[English] 日本語
Yorodumi
- PDB-7yr7: Cryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yr7
TitleCryo-EM structure of Pseudomonas aeruginosa RsmZ RNA in complex with three RsmA protein dimers
Components
  • RsmZ RNA (118-MER)
  • Translational regulator CsrA
KeywordsRNA BINDING PROTEIN/RNA / RNA-protein Complex / RNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of carbohydrate metabolic process / mRNA catabolic process / positive regulation of translational initiation / negative regulation of translational initiation / mRNA 5'-UTR binding / cytoplasm
Similarity search - Function
Translational regulator CsrA / Carbon storage regulator superfamily / Global regulator protein family
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Translational regulator CsrA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsJia, X. / Pan, Z. / Yuan, Y. / Luo, B. / Luo, Y. / Mukherjee, S. / Jia, G. / Liu, L. / Ling, X. / Yang, X. ...Jia, X. / Pan, Z. / Yuan, Y. / Luo, B. / Luo, Y. / Mukherjee, S. / Jia, G. / Liu, L. / Ling, X. / Yang, X. / Wu, Y. / Liu, T. / Miao, Z. / Wei, X. / Bujnicki, J.M. / Zhao, K. / Su, Z.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
National Natural Science Foundation of China (NSFC)32070049 China
National Natural Science Foundation of China (NSFC)31970131 China
Other government20822401D4057
CitationJournal: Cell Res / Year: 2023
Title: Structural basis of sRNA RsmZ regulation of Pseudomonas aeruginosa virulence.
Authors: Xinyu Jia / Zhiling Pan / Yang Yuan / Bingnan Luo / Yongbo Luo / Sunandan Mukherjee / Guowen Jia / Liu Liu / Xiaobin Ling / Xiting Yang / Zhichao Miao / Xiawei Wei / Janusz M Bujnicki / ...Authors: Xinyu Jia / Zhiling Pan / Yang Yuan / Bingnan Luo / Yongbo Luo / Sunandan Mukherjee / Guowen Jia / Liu Liu / Xiaobin Ling / Xiting Yang / Zhichao Miao / Xiawei Wei / Janusz M Bujnicki / Kelei Zhao / Zhaoming Su /
History
DepositionAug 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.initial_refinement_model_id / _em_admin.last_update
Revision 1.2Mar 12, 2025Group: Data collection / Database references / Structure summary
Category: em_admin / pdbx_database_related / pdbx_entry_details
Item: _em_admin.last_update
Revision 1.1Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / pdbx_database_related / Data content type: EM metadata / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Translational regulator CsrA
E: Translational regulator CsrA
G: Translational regulator CsrA
B: Translational regulator CsrA
A: RsmZ RNA (118-MER)
C: Translational regulator CsrA
D: Translational regulator CsrA


Theoretical massNumber of molelcules
Total (without water)75,5917
Polymers75,5917
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Translational regulator CsrA / Carbon storage regulator


Mass: 6198.266 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: csrA, PAMH27_4484 / Production host: Escherichia coli (E. coli) / References: UniProt: V6AK05
#2: RNA chain RsmZ RNA (118-MER)


Mass: 38400.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: RNP1-6 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 59.7 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameCategory
7UCSF Chimeramodel fitting
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 483925 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12MF0

2mf0

12MF01PDBexperimental model
24KJI

4kji

14KJI2PDBexperimental model
31VPZ

1vpz

11VPZ3PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0065396
ELECTRON MICROSCOPYf_angle_d1.2847871
ELECTRON MICROSCOPYf_dihedral_angle_d15.5772988
ELECTRON MICROSCOPYf_chiral_restr0.0631015
ELECTRON MICROSCOPYf_plane_restr0.008558

+
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