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

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Basic information

Entry
Database: PDB / ID: 3dsv
TitleCrystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with mono-prenylated peptide Ser-Cys-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
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-70 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.035, 90.613, 114.376
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, 498 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.: 495 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE DEPOSITORS HAVE SOAKED THE CRYSTALS WITH THE MONOPRENYLATED PEPTIDE, SER-CYS-SER-CYS(GG), BUT ...THE DEPOSITORS HAVE SOAKED THE CRYSTALS WITH THE MONOPRENYLATED PEPTIDE, SER-CYS-SER-CYS(GG), BUT CAN ONLY SEE MINOR FRACTIONS OF THIS MOLECULE. GG IS GER (GERAN-8-YL GERAN) AND IS COVALENTLY BOUND TO THE C-TERMINAL CYS OF THE PEPTIDE. 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: 2.31 Å3/Da / Density % sol: 46.65 %
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: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 41395 / Num. obs: 41339 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 18.5 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.085 / Net I/σ(I): 31
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 16.5 % / Mean I/σ(I) obs: 11.1 / Num. unique all: 5293 / Rsym value: 0.379 / % possible all: 99.7

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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: 2.1→29.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.34 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21114 2071 5 %RANDOM
Rwork0.14927 ---
obs0.15231 39268 99.92 %-
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: 25.886 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å20 Å2
2---0.44 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5093 0 17 495 5605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225233
X-RAY DIFFRACTIONr_bond_other_d00.024705
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.967110
X-RAY DIFFRACTIONr_angle_other_deg3.7453.00110897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.9815648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76624.108241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37315874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9371530
X-RAY DIFFRACTIONr_chiral_restr0.1040.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025847
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021070
X-RAY DIFFRACTIONr_nbd_refined0.220.21283
X-RAY DIFFRACTIONr_nbd_other0.2340.24394
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22607
X-RAY DIFFRACTIONr_nbtor_other0.1070.22354
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2367
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0740.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4430.268
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0170.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.11.53213
X-RAY DIFFRACTIONr_mcbond_other1.0341.51303
X-RAY DIFFRACTIONr_mcangle_it1.96825152
X-RAY DIFFRACTIONr_scbond_it2.39432020
X-RAY DIFFRACTIONr_scangle_it3.7014.51955
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
Rfree0.224 159 -
Rwork0.14 2835 -
obs--99.77 %
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)
10.06710.01460.14860.13650.13550.4086-0.0043-0.0053-0.02510.0033-0.0069-0.01610.0029-0.00230.0112-0.02290.00460.0017-0.01770.0069-0.01313.55886.910616.6044
20.21850.05850.00870.26850.15070.19490.0073-0.00280.0159-0.0053-0.03230.0087-0.015-0.0290.025-0.02190.0090.0003-0.0168-0.0035-0.01753.063226.218517.8296
3000000000000000000000-0.55617.013123.4727
400000000000000000000.00010-8.357243.805228.9737
50.01330.00060.00440.0457-0.00070.00150.0016-0.0073-0.00480.00990.00340.003-0.0043-0.0027-0.005-0.0022-0.00210.0035-0.00020.001-0.01439.650916.889315.8552
64.9754-12.67658.273932.2975-21.080413.75910.1063-0.00030.1450.20950.1791-0.17570.49150.0496-0.2853-0.0005-0.00030.000200.0005-0.00016.517423.740919.1882
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3292 - 330
2X-RAY DIFFRACTION2BB5 - 3315 - 331
3X-RAY DIFFRACTION3BC332
4X-RAY DIFFRACTION4BD333
5X-RAY DIFFRACTION5AF331 - 562
6X-RAY DIFFRACTION5BG335 - 597
7X-RAY DIFFRACTION6BE334

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