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- PDB-6j7f: Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP -

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Basic information

Entry
Database: PDB / ID: 6j7f
TitleComplex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), 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 / SNARE complex ...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 / SNARE complex / SNAP receptor activity / 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 / visual perception / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 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 / Geranylgeranyl transferase type-2 subunit beta / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Prenyltransferase subunit beta ...YKT6, SNARE motif / Geranylgeranyl transferase type-2 subunit beta / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / 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 / Mainly Alpha
Similarity search - Domain/homology
DIPHOSPHATE / FARNESYL / GERAN-8-YL GERAN / L(+)-TARTARIC ACID / 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: 2.883 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 1.1Nov 22, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id
Revision 1.2May 28, 2025Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)98,3087
Polymers97,5033
Non-polymers8054
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-12 kcal/mol
Surface area34950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.415, 119.415, 210.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 3 types, 3 molecules ABC

#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: 22145.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: farnesyl-Ykt6 (C-terminal methylated) / 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

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Non-polymers , 4 types, 4 molecules

#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H34 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2

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Details

Has protein modificationY

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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: 3.85 Å3/Da / Density % sol: 68.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1M Ammonium Tartrate dibasic pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 35109 / % possible obs: 99.9 % / Redundancy: 16.2 % / Rsym value: 0.136 / Net I/σ(I): 12.3
Reflection shellResolution: 2.88→2.93 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1721 / Rsym value: 0.512 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J6X

6j6x


Resolution: 2.883→48.185 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.77
RfactorNum. reflection% reflection
Rfree0.2494 1745 4.98 %
Rwork0.2056 --
obs0.2079 35058 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.883→48.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6479 0 54 0 6533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026679
X-RAY DIFFRACTIONf_angle_d0.59051
X-RAY DIFFRACTIONf_dihedral_angle_d9.9742459
X-RAY DIFFRACTIONf_chiral_restr0.021006
X-RAY DIFFRACTIONf_plane_restr0.0031152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8826-2.96740.38381530.33042654X-RAY DIFFRACTION98
2.9674-3.06320.33011290.30622759X-RAY DIFFRACTION100
3.0632-3.17260.35181340.28562720X-RAY DIFFRACTION100
3.1726-3.29960.31681520.25552721X-RAY DIFFRACTION100
3.2996-3.44980.28821490.23772725X-RAY DIFFRACTION100
3.4498-3.63160.28471400.21672757X-RAY DIFFRACTION100
3.6316-3.8590.22961460.19882767X-RAY DIFFRACTION100
3.859-4.15680.2251650.18512753X-RAY DIFFRACTION100
4.1568-4.57480.23191190.16182814X-RAY DIFFRACTION100
4.5748-5.23610.22791550.1672796X-RAY DIFFRACTION100
5.2361-6.59430.22641520.20092840X-RAY DIFFRACTION100
6.5943-48.19140.18541510.16743007X-RAY DIFFRACTION100

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