[English] 日本語
Yorodumi
- PDB-2m70: Structural determination of the Citrus sinensis Poly(A)-Binding P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m70
TitleStructural determination of the Citrus sinensis Poly(A)-Binding Protein CsPABP1
ComponentsPoly(A)-binding protein 1
KeywordsPROTEIN BINDING / Poly(A)-binding protein / Citrus sinensis / CsPABP1
Function / homology
Function and homology information


RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Poly(A)-binding protein 1
Similarity search - Component
Biological speciesCitrus sinensis (sweet orange)
MethodSOLUTION NMR / torsion angle dynamics, distance geometry
Model detailsfewest violations, model1
AuthorsSforca, M.L. / Domingues, M.N. / Zeri, A.C.M. / Benedetti, C.E.
CitationJournal: To be Published
Title: Structural determination of the Citrus sinensis Poly(A)-Binding Protein CsPABP1
Authors: Sforca, M.L. / Domingues, M.N. / Zeri, A.C.M. / Benedetti, C.E.
History
DepositionApr 16, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly(A)-binding protein 1


Theoretical massNumber of molelcules
Total (without water)17,1871
Polymers17,1871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein Poly(A)-binding protein 1


Mass: 17187.125 Da / Num. of mol.: 1 / Fragment: UNP residues 57-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus sinensis (sweet orange) / Production host: Escherichia coli (E. coli) / References: UniProt: G3LUH8

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1333D HN(CA)CB
1433D CBCA(CO)NH
1533D HCACO
1633D HNCO
1723D (H)CCH-TOCSY
1823D CCH-TOCSY
1922D 1H-13C HSQC aliphatic
11022D 1H-13C HSQC aromatic
11113D 1H-15N TOCSY
11213D 1H-15N NOESY
11323D 1H-13C NOESY aliphatic
11422D 1H-13C HSQC aromatic

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-98% 15N] entity-1, 50 mM sodium phosphate-2, 20 mM sodium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-99% 13C; U-99% 15N] entity-4, 50 mM sodium phosphate-5, 20 mM sodium chloride-6, 100% D2O100% D2O
30.6 mM [U-99% 13C; U-99% 15N] entity-7, 50 mM sodium phosphate-8, 20 mM sodium chloride-9, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMentity-1[U-98% 15N]1
50 mMsodium phosphate-21
20 mMsodium chloride-31
0.6 mMentity-4[U-99% 13C; U-99% 15N]2
50 mMsodium phosphate-52
20 mMsodium chloride-62
0.6 mMentity-7[U-99% 13C; U-99% 15N]3
50 mMsodium phosphate-83
20 mMsodium chloride-93
Sample conditionsIonic strength: 0.7 / pH: 6.4 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANArefinement
RefinementMethod: torsion angle dynamics, distance geometry / Software ordinal: 1
NMR constraintsNOE constraints total: 2416 / NOE intraresidue total count: 708 / NOE long range total count: 499 / NOE medium range total count: 524 / NOE sequential total count: 685
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Representative conformer: 1

+
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