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- PDB-1n4p: Protein Geranylgeranyltransferase type-I Complexed with Geranylge... -

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Basic information

Entry
Database: PDB / ID: 1n4p
TitleProtein Geranylgeranyltransferase type-I Complexed with Geranylgeranyl Diphosphate
Components
  • Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
  • Geranylgeranyl transferase type-1 subunit beta
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE / protein geranylgeranyltransferase type-I / GGTase / geranylgeranyl / protein prenylation / CaaX / lipid modification / rap2b
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / positive regulation of tubulin deacetylation / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of nitric-oxide synthase biosynthetic process / microtubule associated complex / forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / heterocyclic compound binding / enzyme-linked receptor protein signaling pathway / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / positive regulation of nitric-oxide synthase biosynthetic process / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / alpha-tubulin binding / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / response to inorganic substance / Signalling to RAS / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of cell cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / homeostasis of number of cells within a tissue / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / striated muscle cell differentiation / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / response to cytokine / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / cytoplasmic side of plasma membrane / Signaling by SCF-KIT
Similarity search - Function
Geranylgeranyl transferase type-1 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 ...Geranylgeranyl transferase type-1 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 / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
GERAN-8-YL GERAN / GERANYLGERANYL DIPHOSPHATE / GTPase KRas / Geranylgeranyl transferase type-1 subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsTaylor, J.S. / Reid, T.S. / Casey, P.J. / Beese, L.S.
CitationJournal: EMBO J. / Year: 2003
Title: Structure of mammalian protein geranylgeranyltransferase type-I
Authors: Taylor, J.S. / Reid, T.S. / Terry, K.L. / Casey, P.J. / Beese, L.S.
History
DepositionNov 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Geranylgeranyl transferase type-1 subunit beta
C: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
D: Geranylgeranyl transferase type-1 subunit beta
E: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
F: Geranylgeranyl transferase type-1 subunit beta
G: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
H: Geranylgeranyl transferase type-1 subunit beta
I: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
J: Geranylgeranyl transferase type-1 subunit beta
K: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
L: Geranylgeranyl transferase type-1 subunit beta
M: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
N: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)525,91037
Polymers521,94714
Non-polymers3,96323
Water18,4471024
1
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1165
Polymers86,5642
Non-polymers5513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
D: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1516
Polymers86,5642
Non-polymers5874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
F: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1165
Polymers86,5642
Non-polymers5513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
H: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1516
Polymers86,5642
Non-polymers5874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
J: Geranylgeranyl transferase type-1 subunit beta
M: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6717
Polymers87,8453
Non-polymers8264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
L: Geranylgeranyl transferase type-1 subunit beta
N: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7068
Polymers87,8453
Non-polymers8615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)272.338, 271.566, 185.425
Angle α, β, γ (deg.)90.00, 131.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / CAAX farnesyltransferase subunit alpha / FTase-alpha / Ras proteins prenyltransferase subunit alpha ...CAAX farnesyltransferase subunit alpha / FTase-alpha / Ras proteins prenyltransferase subunit alpha / Type I protein geranyl-geranyltransferase subunit alpha / GGTase-I-alpha


Mass: 44098.145 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta / Plasmid: ATCC 63134 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein
Geranylgeranyl transferase type-1 subunit beta / Geranylgeranyl transferase type I subunit beta / GGTase-I-beta / Type I protein geranyl- ...Geranylgeranyl transferase type I subunit beta / GGTase-I-beta / Type I protein geranyl-geranyltransferase subunit beta


Mass: 42466.176 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pggt1b / Plasmid: ATCC 63134 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P53610, protein geranylgeranyltransferase type I

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Protein/peptide , 1 types, 2 molecules MN

#3: Protein/peptide Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b / / KKKSKTKCVIL Peptide


Mass: 1280.685 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE GERANYLGERANYL LIPID WAS ADDED BY THE ENZYME.
Source: (synth.) Homo sapiens (human) / References: UniProt: P01116*PLUS

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Non-polymers , 5 types, 1047 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE / Geranylgeranyl pyrophosphate


Mass: 450.443 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H36O7P2
#7: Chemical ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H34
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1024 / 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: 5.48 Å3/Da / Density % sol: 77.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: ammonium sulfate, sodium citrate, dithiothreitol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
21.3 Mammonium sulfate1reservoir
3175 mM1reservoirpH6.5Na3 citrate
420 mMdithiothreitol1reservoir
5100 mMMES1reservoirpH6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 19, 2002 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.65→29.92 Å / Num. all: 286863 / Num. obs: 286863 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 60.8 Å2 / Rsym value: 0.077 / Net I/σ(I): 14
Reflection shellResolution: 2.65→2.74 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.5 / % possible all: 91.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 1038571 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 91.5 % / Rmerge(I) obs: 0.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→29.92 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: ncs restraints employed during refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.228 14289 5 %RANDOM
Rwork0.204 ---
all0.204 286863 --
obs0.204 285197 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.0629 Å2 / ksol: 0.374513 e/Å3
Displacement parametersBiso mean: 53.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.77 Å20 Å2-3.95 Å2
2--11.75 Å20 Å2
3----5.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.65→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32190 0 229 1024 33443
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 2197 4.9 %
Rwork0.325 42461 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMGGPP.TOP
X-RAY DIFFRACTION4GGPP.PARAMION.TOP
X-RAY DIFFRACTION5GG-CYS.PARAMGG-CYS.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.369 / Rfactor Rwork: 0.344

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