[English] 日本語
Yorodumi
- PDB-9o7t: S. aureus YhaM D193A, 4 N-terminal domains, 2 RNA substrates -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9o7t
TitleS. aureus YhaM D193A, 4 N-terminal domains, 2 RNA substrates
Components
  • Cmp-binding-factor 1
  • RNA
KeywordsRNA BINDING PROTEIN/RNA / exonuclease / translation / RNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


rRNA 3'-end processing / exonuclease activity / nucleic acid binding
Similarity search - Function
: / HD domain profile. / HD domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / Cmp-binding-factor 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Streptococcus pyogenes (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsMattingly, J.M. / Tanquary, J.R. / Dunham, C.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121359 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI150986 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM093278 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM8367 United States
CitationJournal: To Be Published
Title: Structural insights into RNA recognition by the Staphylococcus aureus exoribonuclease YhaM
Authors: Mattingly, J.M. / Tanquary, J.R. / Liponska, A. / Yap, M.N.F. / Dunham, C.M.
History
DepositionApr 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cmp-binding-factor 1
B: Cmp-binding-factor 1
C: Cmp-binding-factor 1
D: Cmp-binding-factor 1
E: Cmp-binding-factor 1
F: Cmp-binding-factor 1
G: RNA
H: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,82826
Polymers230,9678
Non-polymers86118
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Cmp-binding-factor 1


Mass: 35785.797 Da / Num. of mol.: 6 / Mutation: D193A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cbf1, SAUSA300_1791 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2XHZ3
#2: RNA chain RNA


Mass: 8125.965 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1YhaM D193A hexamer, 4 N-terminal domains, 2 RNA substratesCOMPLEX#20MULTIPLE SOURCES
2YhaM D193A hexamer, 4 N-terminal domainsCOMPLEX#11RECOMBINANT
3RNA substratesCOMPLEX#21SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Staphylococcus aureus (bacteria)1280
33Streptococcus pyogenes (bacteria)160490
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMsodium dihydrogen phosphateNaH2PO41
2150 mMsodium chlorideNaCl1
37 mMmagnesium chlorideMgCl21
41 % v/vglycerolC3H8O31
SpecimenConc.: 1.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.6 sec. / Electron dose: 47 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14007
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

-
Processing

EM software
IDNameVersionCategoryDetails (eV)
1Topaz0.2.5particle selection
2Leginonimage acquisition
4cryoSPARC4.5.3CTF correctionPatch CTF Estimation
9cryoSPARC4.5.3initial Euler assignmentHomogeneous Refinement
10cryoSPARC4.5.3final Euler assignmentHomogeneous Refinement
11cryoSPARC4.5.3classificationcryoSPARC 3D classification (without particle alilgnments)
12cryoSPARC4.5.33D reconstructionHomogeneous Refinement
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8389618
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78085 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 101 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient (CCmask)
Details: Model was built into main EM map de novo using ModelAngelo, then flexibly fit using PHENIX real-space model refinement.
Atomic model buildingDetails: Initial model built de novo using ModelAngelo / Source name: Other / Type: other

+
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