[English] 日本語
Yorodumi
- PDB-3cpj: Crystal structure of Ypt31 in complex with yeast Rab-GDI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cpj
TitleCrystal structure of Ypt31 in complex with yeast Rab-GDI
Components
  • GTP-binding protein YPT31/YPT8
  • Rab GDP-dissociation inhibitor
KeywordsPROTEIN TRANSPORT / Rab GTPase / prenylation / vesicular transport / Acetylation / Golgi apparatus / GTP-binding / Lipoprotein / Membrane / Nucleotide-binding / Cytoplasm / GTPase activation / Phosphoprotein
Function / homology
Function and homology information


Rab GDP-dissociation inhibitor activity / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / early endosome to Golgi transport / small GTPase-mediated signal transduction / exocytosis / vesicle-mediated transport / Neutrophil degranulation / GTPase activator activity / trans-Golgi network ...Rab GDP-dissociation inhibitor activity / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / early endosome to Golgi transport / small GTPase-mediated signal transduction / exocytosis / vesicle-mediated transport / Neutrophil degranulation / GTPase activator activity / trans-Golgi network / recycling endosome / autophagy / protein transport / mitochondrial outer membrane / endosome / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Rab GDI protein / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / small GTPase Rab1 family profile. / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Rab GDI protein / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / small GTPase Rab1 family profile. / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Small GTPase / Ras family / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein YPT31/YPT8 / Rab GDP-dissociation inhibitor
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKravchenko, S. / Ignatev, A. / Goody, R.S. / Rak, A. / Pylypenko, O.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism.
Authors: Ignatev, A. / Kravchenko, S. / Rak, A. / Goody, R.S. / Pylypenko, O.
History
DepositionMar 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: Rab GDP-dissociation inhibitor
B: GTP-binding protein YPT31/YPT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3186
Polymers75,7792
Non-polymers5384
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-52.1 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.940, 61.430, 92.750
Angle α, β, γ (deg.)90.00, 103.68, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules GB

#1: Protein Rab GDP-dissociation inhibitor / Rab GDI / Secretory pathway GDP dissociation inhibitor


Mass: 51271.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39958
#2: Protein GTP-binding protein YPT31/YPT8 / Rab GTPase YPT31


Mass: 24508.014 Da / Num. of mol.: 1 / Mutation: D58E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38555

-
Non-polymers , 4 types, 456 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.931 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.35→19.79 Å / Num. all: 30772 / Num. obs: 30683 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.35→2.4 Å / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ukv, chain G

1ukv


Resolution: 2.35→19.79 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.889 / SU B: 7.523 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.389 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25523 1512 5 %RANDOM
Rwork0.19875 ---
all0.20156 28714 --
obs0.20156 28714 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.168 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4749 0 31 452 5232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224875
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.9736594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4145595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73924.398216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04115850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9341523
X-RAY DIFFRACTIONr_chiral_restr0.0710.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023625
X-RAY DIFFRACTIONr_nbd_refined0.190.22231
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23325
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2420
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.213
X-RAY DIFFRACTIONr_mcbond_it0.4721.53075
X-RAY DIFFRACTIONr_mcangle_it0.83224807
X-RAY DIFFRACTIONr_scbond_it1.07932065
X-RAY DIFFRACTIONr_scangle_it1.7914.51787
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 109 -
Rwork0.231 2072 -
obs--100 %

+
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