[English] 日本語
Yorodumi
- PDB-3pz1: Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pz1
TitleCrystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3
Components(Geranylgeranyl transferase type-2 subunit ...) x 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein prenylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
Chem-3PZ / 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: 1.95 Å
AuthorsGuo, Z. / Bon, R.S. / Stigter, E.A. / Waldmann, H. / Alexandrov, K. / Blankenfeldt, W. / Goody, R.S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: Structure-Guided Development of Selective RabGGTase Inhibitors.
Authors: Bon, R.S. / Guo, Z. / Stigter, E.A. / Wetzel, S. / Menninger, S. / Wolf, A. / Choidas, A. / Alexandrov, K. / Blankenfeldt, W. / Goody, R.S. / Waldmann, H.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 15, 2014Group: Database references / Source and taxonomy
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)76,2059
Polymers75,2602
Non-polymers9467
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-20 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.554, 90.583, 114.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
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 geranyl-geranyltransferase subunit alpha / ...Geranylgeranyl transferase type II subunit alpha / Rab geranyl-geranyltransferase subunit alpha / Rab GG transferase alpha / Rab GGTase alpha / Rab geranylgeranyltransferase subunit alpha


Mass: 38498.652 Da / Num. of mol.: 1
Fragment: Fusion of residues 1-237 and 353-441 with linker AGSG
Source method: isolated from a genetically manipulated source
Details: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET3 0a
Source: (gene. exp.) Rattus norvegicus (Norway rat) / 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 / Rab geranyl-geranyltransferase ...Geranylgeranyl transferase type II subunit beta / GGTase-II-beta / Rab geranyl-geranyltransferase subunit beta / Rab GG transferase beta / Rab GGTase beta / Rab geranylgeranyltransferase subunit beta / Type II protein geranyl-geranyltransferase subunit beta


Mass: 36760.965 Da / Num. of mol.: 1 / Fragment: UNP residues 10-339
Source method: isolated from a genetically manipulated source
Details: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET3 0a
Source: (gene. exp.) Rattus norvegicus (Norway rat) / 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

-
Non-polymers , 5 types, 406 molecules

#3: Chemical ChemComp-3PZ / (3R)-3-benzyl-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-7-carbonitrile


Mass: 527.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H29N5O3S
#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: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9764 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 2, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 51239 / Num. obs: 50703 / % possible obs: 99 % / Observed criterion σ(I): 5 / Redundancy: 4.1 % / Biso Wilson estimate: 31.8 Å2 / Rsym value: 0.048 / Net I/σ(I): 19.7
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 6920 / Rsym value: 0.331 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DSS

3dss


Resolution: 1.95→29.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.142 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23191 2542 5 %RANDOM
Rwork0.18227 ---
obs0.18469 48147 98.97 %-
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: 29.089 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4991 0 56 399 5446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225270
X-RAY DIFFRACTIONr_bond_other_d00.023551
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9697179
X-RAY DIFFRACTIONr_angle_other_deg4.1583.0018635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4745662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3524.082245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68815889
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1121532
X-RAY DIFFRACTIONr_chiral_restr0.0750.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025870
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021074
X-RAY DIFFRACTIONr_nbd_refined0.2140.21280
X-RAY DIFFRACTIONr_nbd_other0.2290.23541
X-RAY DIFFRACTIONr_nbtor_refined0.180.22611
X-RAY DIFFRACTIONr_nbtor_other0.1060.22245
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2332
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3540.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.228
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0490.21
X-RAY DIFFRACTIONr_mcbond_it1.0631.53193
X-RAY DIFFRACTIONr_mcbond_other2.7351.51283
X-RAY DIFFRACTIONr_mcangle_it1.81125143
X-RAY DIFFRACTIONr_scbond_it2.29632077
X-RAY DIFFRACTIONr_scangle_it3.4554.52017
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 183 -
Rwork0.201 3488 -
obs--98.6 %
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)
100.0002-0.00010.001-0.00040.0002-0.000100.0002-0.0003-0.000100.0002-0.00010.00020.01340.0001-0.0002-0.0031-0.0001-0.00213.99326.754616.3724
2000000-0.000100-0.000300-0.00010.000200.0137-0.00010.0001-0.00310-0.00183.00525.724218.0624
30.0181-0.0022-0.18890.00030.02321.967-0.0454-0.042-0.0364-0.0015-0.00210.0299-0.00810.08830.0474-0.00010.0004-0.0002-0.00030.0002-0.00044.189719.887427.0949
40000000000000000.00230.0001-0.00060.002-0.00080.0021-0.49116.772623.4063
5000000000000000000000-8.376843.547629.1322
60.0004-0.00050.00080.0017-0.00020.0021-0.0004-0.00030.0001-0.00050000.00010.00030.01290.00010.0002-0.003-0.0001-0.00197.706416.073814.8533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 330
2X-RAY DIFFRACTION2B5 - 331
3X-RAY DIFFRACTION3B1
4X-RAY DIFFRACTION4B332
5X-RAY DIFFRACTION5B333
6X-RAY DIFFRACTION6A331 - 513
7X-RAY DIFFRACTION6B338 - 553

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more