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- PDB-4lhy: Crystal structure of GDP-bound Rab8:Rabin8 -

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Basic information

Entry
Database: PDB / ID: 4lhy
TitleCrystal structure of GDP-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


Golgi to plasma membrane transport vesicle / ciliary basal body-plasma membrane docking / neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / protein localization to organelle / negative regulation of filopodium assembly / proximal dendrite / VxPx cargo-targeting to cilium ...Golgi to plasma membrane transport vesicle / ciliary basal body-plasma membrane docking / neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / protein localization to organelle / negative regulation of filopodium assembly / proximal dendrite / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / BBSome-mediated cargo-targeting to cilium / Golgi to plasma membrane transport / 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 / protein targeting to membrane / 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 / guanyl-nucleotide exchange factor activity / 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 / protein transport / synaptic vesicle / GTPase binding / lamellipodium / 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 / 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 / Rab-3A-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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)79,4309
Polymers78,4486
Non-polymers9823
Water0
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)39,6674
Polymers39,2243
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-47 kcal/mol
Surface area17840 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)39,7635
Polymers39,2243
Non-polymers5392
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-60 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.587, 164.765, 166.421
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-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
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / 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: 3.52 Å3/Da / Density % sol: 65.07 %
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 hour at 4 C, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.984 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: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.1→20.1 Å / Num. all: 20523 / Num. obs: 20118 / % possible obs: 98 % / Observed criterion σ(F): 8.3 / Observed criterion σ(I): 13.56

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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: 3.1→20.08 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.852 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.459 / ESU R Free: 0.494 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31031 1003 5 %RANDOM
Rwork0.28848 ---
obs0.28957 19035 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.471 Å2
Baniso -1Baniso -2Baniso -3
1-2.68 Å20 Å20 Å2
2--3.74 Å20 Å2
3----6.42 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 61 0 4788
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.017
X-RAY DIFFRACTIONr_bond_other_d0
X-RAY DIFFRACTIONr_angle_refined_deg1.708
X-RAY DIFFRACTIONr_angle_other_deg4.425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.287
X-RAY DIFFRACTIONr_chiral_restr0.082
X-RAY DIFFRACTIONr_gen_planes_refined0.005
X-RAY DIFFRACTIONr_gen_planes_other0.005
X-RAY DIFFRACTIONr_nbd_refined0.27
X-RAY DIFFRACTIONr_nbd_other0.24
X-RAY DIFFRACTIONr_nbtor_refined0.201
X-RAY DIFFRACTIONr_nbtor_other0.117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.182
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.087
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.531
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 57 -
Rwork0.377 1381 -
obs--97.96 %
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)
10.4308-0.1607-0.34611.07640.20372.2153-0.0313-0.0642-0.0132-0.01270.0011-0.0069-0.04890.00980.03020.01050.0146-0.0079-0.0604-0.0001-0.069826.3347-30.9902-39.4307
20.3657-0.02640.33910.85491.34142.5016-0.0433-0.1519-0.0167-0.0826-0.10180.1394-0.1328-0.37270.14510.00740.0511-0.0461-0.0224-0.0482-0.04719.3074-35.8434-78.1721
30.68011.4523-0.155814.1863-1.81430.2337-0.2219-0.04650.06890.61850.2640.2232-0.2939-0.2331-0.04220.12230.1079-0.106-0.2923-0.0216-0.192315.271-35.9037-93.5573
40.6779-1.58080.477913.9463-0.45470.3793-0.1631-0.0968-0.1760.86680.239-1.2349-0.21290.2164-0.07590.0767-0.002-0.0976-0.2808-0.0461-0.242624.0472-37.706-92.2059
57.1101-7.7788-1.78589.46241.49960.66520.29430.28360.6573-0.6557-0.3443-0.5717-0.02530.0720.050.07580.05840.0123-0.30850.0187-0.20920.1692-34.2992-24.3594
64.9362-4.5149-0.04935.2512-0.7720.59570.30540.4095-0.401-0.7887-0.35740.4990.4141-0.31380.0520.1028-0.00970.0101-0.2366-0.0351-0.240715.6759-42.4146-26.5957
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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