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- PDB-3c72: Engineered RabGGTase in complex with a peptidomimetic inhibitor -

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Basic information

Entry
Database: PDB / ID: 3c72
TitleEngineered RabGGTase in complex with a peptidomimetic inhibitor
Components(Geranylgeranyl transferase type-2 subunit ...) x 2
KeywordsTRANSFERASE / peptide inhibitor / Rab prenylation / Metal-binding / Prenyltransferase / Phosphoprotein
Function / homology
Function and homology information


isoprenoid binding / 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 / Rab geranylgeranyltransferase activity / protein geranylgeranylation / 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 and squalene oxidase repeat / 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
Chem-CX1 / 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: 2.3 Å
AuthorsGuo, Z. / Wu, Y.W. / Tan, K.T. / Bon, R.S. / Guiu-Rozas, E. / Delon, C. / Nguyen, U.T. / Wetzel, S. / Arndt, S. / Goody, R.S. ...Guo, Z. / Wu, Y.W. / Tan, K.T. / Bon, R.S. / Guiu-Rozas, E. / Delon, C. / Nguyen, U.T. / Wetzel, S. / Arndt, S. / Goody, R.S. / Blankenfeldt, W. / Alexandrov, K. / Waldmann, H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2008
Title: Development of selective RabGGTase inhibitors and crystal structure of a RabGGTase-inhibitor complex.
Authors: Guo, Z. / Wu, Y.W. / Tan, K.T. / Bon, R.S. / Guiu-Rozas, E. / Delon, C. / Nguyen, T.U. / Wetzel, S. / Arndt, S. / Goody, R.S. / Blankenfeldt, W. / Alexandrov, K. / Waldmann, H.
History
DepositionFeb 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Aug 30, 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)76,3055
Polymers75,5862
Non-polymers7193
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.192, 91.671, 115.439
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: 38693.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rabggta, Ggta / Plasmid: pGATEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q08602, protein geranylgeranyltransferase type II
#2: Protein Geranylgeranyl transferase type-2 subunit beta / Geranylgeranyl transferase type II subunit beta / Rab geranylgeranyltransferase subunit beta / Rab ...Geranylgeranyl transferase type II 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) / Gene: Rabggtb, Ggtb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q08603, protein geranylgeranyltransferase type II

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Non-polymers , 4 types, 194 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-CX1 / N-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-L-tyrosine


Mass: 613.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H35N5O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 14% (w/v) PEG 3350, 0.2 M Ca-Acetate, 0.1 M HEPES, cocrystallization with 5 mM inhibitor, 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: 0.9797 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2006 / Details: Si(111) monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 31830 / % possible obs: 99.7 % / Observed criterion σ(I): 4.7 / Redundancy: 5.7 % / Biso Wilson estimate: 50 Å2 / Rsym value: 5.2 / Net I/σ(I): 20
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 3742 / Rsym value: 40.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LTX

1ltx


Resolution: 2.3→19.88 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.187 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS bodies have been assigned with TLSMD
RfactorNum. reflection% reflectionSelection details
Rfree0.25617 1587 5 %RANDOM
Rwork0.18908 ---
obs0.19242 30241 99.95 %-
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: 31.217 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4988 0 47 191 5226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225187
X-RAY DIFFRACTIONr_bond_other_d0.0020.023474
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9667050
X-RAY DIFFRACTIONr_angle_other_deg1.0613.0018416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7265633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57524.091242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28915855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6551531
X-RAY DIFFRACTIONr_chiral_restr0.0930.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021061
X-RAY DIFFRACTIONr_nbd_refined0.2170.21280
X-RAY DIFFRACTIONr_nbd_other0.1950.23601
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22480
X-RAY DIFFRACTIONr_nbtor_other0.0950.22496
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2206
X-RAY DIFFRACTIONr_metal_ion_refined0.1580.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0840.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.211
X-RAY DIFFRACTIONr_mcbond_it0.8781.53246
X-RAY DIFFRACTIONr_mcbond_other0.1951.51271
X-RAY DIFFRACTIONr_mcangle_it1.45125059
X-RAY DIFFRACTIONr_scbond_it2.132250
X-RAY DIFFRACTIONr_scangle_it2.9584.51988
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 122 -
Rwork0.207 2168 -
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)
159.808127.1807-6.871143.4898-19.130133.73131.1676-0.7535-2.0456-0.7917-0.58970.52760.8213-0.211-0.5780.14420.00020.00420.14780.00310.1439-0.960218.129849.31
21.3703-0.49761.5752.04340.53844.9028-0.1306-0.1379-0.0530.39190.0864-0.3359-0.06890.09010.04420.05810.0471-0.01940.15070.08960.173121.592413.270832.6668
31.8481-0.68960.79911.58770.36722.45540.15990.2331-0.1511-0.1691-0.05910.05930.3580.0854-0.10080.11630.06290.01590.06840.0010.15566.6433-0.884-3.0884
41.4149-0.08960.13041.9630.57391.8851-0.0684-0.19790.190.2427-0.05830.0798-0.1461-0.31140.1267-0.02650.05860.03380.0445-0.01860.05257.199130.052121.0606
52.12380.54930.76312.67521.17292.19070.0294-0.28820.1672-0.0227-0.1670.40150.0464-0.72250.1376-0.02920.05970.0240.2704-0.01220.1443-4.213220.78613.6511
68.264-8.1425-0.154929.9989-15.916911.75341.0647-1.1808-1.5741-1.15920.13744.8601-1.47770.838-1.20210.00040.00090.00030.0013-0.0035-0.00326.382520.740723.2462
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA16 - 2520 - 29
2X-RAY DIFFRACTION2AA26 - 17830 - 182
3X-RAY DIFFRACTION3AA179 - 330183 - 334
4X-RAY DIFFRACTION4BB7 - 2087 - 208
5X-RAY DIFFRACTION5BB209 - 331209 - 331
6X-RAY DIFFRACTION6BE3341

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