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- PDB-1ltx: Structure of Rab Escort Protein-1 in complex with Rab geranylgera... -

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Basic information

Entry
Database: PDB / ID: 1ltx
TitleStructure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid
Components
  • (RAB GERANYLGERANYLTRANSFERASE ...) x 2
  • AAAA
  • Rab Escort Protein 1
KeywordsTransferase/Protein binding / RAB PRENYLATION / PRENYLTRANSFERASE / LUCINE-RICH REPEATS / POST-TRANSLATIONAL MODIFICATION / Transferase-Protein binding COMPLEX
Function / homology
Function and homology information


RAB GEFs exchange GTP for GDP on RABs / 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 / protein targeting to membrane / GDP-dissociation inhibitor activity ...RAB GEFs exchange GTP for GDP on RABs / 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 / protein targeting to membrane / GDP-dissociation inhibitor activity / small GTPase-mediated signal transduction / blood vessel development / vesicle-mediated transport / GTPase activator activity / intracellular protein transport / small GTPase binding / protein-containing complex binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Rab protein geranylgeranyltransferase component A / : / RAE1/2 domain I, C-terminal region / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Rab geranylgeranyltransferase, alpha subunit, insert-domain / Rab geranylgeranyltransferase, alpha subunit, insert-domain superfamily / Rab geranylgeranyl transferase alpha-subunit, insert domain ...Rab protein geranylgeranyltransferase component A / : / RAE1/2 domain I, C-terminal region / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / 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 / Rab geranylgeranyltransferase alpha-subunit, insert domain / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / 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 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Leucine-rich repeat domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / FAD/NAD(P)-binding domain superfamily / Alpha Horseshoe / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FARNESYL / Rab proteins geranylgeranyltransferase component A 1 / 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: 2.7 Å
AuthorsPylypenko, O. / Rak, A. / Reents, R. / Niculae, A. / Thoma, N.H. / Waldmann, H. / Schlichting, I. / Goody, R.S. / Alexandrov, K.
Citation
Journal: Mol.Cell / Year: 2003
Title: Structure of Rab Escort Protein-1 in Complex with Rab Geranylgeranyltransferase
Authors: Pylypenko, O. / Rak, A. / Reents, R. / Niculae, A. / Sidorovitch, V. / Cioaca, M.D. / Bessolitsyna, E. / Thoma, N.H. / Waldmann, H. / Schlichting, I. / Goody, R.S. / Alexandrov, K.
#1: Journal: J.STRUCT.BIOL. / Year: 2001
Title: Crystallization and Preliminary X-ray Diffraction Analysis of the Rab Escort Protein-1 in Complex with Rab Geranylgeranyltransferase
Authors: Rak, A. / Reents, R. / Pylypenko, O. / Niculae, A. / Sidorovitch, V. / Thoma, N.H. / Waldmann, H. / Schlichting, I. / Goody, R.S. / Alexandrov, K.
History
DepositionMay 21, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_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_conn.ptnr2_label_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
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT
B: RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT
R: Rab Escort Protein 1
P: AAAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,0777
Polymers174,7704
Non-polymers3073
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.7, 197.3, 85.3
Angle α, β, γ (deg.)90.00, 112.8, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RAB GERANYLGERANYLTRANSFERASE ... , 2 types, 2 molecules AB

#1: Protein RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT


Mass: 64981.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pGATEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: Q08602, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT / Geranylgeranyl transferase type II beta subunit


Mass: 36892.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: Q08603, Transferases; Transferring alkyl or aryl groups, other than methyl groups

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Protein / Protein/peptide , 2 types, 2 molecules RP

#3: Protein Rab Escort Protein 1 / Rab proteins geranylgeranyltransferase component A 1


Mass: 72594.219 Da / Num. of mol.: 1 / Mutation: A473T, G483A, Q231K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P37727
#4: Protein/peptide AAAA


Mass: 302.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PUTATIVE PEPTIDE.

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Non-polymers , 4 types, 106 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG 3350, 100mM KSCN, 100mM Namalonate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion
Details: used microseeding, Rak, A., (2001) J.STRUCT.BIOL., 136, 158.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
220 %PEG33501reservoir
3100 mMKSCN1reservoir
4100 mMNamalonate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.7→19.7 Å / Num. all: 54362 / Num. obs: 54362 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 53.8 Å2 / Rsym value: 0.094 / Net I/σ(I): 9.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.25 / Num. unique all: 3716 / Rsym value: 0.364 / % possible all: 62.5
Reflection
*PLUS
Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 62.5 % / Num. unique obs: 3716 / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
ProDCdata collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DCE

1dce


Resolution: 2.7→19.74 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2824477.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2714 5 %RANDOM
Rwork0.224 ---
all0.224 54362 --
obs0.224 54362 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.0783 Å2 / ksol: 0.342551 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10754 0 17 103 10874
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 337 4.6 %
Rwork0.346 6982 -
obs--76.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4FPP+.PARAM
Refinement
*PLUS
Highest resolution: 2.8 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.274
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.37
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å

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