[English] 日本語
Yorodumi
- PDB-6j7x: Complex of GGTaseIII, farnesyl-Ykt6, and GGPP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j7x
TitleComplex of GGTaseIII, farnesyl-Ykt6, and GGPP
Components
  • Geranylgeranyl transferase type-2 subunit beta
  • Protein prenyltransferase alpha subunit repeat-containing protein 1
  • Synaptobrevin homolog YKT6
KeywordsLIPID BINDING PROTEIN / lipid transferase
Function / homology
Function and homology information


protein prenyltransferase activity / protein geranylgeranyltransferase type II / Rab-protein geranylgeranyltransferase complex / vesicle targeting / protein-cysteine S-palmitoyltransferase activity / basal dendrite / Rab geranylgeranyltransferase activity / protein geranylgeranylation / Intra-Golgi traffic / SNAP receptor activity ...protein prenyltransferase activity / protein geranylgeranyltransferase type II / Rab-protein geranylgeranyltransferase complex / vesicle targeting / protein-cysteine S-palmitoyltransferase activity / basal dendrite / Rab geranylgeranyltransferase activity / protein geranylgeranylation / Intra-Golgi traffic / SNAP receptor activity / SNARE complex / RAB geranylgeranylation / apical dendrite / vesicle docking involved in exocytosis / retrograde transport, endosome to Golgi / COPII-mediated vesicle transport / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / CDC42 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / COPI-mediated anterograde transport / RAC1 GTPase cycle / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / visual perception / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle membrane / protein modification process / small GTPase binding / protein transport / endosome / cadherin binding / Golgi membrane / neuronal cell body / endoplasmic reticulum / Golgi apparatus / mitochondrion / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
YKT6, SNARE motif / Longin domain / Geranylgeranyl transferase type-2 subunit beta / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin / v-SNARE, coiled-coil homology domain ...YKT6, SNARE motif / Longin domain / Geranylgeranyl transferase type-2 subunit beta / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase alpha-alpha toroid domain / Glycosyltransferase - #20 / Longin-like domain superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Beta-Lactamase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / GERANYLGERANYL DIPHOSPHATE / Synaptobrevin homolog YKT6 / Geranylgeranyl transferase type-2 subunit beta / Protein prenyltransferase alpha subunit repeat-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGoto-Ito, S. / Yamagata, A. / Sato, Y. / Fukai, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyCREST JPMJCR12M5 Japan
Japan Society for the Promotion of ScienceKAKENHI 16K08574 Japan
Japan Society for the Promotion of ScienceKAKENHI 16H05148 Japan
CitationJournal: Embo J. / Year: 2020
Title: A SNARE geranylgeranyltransferase essential for the organization of the Golgi apparatus.
Authors: Shirakawa, R. / Goto-Ito, S. / Goto, K. / Wakayama, S. / Kubo, H. / Sakata, N. / Trinh, D.A. / Yamagata, A. / Sato, Y. / Masumoto, H. / Cheng, J. / Fujimoto, T. / Fukai, S. / Horiuchi, H.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 28, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein prenyltransferase alpha subunit repeat-containing protein 1
B: Geranylgeranyl transferase type-2 subunit beta
C: Synaptobrevin homolog YKT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3015
Polymers97,8053
Non-polymers4962
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-23 kcal/mol
Surface area34760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.169, 119.169, 211.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Protein prenyltransferase alpha subunit repeat-containing protein 1


Mass: 37986.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTAR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6K3
#2: Protein Geranylgeranyl transferase type-2 subunit beta / Geranylgeranyl transferase type II subunit beta / GGTase-II-beta / Rab geranyl-geranyltransferase ...Geranylgeranyl transferase type II subunit beta / GGTase-II-beta / Rab geranyl-geranyltransferase subunit beta / Rab GGTase beta / Rab geranylgeranyltransferase subunit beta / Type II protein geranyl-geranyltransferase subunit beta


Mass: 37371.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABGGTB, GGTB / Production host: Escherichia coli (E. coli)
References: UniProt: P53611, protein geranylgeranyltransferase type II
#3: Protein Synaptobrevin homolog YKT6


Mass: 22446.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YKT6 / Production host: Escherichia coli (E. coli)
References: UniProt: O15498, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#4: Chemical ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE


Mass: 450.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H36O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.12 Å3/Da / Density % sol: 70.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M NaFormate pH 7, 11% PEG 3350, 30% EG

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 39710 / % possible obs: 98.1 % / Redundancy: 21.2 % / Rsym value: 0.114 / Net I/σ(I): 30.7
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 1.52 / Num. unique obs: 1520 / Rsym value: 0.678 / % possible all: 87.5

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J74

6j74


Resolution: 2.75→48.237 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 1984 5.02 %
Rwork0.2114 --
obs0.2134 39494 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→48.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 32 0 6430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026575
X-RAY DIFFRACTIONf_angle_d0.5218909
X-RAY DIFFRACTIONf_dihedral_angle_d10.6392426
X-RAY DIFFRACTIONf_chiral_restr0.02990
X-RAY DIFFRACTIONf_plane_restr0.0031131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7501-2.81880.35191310.29742408X-RAY DIFFRACTION90
2.8188-2.89510.32651400.27952603X-RAY DIFFRACTION97
2.8951-2.98020.28581440.26232630X-RAY DIFFRACTION98
2.9802-3.07640.33631390.26472616X-RAY DIFFRACTION98
3.0764-3.18630.3261510.25222652X-RAY DIFFRACTION98
3.1863-3.31390.29131410.24922673X-RAY DIFFRACTION99
3.3139-3.46470.26571400.2392675X-RAY DIFFRACTION99
3.4647-3.64730.29591440.23652664X-RAY DIFFRACTION99
3.6473-3.87570.28111160.21592714X-RAY DIFFRACTION99
3.8757-4.17480.27411490.21242695X-RAY DIFFRACTION99
4.1748-4.59460.21091300.18352738X-RAY DIFFRACTION99
4.5946-5.25880.22351520.18632734X-RAY DIFFRACTION99
5.2588-6.62280.27211660.22372776X-RAY DIFFRACTION99
6.6228-48.24420.19051410.17822932X-RAY DIFFRACTION99

+
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