323
X-RAY DIFFRACTIONr_mcangle_it1.99524969
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.11831660
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4154.51586
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: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 68 -
Rwork0.353 1301 -
obs--99.78 %
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)
10.8271-0.1223-0.27161.06040.22872.2538-0.01630.03540.03110.0047-0.0128-0.0113-0.0656-0.01730.0292-0.13630.0257-0.00760.02750.0060.002426.7985-31.0397-39.5516
20.50990.16560.35160.94130.66622.891-0.0452-0.1411-0.0098-0.0987-0.09310.0997-0.2782-0.36050.1383-0.19750.0732-0.07860.0683-0.02220.02689.1623-36.1337-78.4482
30.37470.62840.04797.5735-0.48070.0558-0.2456-0.0522-0.08930.24050.28720.1849-0.234-0.3366-0.04160.03640.0767-0.083-0.1135-0.0129-0.049915.0812-36.0304-93.7431
40.5396-1.23480.06248.85710.68120.1704-0.2723-0.066-0.15410.69310.3538-1.1987-0.07140.3163-0.0816-0.0963-0.014-0.1361-0.05740.0037-0.103523.7574-37.9582-92.3286
54.8244-5.55-1.57726.95191.26811.04170.0073-0.32930.3952-0.56360.1538-0.2662-0.09690.1685-0.1611-0.09670.05630.0556-0.11880.0138-0.06920.3717-34.2596-24.3311
65.1497-6.07740.40578.0332-0.99220.33820.39310.1926-0.4705-1.097-0.27240.75240.4065-0.5249-0.12070.00540.0263-0.009-0.0988-0.0385-0.084315.7792-41.8464-26.4082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 177
2X-RAY DIFFRACTION2B3 - 177
3X-RAY DIFFRACTION3C157 - 228
4X-RAY DIFFRACTION4D157 - 227
5X-RAY DIFFRACTION5E157 - 232
6X-RAY DIFFRACTION6F157 - 232

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