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- PDB-6j7x: Complex of GGTaseIII, farnesyl-Ykt6, and GGPP -

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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 / protein-cysteine S-palmitoyltransferase activity / Rab-protein geranylgeranyltransferase complex / vesicle targeting / basal dendrite / Intra-Golgi traffic / Rab geranylgeranyltransferase activity / protein geranylgeranylation / SNARE complex ...protein prenyltransferase activity / protein geranylgeranyltransferase type II / protein-cysteine S-palmitoyltransferase activity / Rab-protein geranylgeranyltransferase complex / vesicle targeting / basal dendrite / Intra-Golgi traffic / Rab geranylgeranyltransferase activity / protein geranylgeranylation / 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 / COPI-mediated anterograde transport / transport vesicle / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RAC1 GTPase cycle / endoplasmic reticulum-Golgi intermediate compartment membrane / visual perception / cytoplasmic vesicle membrane / protein modification process / small GTPase binding / protein transport / endosome / cadherin binding / Golgi membrane / neuronal cell body / Golgi apparatus / endoplasmic reticulum / mitochondrion / zinc ion binding / plasma membrane / cytosol / cytoplasm
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. / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / 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 / 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: To Be Published
Title: Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP
Authors: Goto-Ito, S. / Shirakawa, R. / Fukai, S.
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

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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)98,3015
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

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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

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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: 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

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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 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

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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

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