[English] 日本語
Yorodumi
- PDB-7zew: Complex Cyp33-RRM : AAUAAA RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zew
TitleComplex Cyp33-RRM : AAUAAA RNA
Components
  • Peptidyl-prolyl cis-trans isomerase E
  • RNA (5'-R(*AP*AP*UP*AP*AP*A)-3')
KeywordsTRANSCRIPTION / RRM / RNA BINDING PROTEIN-STRUCTURAL PROTEIN COMPLEX / HISTONE 3 / H3K4me3 / EPIGENETIC / MLL1 Transcription regulation / infant leukemia
Function / homology
Function and homology information


poly(A) binding / U2-type catalytic step 2 spliceosome / cyclosporin A binding / protein peptidyl-prolyl isomerization / positive regulation of viral genome replication / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Transcription-Coupled Nucleotide Excision Repair (TC-NER) ...poly(A) binding / U2-type catalytic step 2 spliceosome / cyclosporin A binding / protein peptidyl-prolyl isomerization / positive regulation of viral genome replication / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA splicing, via spliceosome / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein folding / secretory granule lumen / ficolin-1-rich granule lumen / nuclear speck / intracellular membrane-bounded organelle / mRNA binding / Neutrophil degranulation / regulation of DNA-templated transcription / RNA binding / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / RNA recognition motif / RNA recognition motif ...Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / 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
Similarity search - Domain/homology
RNA / Peptidyl-prolyl cis-trans isomerase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBlatter, M. / Allain, F. / Meylan, C.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Sci Adv / Year: 2023
Title: RNA binding induces an allosteric switch in Cyp33 to repress MLL1-mediated transcription.
Authors: Blatter, M. / Meylan, C. / Clery, A. / Giambruno, R. / Nikolaev, Y. / Heidecker, M. / Solanki, J.A. / Diaz, M.O. / Gabellini, D. / Allain, F.H.
History
DepositionMar 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Jun 19, 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: Peptidyl-prolyl cis-trans isomerase E
B: RNA (5'-R(*AP*AP*UP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)15,0972
Polymers15,0972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 250structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase E / PPIase E / Cyclophilin E / Cyclophilin-33 / Rotamase E


Mass: 13189.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIE, CYP33 / Plasmid: PTYB12 / Details (production host): NdeI plus XhoI / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNP9, peptidylprolyl isomerase
#2: RNA chain RNA (5'-R(*AP*AP*UP*AP*AP*A)-3')


Mass: 1907.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC aliphatic
132isotropic12D 1H-13C HSQC aromatic
141isotropic22D 1H-13C HSQC aliphatic
151isotropic22D 1H-13C HSQC aromatic
181isotropic13D 1H-15N NOESY
172isotropic13D 1H-13C NOESY aliphatic
162isotropic13D 1H-13C NOESY aromatic
192isotropic13D F3-FILTERED- F2-EDITED 13C NOESY
1102isotropic12D F2- FILTERED NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM RNA (5'-R(*AP*AP*UP*AP*AP*A)-3'), 40 mM sodium chloride, 40 mM sodium phosphate, 90% H2O/10% D2O15N90% H2O/10% D2O
solution21 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM RNA (5'-R(*AP*AP*UP*AP*AP*A)-3'), 40 mM sodium chloride, 40 mM sodium phosphate, 90% H2O/10% D2O13C15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPEPTIDYL-PROLYL CIS-TRANS ISOMERASE E[U-100% 15N]1
1 mMRNA (5'-R(*AP*AP*UP*AP*AP*A)-3')natural abundance1
40 mMsodium chloridenatural abundance1
40 mMsodium phosphatenatural abundance1
1 mMPEPTIDYL-PROLYL CIS-TRANS ISOMERASE E[U-100% 13C; U-100% 15N]2
1 mMRNA (5'-R(*AP*AP*UP*AP*AP*A)-3')natural abundance2
40 mMsodium chloridenatural abundance2
40 mMsodium phosphatenatural abundance2
Sample conditionsIonic strength: 80 mM / Label: standard / pH: 7 / Pressure: AMBIENT Pa / Temperature: 310.15 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9001
Bruker AVANCE IIIBrukerAVANCE III7002

-
Processing

NMR software
NameVersionDeveloperClassification
Amber10Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3.96Guntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / 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