[English] 日本語
Yorodumi
- PDB-1a4t: SOLUTION STRUCTURE OF PHAGE P22 N PEPTIDE-BOX B RNA COMPLEX, NMR,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a4t
TitleSOLUTION STRUCTURE OF PHAGE P22 N PEPTIDE-BOX B RNA COMPLEX, NMR, 20 STRUCTURES
Components
  • 20-MER BASIC PEPTIDE
  • BOXB RNA
KeywordsTRANSCRIPTION/RNA / BACTERIOPHAGE TRANSCRIPTIONAL ANTITERMINATION / PEPTIDE-RNA RECOGNITION / GNRA LOOP / BENT ALPHA-HELICAL PEPTIDE / TRANSCRIPTION REGULATION / TRANSCRIPTION-RNA COMPLEX
Function / homologyDNA-templated transcription termination / RNA / RNA (> 10) / Probable regulatory protein N
Function and homology information
Biological speciesEnterobacteria phage P22 (virus)
MethodSOLUTION NMR / distance geometry
AuthorsCai, Z. / Gorin, A.A. / Frederick, R. / Ye, X. / Hu, W. / Majumdar, A. / Kettani, A. / Patel, D.J.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex.
Authors: Cai, Z. / Gorin, A. / Frederick, R. / Ye, X. / Hu, W. / Majumdar, A. / Kettani, A. / Patel, D.J.
History
DepositionFeb 4, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BOXB RNA
B: 20-MER BASIC PEPTIDE


Theoretical massNumber of molelcules
Total (without water)7,2462
Polymers7,2462
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100DESCRIBED BELOW
Representative

-
Components

#1: RNA chain BOXB RNA


Mass: 4829.969 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein/peptide 20-MER BASIC PEPTIDE


Mass: 2415.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / References: UniProt: P04891

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE BELOW

-
Sample preparation

Sample conditionspH: 5.7 / Temperature: 297 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VARIAN UNITY INOVAVarianVARIAN UNITY INOVA5001
Varian VARIAN UNITY INOVAVarianVARIAN UNITY INOVA6002

-
Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.8BRUNGERrefinement
2D SPECTRA WERE PROCESSED WITH VNMR (VARIAN), ANALYZED WITH FELIX (BIOSYM/MSI); 3D SPECTRA WERE PROCESSED WITH NMRPIPE, ANALYZED WITH PIPP (DELAGLIO); 3D SPECTRA WERE PROCESSED WITH NMRPIPE AND ANALYZED WITH PIPP (DELAGLIOstructure solution
F. ET AL.AL.structure solution
J. BIOMOL. NMR V6V6structure solution
P277structure solution
1995)structure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: A TOTAL OF 100 INITIAL STRUCTURES OF THE COMPLEX WERE GENERATED USING THE X-PLOR METRIC MATRIX DISTANCE GEOMETRY PROTOCOL GUIDED BY THE NOE DISTANCE RESTRAINTS. ALL THE DISTANCE WERE ...Details: A TOTAL OF 100 INITIAL STRUCTURES OF THE COMPLEX WERE GENERATED USING THE X-PLOR METRIC MATRIX DISTANCE GEOMETRY PROTOCOL GUIDED BY THE NOE DISTANCE RESTRAINTS. ALL THE DISTANCE WERE SUBJECTED TO TWO ROUNDS OF MOLECULAR DYNAMICS REFINEMENT WITH THE NONBO NDED INTERACTIONS SUBJECTED TO A REPULSIVE FORCE FIELD IN THE INITIAL ROUND AND A CHARMM-22 FORCE FIELD CONTAINING VAN DER WAALS AND HYDROGEN BOND (WITH WELL DEPTH OF 3 KCAL/MOL) ENERGY TERM IN THE SUBSEQUENT ROUND. THE ELECTROSTATIC ENERGY TERM WAS TURNE D OFF DURING BOTH ROUNDS OF THE COMPUTATIONS. THE MOLECULAR DYNAMICS PROTOCOL DURING EACH ROUND OF THE COMPUTATIONS WAS AS FOLLOWS. THE STRUCTURES WERE HEATED TO 1000K AND EQUILIBRATED AT THIS TEMPERATURE FOR 0.8 PS, FOLLOWED BY GRADUAL COOLING TO 300 K O VER 48 PS AND SUBSEQUENT EQUILIBRATION AT THIS TEMPERATURE FOR 6 PS. THE RESULTING STRUCTURES WERE SUBJECTED TO 2,000 CYCLES OF ENERGY MINIMIZATION. THE FORCE CONSTANTS FOR NOE DISTANCE RESTRAINTS AND COUPLING CONSTANT BASED DIHEDRAL ANGLE RESTRAINTS WERE MAINTAINED AT VALUES 50 KCAL/MOL A A AND 25 KCAL/MOL RAD RAD, RESPECTIVELY THROUGHOUT THE CALCULATIONS. A FORCE CONSTANT OF 60 KCAL/MOL A A WAS APPLIED TO MAINTAIN HYDROGEN BONDING DISTANCE RESTRAINTS FOR WATSON-CRICK BASE PAIRS IN THE RNA STEM OF THE CO MPLEX. A SUBSET OF 27 REFINED STRUCTURES WERE SELECTED BASED ON THEIR LOWER VALUES OF TOTAL ENERGY, VAN DER WAALS ENERGY AND NOE VIOLATIONS ENERGY. THESE 27 REFINED STRUCTURES DEFINED A NOTICEABLE CONVERGED SUBSET (~10 KCAL/MOL VARIATION OF TOTAL ENERGY W ITHIN SUBSET) AND WERE SEPARATED BY A GAP OF ~120 KCAL/MOL OF TOTAL ENERGY FROM THE REST OF THE ENSEMBLE OF REFINED STRUCTURES. THE 20 STRUCTURES OF THE COMPLEX WITH THE LOWEST NUMBER OF NOE VIOLATIONS EXHIBITED PAIRWISE R.M.S.D. VALUE FOR ALL HEAVY ATOMS OF 1.27 A.
NMR ensembleConformer selection criteria: DESCRIBED BELOW / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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