[English] 日本語
Yorodumi
- EMDB-37683: Cryo-EM structure of SIR2/HerA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37683
TitleCryo-EM structure of SIR2/HerA complex
Map data
Sample
  • Complex: Cryo-EM structure of a bacterial protein
    • Protein or peptide: Helicase HerA central domain-containing protein
    • Protein or peptide: SIR2-like domain-containing protein
Keywordsbacterial immune proteins / IMMUNE SYSTEM
Function / homologySIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / SIR2-like domain-containing protein
Function and homology information
Biological speciesPaenibacillus sp. 453mf (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsYu G / Liao F / Li X / Li Z / Zhang H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200496 China
CitationJournal: To Be Published
Title: Cryo-EM structure of a bacterial protein
Authors: Yu G / Liao F / Li X / Li Z / Zhang H
History
DepositionOct 7, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37683.png

Downloads & links

-
Map

FileDownload / File: emd_37683.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 440 pix.
= 435.2 Å		0.99 Å/pix.
x 440 pix.
= 435.2 Å		0.99 Å/pix.
x 440 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98909 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.0150985 - 2.1382077
Average (Standard dev.)-0.0009773322 (±0.05083302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 435.19962 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Cryo-EM structure of a bacterial protein

EntireName: Cryo-EM structure of a bacterial protein
Components
  • Complex: Cryo-EM structure of a bacterial protein
    • Protein or peptide: Helicase HerA central domain-containing protein
    • Protein or peptide: SIR2-like domain-containing protein

-
Supramolecule #1: Cryo-EM structure of a bacterial protein

SupramoleculeName: Cryo-EM structure of a bacterial protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Paenibacillus sp. 453mf (bacteria)
Molecular weightTheoretical: 400 KDa

-
Macromolecule #1: Helicase HerA central domain-containing protein

MacromoleculeName: Helicase HerA central domain-containing protein / type: protein_or_peptide / ID: 1 / Details: WP_091160506.1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Paenibacillus sp. 453mf (bacteria)
Molecular weightTheoretical: 77.626344 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIGVNRMTEA STYIGTVQDV NGANIRVVLD INTISSLKFV DGQGYRIGQI GSFVRIPIGY INLFGIVSQV GAGAVPDKLL EVEPYGHRW ISVQLVGEEG IKKEFERGVS QYPTIGDKVH IVTEPDLKKI YGTQNKKYIS LGNIASVDSI PALVNIDTLV T RHSAVLGS ...String:
MIGVNRMTEA STYIGTVQDV NGANIRVVLD INTISSLKFV DGQGYRIGQI GSFVRIPIGY INLFGIVSQV GAGAVPDKLL EVEPYGHRW ISVQLVGEEG IKKEFERGVS QYPTIGDKVH IVTEPDLKKI YGTQNKKYIS LGNIASVDSI PALVNIDTLV T RHSAVLGS TGSGKSTTVT SILQRISDMS QFPSARIIVF DIHGEYAAAF KGKAKVYKVT PSNNELKLSI PYWALTCDEF LS VAFGGLE GSGRNALIDK IYELKLQTLK RQEYEGINED SLTVDTPIPF SIHKLWFDLY RAEISTHYVQ GSHSEENEAL LLG EDGNPV QKGDSLKVVP PIYMPHTQAQ GATKIYLSNR GKNIRKPLEG LASLLKDPRY EFLFNADDWS VNLDGKTNKD LDAL LETWV GSEESISIFD LSGMPSSILD TLIGILIRIL YDSLFWSRNQ PEGGRERPLL VVLEEAHTYL GKDSRGIAID GVRKI VKEG RKYGIGMMLV SQRPSEIDST ILSQCGTLFA LRMNNSSDRN HVLGAVSDSF EGLMGMLPTL RTGEAIIIGE SVRLPM RTI ISPPPFGRRP DSLDPDVTAK WSNNRVQGDY KEVLTLWRQK KVRSQRIVEN IKRLPVVNEG EMTDMVREMV TSSNILS IG YEADSMTLEI EFNHGLVYQY YDVPETLHTE LLAAESHGKF FNSQIKNNYR FSRI

-
Macromolecule #2: SIR2-like domain-containing protein

MacromoleculeName: SIR2-like domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Paenibacillus sp. 453mf (bacteria)
Molecular weightTheoretical: 43.60948 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDHSITASYY DTTQQLSLLK HVLSEDKRPI AFIIAAGCPV SIRHNDAPLI PDVAGLTRKI SDSFGGNPDS LLMKIIQNLK TTIPNPTIE DILSYIRLLQ QIPMSGKIHD VENSVINALE ESICELIEEE VNVDLPGNAT PYHKIAAWIN SINREHQVEI F TTNYDLLM ...String:
MDHSITASYY DTTQQLSLLK HVLSEDKRPI AFIIAAGCPV SIRHNDAPLI PDVAGLTRKI SDSFGGNPDS LLMKIIQNLK TTIPNPTIE DILSYIRLLQ QIPMSGKIHD VENSVINALE ESICELIEEE VNVDLPGNAT PYHKIAAWIN SINREHQVEI F TTNYDLLM EQALEELNVP YFDGFVGSKR AFFDIRTIEE NKLPSRWSKL WKLHGSINWQ LDKQTQTIWR GTPSKGCSLI HP SHLKYDQ SRKMPYLVMM DQLKLFLNQP SAILITCGYS YKDQHINEVL SQGLQTNPNA LIYGLQYDVL ENYQEAKDMA LKR SNLILL AKDRAIIGKK EGEWKPDPQS SQDNDPLLFF KLGDFQHLAS FLEEISQYDW SKQND

UniProtKB: SIR2-like domain-containing protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63638
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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