[English] 日本語
Yorodumi
- PDB-4lhy: Crystal structure of GDP-bound Rab8:Rabin8 -

+
Open data


ID or keywords:

Loading...

-
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


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 membrane / endosome / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
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)39,6674
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

-
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


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more