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- PDB-6j6x: Crystal structure of apo GGTaseIII -

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Basic information

Entry
Database: PDB / ID: 6j6x
TitleCrystal structure of apo GGTaseIII
Components
  • Geranylgeranyl transferase type-2 subunit beta
  • Protein prenyltransferase alpha subunit repeat-containing protein 1
KeywordsLIPID BINDING PROTEIN / lipid transferase
Function / homology
Function and homology information


protein prenyltransferase activity / protein geranylgeranyltransferase type II / Rab-protein geranylgeranyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / RAB geranylgeranylation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / endoplasmic reticulum to Golgi vesicle-mediated transport / visual perception / protein modification process ...protein prenyltransferase activity / protein geranylgeranyltransferase type II / Rab-protein geranylgeranyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / RAB geranylgeranylation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / endoplasmic reticulum to Golgi vesicle-mediated transport / visual perception / protein modification process / small GTPase binding / mitochondrion / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Geranylgeranyl transferase type-2 subunit beta / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase ...Geranylgeranyl transferase type-2 subunit beta / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
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: 2.962 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 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.3May 28, 2025Group: Database references / Category: citation / citation_author
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,8615
Polymers79,6012
Non-polymers2613
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-36 kcal/mol
Surface area27170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.540, 88.540, 647.581
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 42228.938 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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
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: 4.6 Å3/Da / Density % sol: 77.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.04M MgCl2, 0.05M NaCacodylate pH 6, 5% MPD, 8mM CHAPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.044 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 2.96→50 Å / Num. obs: 33185 / % possible obs: 100 % / Redundancy: 69.8 % / Rmerge(I) obs: 0.204 / Net I/σ(I): 29
Reflection shellResolution: 2.96→3.01 Å / Redundancy: 59.5 % / Rmerge(I) obs: 1.848 / Num. unique obs: 1568 / CC1/2: 0.578 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DSS, 1DCE

3dss

1dce


Resolution: 2.962→49.475 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 29.37
RfactorNum. reflection% reflection
Rfree0.2975 1565 4.74 %
Rwork0.2659 --
obs0.2674 32986 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.962→49.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 17 0 4681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024792
X-RAY DIFFRACTIONf_angle_d0.5176499
X-RAY DIFFRACTIONf_dihedral_angle_d10.3341739
X-RAY DIFFRACTIONf_chiral_restr0.02719
X-RAY DIFFRACTIONf_plane_restr0.002817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9619-3.05750.38171530.3432732X-RAY DIFFRACTION100
3.0575-3.16680.34771350.32912799X-RAY DIFFRACTION100
3.1668-3.29360.34521320.31532767X-RAY DIFFRACTION100
3.2936-3.44340.30191420.28912779X-RAY DIFFRACTION100
3.4434-3.62490.29481270.27762797X-RAY DIFFRACTION100
3.6249-3.8520.29361410.28072845X-RAY DIFFRACTION100
3.852-4.14920.26371280.27092832X-RAY DIFFRACTION100
4.1492-4.56650.26971510.25362838X-RAY DIFFRACTION100
4.5665-5.22670.28791470.25972906X-RAY DIFFRACTION100
5.2267-6.58260.34151590.29242927X-RAY DIFFRACTION100
6.5826-49.48150.27851500.22783199X-RAY DIFFRACTION99

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