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

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Basic information

Entry
Database: PDB / ID: 3dsu
TitleCrystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with farnesyl pyrophosphate
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
FARNESYL DIPHOSPHATE / 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: 1.9 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 / 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 / _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)75,8225
Polymers75,3342
Non-polymers4883
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-65 kcal/mol
Surface area25590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.875, 90.877, 114.240
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, 461 molecules

#3: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 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: 0.9998 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 7, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.9→29.4 Å / Num. all: 55583 / Num. obs: 54566 / % possible obs: 98.2 % / Observed criterion σ(I): 5 / Redundancy: 5.7 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.046 / Net I/σ(I): 22.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 7660 / Rsym value: 0.402 / % possible all: 98.1

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Processing

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

3dss


Resolution: 1.9→29.19 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.797 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.551 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21548 2731 5 %RANDOM
Rwork0.15927 ---
obs0.16204 51834 98.21 %-
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: 25.392 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5023 0 26 458 5507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225174
X-RAY DIFFRACTIONr_bond_other_d0.0010.024651
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9637039
X-RAY DIFFRACTIONr_angle_other_deg0.9643.00110785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1165647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08924.17235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52415868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5731528
X-RAY DIFFRACTIONr_chiral_restr0.1270.2780
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021053
X-RAY DIFFRACTIONr_nbd_refined0.2190.21253
X-RAY DIFFRACTIONr_nbd_other0.190.24708
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22586
X-RAY DIFFRACTIONr_nbtor_other0.0860.22699
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2336
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.250.21
X-RAY DIFFRACTIONr_metal_ion_refined0.080.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.259
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1240.23
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1191.53238
X-RAY DIFFRACTIONr_mcbond_other0.5251.51286
X-RAY DIFFRACTIONr_mcangle_it1.8225088
X-RAY DIFFRACTIONr_scbond_it2.33632208
X-RAY DIFFRACTIONr_scangle_it3.584.51941
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 196 -
Rwork0.186 3759 -
obs--97.99 %
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)
13.6491-2.71721.44683.0281-1.6052.2383-0.4964-0.37-0.01020.56790.3327-0.0755-0.4581-0.2390.16370.20070.0754-0.05550.02440.0113-0.091919.466422.351543.1296
20.84930.48241.03970.92031.51933.42590.0417-0.0098-0.121-0.04430.0334-0.16020.08740.1308-0.0750.11880.0280.01730.01570.03520.040618.88843.388316.1981
31.6118-1.4538-0.8242.15931.17011.34240.08520.0973-0.1331-0.2425-0.11470.21540.0211-0.15250.02950.13240.0052-0.01520.0022-0.0209-0.02570.6566-0.9832-7.1091
40.67540.3995-0.3680.2372-0.21250.23570.0364-0.4286-0.38820.8819-0.23220.45160.4113-0.31740.19580.14550.00240.09920.1701-0.13120.0775-10.681222.42429.5029
50.44280.20.17820.7910.40510.60640.0091-0.02740.0505-0.0259-0.0634-0.0022-0.0472-0.08380.05430.13480.02180.00730.0388-0.00390.00738.366627.44917.1068
61.45350.7134-0.07212.3230.26781.2352-0.0132-0.11140.1611-0.0267-0.22560.285-0.1535-0.34870.23880.0190.0517-0.01380.0667-0.0818-0.0475-6.8225.702216.1322
70.10710.08270.1170.12510.02690.2072-0.0085-0.02260.02430.01780.00580.046-0.0116-0.04420.00260.15510.00470.00560.0912-0.00350.06099.511916.268215.2773
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA17 - 9618 - 97
2X-RAY DIFFRACTION2AA97 - 24498 - 245
3X-RAY DIFFRACTION3AA245 - 330246 - 331
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 - 541
11X-RAY DIFFRACTION7BG335 - 581

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