[English] 日本語
Yorodumi
- PDB-3epk: Crystallographic snapshots of eukaryotic dimethylallyltransferase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3epk
TitleCrystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism
Components
  • tRNA
  • tRNA isopentenyltransferase
KeywordsTransferase/RNA / Transferase / Alternative initiation / ATP-binding / Cytoplasm / Mitochondrion / Nucleotide-binding / Nucleus / tRNA processing / Transferase-RNA COMPLEX
Function / homology
Function and homology information


tRNA dimethylallyltransferase / tRNA dimethylallyltransferase activity / tRNA modification / tRNA binding / nucleolus / mitochondrion / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
tRNA isopentenyltransferase, eukaryotes / Histone, subunit A - #140 / IPP transferase / Dimethylallyltransferase / IPP transferase / Classic Zinc Finger / Histone, subunit A / Double Stranded RNA Binding Domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...tRNA isopentenyltransferase, eukaryotes / Histone, subunit A - #140 / IPP transferase / Dimethylallyltransferase / IPP transferase / Classic Zinc Finger / Histone, subunit A / Double Stranded RNA Binding Domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIMETHYLALLYL S-THIOLODIPHOSPHATE / PYROPHOSPHATE / RNA / RNA (> 10) / tRNA dimethylallyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsHuang, R.H. / Zhou, C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism.
Authors: Zhou, C. / Huang, R.H.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 2, 2019Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / entity / struct_ref_seq
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 2.1Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: tRNA isopentenyltransferase
E: tRNA
B: tRNA isopentenyltransferase
F: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,75722
Polymers140,8464
Non-polymers91118
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: tRNA isopentenyltransferase
E: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,92111
Polymers70,4232
Non-polymers4989
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-96 kcal/mol
Surface area27920 Å2
MethodPISA
3
B: tRNA isopentenyltransferase
F: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,83711
Polymers70,4232
Non-polymers4149
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-98 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.854, 209.844, 125.501
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain A,B, using restrain)
NCS domain segments:

Dom-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 13 - 415 / Label seq-ID: 1 - 403

Component-IDAuth asym-IDLabel asym-ID
1AA
2BC

-
Components

-
Protein / RNA chain , 2 types, 4 molecules ABEF

#1: Protein tRNA isopentenyltransferase / Isopentenyl-diphosphate: tRNA isopentenyltransferase / IPP transferase / IPTase / IPPT


Mass: 48199.000 Da / Num. of mol.: 2 / Fragment: UNP residues 13-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MOD5 / Plasmid: pLM-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07884, EC: 2.5.1.8
#2: RNA chain tRNA


Mass: 22224.121 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase

-
Non-polymers , 5 types, 254 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S
#6: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.78 Å3/Da / Density % sol: 67.49 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 6.5
Details: Pentaerythritol propoxylate 426, pH 6.5, vapor diffusion, temperature 278K, VAPOR DIFFUSION
Components of the solutionsName: Pentaerythritol propoxylate 426

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97850.9785
SYNCHROTRONAPS 21-ID-G20.97850.9785
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDNov 12, 2007
MARMOSAIC 300 mm CCD2CCDNov 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 32701

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 3.2→50 Å / Occupancy max: 1.01 / Occupancy min: 1 / FOM work R set: 0.856 / σ(F): 1480
RfactorNum. reflection% reflection
Rfree0.24 2522 7.1 %
Rwork0.19 --
obs-31221 87.7 %
Solvent computationBsol: 29.081 Å2
Displacement parametersBiso max: 195.4 Å2 / Biso mean: 72.171 Å2 / Biso min: 7.73 Å2
Baniso -1Baniso -2Baniso -3
1--15.356 Å20 Å20 Å2
2--20.315 Å20 Å2
3----4.959 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6678 2944 39 236 9897
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.201
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_scbond_it1.6312
X-RAY DIFFRACTIONc_mcangle_it2.3422
X-RAY DIFFRACTIONc_scangle_it2.7192.5
Refine LS restraints NCSRms: 0.074 / Type: restrain / Weight: 100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5pp.parpp.top

+
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