[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleTracking in atomic detail the functional specializations in viral RecA helicases that occur during evolution.
Journal, issue, pagesNucleic Acids Res, Vol. 41, Issue 20, Page 9396-9410, Year 2013
Publish dateAug 11, 2013
AuthorsKamel El Omari / Christoph Meier / Denis Kainov / Geoff Sutton / Jonathan M Grimes / Minna M Poranen / Dennis H Bamford / Roman Tuma / David I Stuart / Erika J Mancini /
PubMed AbstractMany complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, ...Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected the mechanism of RNA translocation for one such phage, 12, and have now investigated three further highly divergent, cystoviral P4 NTPases (from 6, 8 and 13). High-resolution crystal structures of the set of P4s allow a structure-based phylogenetic analysis, which reveals that these proteins form a distinct subfamily of the RecA-type ATPases. Although the proteins share a common catalytic core, they have different specificities and control mechanisms, which we map onto divergent N- and C-terminal domains. Thus, the RNA loading and tight coupling of NTPase activity with RNA translocation in 8 P4 is due to a remarkable C-terminal structure, which wraps right around the outside of the molecule to insert into the central hole where RNA binds to coupled L1 and L2 loops, whereas in 12 P4, a C-terminal residue, serine 282, forms a specific hydrogen bond to the N7 of purines ring to confer purine specificity for the 12 enzyme.
External linksNucleic Acids Res / PubMed:23939620 / PubMed Central
MethodsX-ray diffraction
Resolution1.7 - 3.1 Å
Structure data

PDB-4blo:
P4 PROTEIN FROM BACTERIOPHAGE PHI6 IN COMPLEX WITH ADP
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-4blp:
P4 PROTEIN FROM BACTERIOPHAGE PHI13
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4blq:
P4 PROTEIN FROM BACTERIOPHAGE PHI8
Method: X-RAY DIFFRACTION / Resolution: 2.79 Å

PDB-4blr:
P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH UTP
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-4bls:
P4 PROTEIN FROM BACTERIOPHAGE PHI12 Q278A MUTANT IN COMPLEX WITH AMPcPP
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-4blt:
P4 PROTEIN FROM BACTERIOPHAGE PHI12 S292A MUTANT IN COMPLEX WITH AMPcPP
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-4bwy:
P4 PROTEIN FROM BACTERIOPHAGE PHI8 (R32)
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-FLC:
CITRATE ANION

ChemComp-GOL:
GLYCEROL

ChemComp-HOH:
WATER

ChemComp-UTP:
URIDINE 5'-TRIPHOSPHATE / UTP*YM

ChemComp-DTT:
2,3-DIHYDROXY-1,4-DITHIOBUTANE

ChemComp-APC:
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / AMP-CPP, energy-carrying molecule analogue*YM

Source
  • pseudomonas phage phi6 (bacteriophage)
  • pseudomonas phage phi13 (bacteriophage)
  • pseudomonas phage phi8 (bacteriophage)
  • pseudomonas phage phi12 (bacteriophage)
KeywordsHYDROLASE / ATPASE / CYSTOVIRIDAE / NTPASE / PACKAGING

+
About Yorodumi Papers

-
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://pdbjlvh1.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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more