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- PDB-3dsx: Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3dsx
TitleCrystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with di-prenylated peptide Ser-Cys(GG)-Ser-Cys(GG) derivated from Rab7
Components(Geranylgeranyl transferase type-2 subunit ...) x 2
KeywordsTRANSFERASE / protein prenylation / Metal-binding / Prenyltransferase / Zinc / Phosphoprotein
Function / homology
Function and homology information


TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / protein geranylgeranyltransferase type II / RAB geranylgeranylation / Rab-protein geranylgeranyltransferase complex / isoprenoid binding / Rab geranylgeranyltransferase activity / protein geranylgeranylation / endoplasmic reticulum to Golgi vesicle-mediated transport / small GTPase binding / zinc ion binding / cytoplasm
Similarity search - Function
Rab geranylgeranyltransferase, alpha subunit, insert-domain / Rab geranylgeranyltransferase, alpha subunit, insert-domain superfamily / Rab geranylgeranyl transferase alpha-subunit, insert domain / Geranylgeranyl transferase type-2 subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat ...Rab geranylgeranyltransferase, alpha subunit, insert-domain / Rab geranylgeranyltransferase, alpha subunit, insert-domain superfamily / Rab geranylgeranyl transferase alpha-subunit, insert domain / Geranylgeranyl transferase type-2 subunit beta / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Leucine-rich repeat domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
GERAN-8-YL GERAN / Geranylgeranyl transferase type-2 subunit alpha / Geranylgeranyl transferase type-2 subunit beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGuo, Z. / Yu, S. / Goody, R.S. / Alexandrov, K. / Blankenfeldt, W.
CitationJournal: Embo J. / Year: 2008
Title: Structures of RabGGTase-substrate/product complexes provide insights into the evolution of protein prenylation
Authors: Guo, Z. / Wu, Y.-W. / Das, D. / Delon, C. / Cramer, J. / Yu, S. / Thuns, S. / Lupilova, N. / Waldmann, H. / Brunsveld, L. / Goody, R.S. / Alexandrov, K. / Blankenfeldt, W.
History
DepositionJul 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 1, 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 / 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.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Geranylgeranyl transferase type-2 subunit alpha
B: Geranylgeranyl transferase type-2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7145
Polymers75,3342
Non-polymers3803
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-65 kcal/mol
Surface area26250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.354, 91.153, 114.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Geranylgeranyl transferase type-2 subunit ... , 2 types, 2 molecules AB

#1: Protein Geranylgeranyl transferase type-2 subunit alpha / Geranylgeranyl transferase type II subunit alpha / Rab geranylgeranyltransferase subunit alpha / ...Geranylgeranyl transferase type II subunit alpha / Rab geranylgeranyltransferase subunit alpha / Rab geranyl-geranyltransferase subunit alpha / Rab GG transferase alpha / Rab GGTase alpha


Mass: 38441.598 Da / Num. of mol.: 1 / Fragment: PFTA domains, UNP residues 1-237 and 353-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET3 0a
Gene: Rabggta, Ggta / Plasmid: pGATEV and pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3)
References: UniProt: Q08602, protein geranylgeranyltransferase type II
#2: Protein Geranylgeranyl transferase type-2 subunit beta / Geranylgeranyl transferase type II subunit beta / GGTase-II-beta / Type II protein geranyl- ...Geranylgeranyl transferase type II subunit beta / GGTase-II-beta / Type II protein geranyl-geranyltransferase subunit beta / Rab geranylgeranyltransferase subunit beta / Rab geranyl-geranyltransferase subunit beta / Rab GG transferase beta / Rab GGTase beta


Mass: 36892.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET3 0a
Gene: Rabggtb, Ggtb / Plasmid: pGATEV and pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3)
References: UniProt: Q08603, protein geranylgeranyltransferase type II

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Non-polymers , 4 types, 300 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H34
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE DEPOSITORS HAVE SOAKED THE CRYSTALS WITH THE DIPRENYLATED PEPTIDE, SER-CYS(GG)-SER-CYS(GG), BUT ...THE DEPOSITORS HAVE SOAKED THE CRYSTALS WITH THE DIPRENYLATED PEPTIDE, SER-CYS(GG)-SER-CYS(GG), BUT CAN ONLY SEE MINOR FRACTIONS OF THIS MOLECULE. GG IS GER (GERAN-8-YL GERAN) AND IS BOUND TO BOTH CYSS OF THE PEPTIDE COVALENTLY. THE PEPTIDE IS DERIVED FROM RAB7.

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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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 2.5% (v/v)DMSO, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9841 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 41909 / Num. obs: 41826 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 7.2 % / Biso Wilson estimate: 39 Å2 / Rsym value: 0.057 / Net I/σ(I): 23.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 6.9 / Num. unique all: 5348 / Rsym value: 0.391 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DB ENTRY 3DSS

3dss


Resolution: 2.1→29.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.084 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22942 2101 5 %RANDOM
Rwork0.16753 ---
obs0.17056 39725 99.85 %-
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: 30.065 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5089 0 22 297 5408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225233
X-RAY DIFFRACTIONr_bond_other_d0.0010.024729
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9627106
X-RAY DIFFRACTIONr_angle_other_deg0.8463.00110940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61223.95238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29415878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5921531
X-RAY DIFFRACTIONr_chiral_restr0.0810.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025820
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021071
X-RAY DIFFRACTIONr_nbd_refined0.2150.21202
X-RAY DIFFRACTIONr_nbd_other0.180.24657
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22611
X-RAY DIFFRACTIONr_nbtor_other0.0870.22807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1661.53268
X-RAY DIFFRACTIONr_mcbond_other0.6991.51302
X-RAY DIFFRACTIONr_mcangle_it1.86725142
X-RAY DIFFRACTIONr_scbond_it2.39732232
X-RAY DIFFRACTIONr_scangle_it3.5764.51958
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 168 -
Rwork0.17 2871 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3093-1.52880.98351.1429-1.14672.296-0.2645-0.2131-0.09990.34770.125-0.0821-0.4295-0.19540.13950.23980.0605-0.0356-0.04140.0187-0.140819.466422.351543.1296
20.54380.27270.39070.71691.32222.8904-0.0392-0.034-0.0902-0.02880.034-0.04370.03220.11740.00520.15410.02890.0055-0.01970.031-0.045918.88843.388316.1981
31.8684-1.7844-0.92061.92981.15610.79330.14110.1473-0.1053-0.2119-0.17960.19610.0128-0.13820.03850.140.0033-0.0082-0.0325-0.0165-0.11340.6566-0.9832-7.1091
40.32350.0838-0.6590.0217-0.17071.3424-0.1125-0.1568-0.46690.64150.0940.28260.1289-0.03420.01840.11690.04640.0778-0.0444-0.10190.0693-10.681222.42429.5029
50.2150.06740.05860.36810.16330.3601-0.0028-0.01050.02-0.0066-0.02760.0069-0.0293-0.05190.03040.17760.01890.006-0.01480.0006-0.06418.366627.44917.1068
60.83720.6365-0.21022.8617-0.13621.0263-0.041-0.03040.0973-0.0572-0.12620.1716-0.1172-0.20110.16720.09170.0614-0.01110.0168-0.0362-0.0921-6.8225.702216.1322
70.14770.05040.08130.10970.05340.062-0.00710.01040.024-0.01170.0011-0.0220.02150.01850.00590.20150.00350.0108-0.00990.006-0.08459.867717.063514.9596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 962 - 97
2X-RAY DIFFRACTION2AA97 - 24498 - 245
3X-RAY DIFFRACTION3AA245 - 329246 - 330
4X-RAY DIFFRACTION4BB5 - 405 - 40
5X-RAY DIFFRACTION5BB41 - 25941 - 259
6X-RAY DIFFRACTION6BB260 - 331260 - 331
7X-RAY DIFFRACTION7BC332
8X-RAY DIFFRACTION7BD333
9X-RAY DIFFRACTION7BE334
10X-RAY DIFFRACTION7AF331 - 477
11X-RAY DIFFRACTION7BG335 - 484

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