[English] 日本語
Yorodumi
- PDB-3zj2: Structure of Nab2p tandem zinc finger 34 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zj2
TitleStructure of Nab2p tandem zinc finger 34
ComponentsNUCLEAR POLYADENYLATED RNA-BINDING PROTEIN NAB2
KeywordsRNA BINDING PROTEIN / CCCH-TYPE ZINC FINGER / MRNA EXPORT / POLY(A) LENGTH CONTROL / POLYADENOSINE RNA BINDING
Function / homology
Function and homology information


: / ribonuclease P RNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 7S RNA binding / poly(A) binding / positive regulation of transcription by RNA polymerase III / poly(A)+ mRNA export from nucleus / regulation of mRNA stability / 5S rRNA binding / tRNA binding ...: / ribonuclease P RNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 7S RNA binding / poly(A) binding / positive regulation of transcription by RNA polymerase III / poly(A)+ mRNA export from nucleus / regulation of mRNA stability / 5S rRNA binding / tRNA binding / mRNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
CCCH zinc finger - #40 / CCCH zinc finger / Nuclear abundant poly(A) RNA-binding protein Nab2, N-terminal / Nuclear polyadenylated RNA-binding 2 protein, CCCH zinc finger 1 / Nab2/ZC3H14, N-terminal domain superfamily / : / : / Nuclear abundant poly(A) RNA-bind protein 2 (Nab2) / Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1 / RNA-binding, Nab2-type zinc finger ...CCCH zinc finger - #40 / CCCH zinc finger / Nuclear abundant poly(A) RNA-binding protein Nab2, N-terminal / Nuclear polyadenylated RNA-binding 2 protein, CCCH zinc finger 1 / Nab2/ZC3H14, N-terminal domain superfamily / : / : / Nuclear abundant poly(A) RNA-bind protein 2 (Nab2) / Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1 / RNA-binding, Nab2-type zinc finger / Nab2-type CCCH zinc finger 4 / Nuclear polyadenylated RNA-binding protein Nab2/ZC3H14 / RNA-binding, Nab2-type zinc finger / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Nuclear polyadenylated RNA-binding protein NAB2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodSOLUTION NMR / CYANA, AMBER
AuthorsMartinez-Lumbreras, S. / Santiveri, C.M. / Mirassou, Y. / Zorrilla, S. / Perez-Canadillas, J.M.
CitationJournal: Structure / Year: 2013
Title: Two Singular Types of Ccch Tandem Zinc Finger in Nab2P Contribute to Polyadenosine RNA Recognition.
Authors: Martinez-Lumbreras, S. / Santiveri, C.M. / Mirassou, Y. / Zorrilla, S. / Perez-Canadillas, J.M.
History
DepositionJan 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Jul 9, 2014Group: Database references / Structure summary
Revision 1.3May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_conn.ptnr2_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: NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN NAB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8303
Polymers7,6991
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50LOWEST TARGET FUNCTION
RepresentativeModel #1

-
Components

#1: Protein NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN NAB2 / NAB2P


Mass: 7698.917 Da / Num. of mol.: 1 / Fragment: ZINC FINGERS 3 AND 4, RESIDUES 333-401
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32505
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHE TWO N-TERMINAL RESIDUES (GS) ARE NOT FROM WILD TYPE SEQUENCE

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-15N HSQC
1211H-15N HMBC
1311H-13C HSQC
141HNCO
151HN(CA) CO
161HNCA
171HN(CA)CB
181CBCA(CO) HN
191H(C)CH- TOCSY
1101(H)CCH- TOCSY
1111(HB) CB(CGCD) HD ARO
1121(HB)CB(CGCDCE)HE ARO
113115N HSQC-NOESY
1141NOESY AND TOCSY
1151(H)CCH-TOCSY
NMR detailsText: NONE

-
Sample preparation

DetailsContents: 90% H2O/10% D2O, 100% D2O
Sample conditionsIonic strength: 25 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 298.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

-
Processing

NMR software
NameVersionDeveloperClassification
Amber7CASE, D.A. ET ALrefinement
NMRPipestructure solution
CcpNmr Analysisstructure solution
CYANAstructure solution
Amberstructure solution
RefinementMethod: CYANA, AMBER / Software ordinal: 1
Details: REFINEMENT PROTOCOL AS DESCRIBED IN THE PRIMARY CITATION
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 50 / 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://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

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