[English] 日本語
Yorodumi
- EMDB-76915: Structure of the HPII Catalase from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-76915
TitleStructure of the HPII Catalase from Escherichia coli
Map dataStructure of the HPII Catalase from Escherichia coli
Sample
  • Organelle or cellular component: HPII catalase
    • Protein or peptide: Catalase
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
KeywordsCatalase / HPII / Heme / Reactive oxygen species / tetramer / OXIDOREDUCTASE
Function / homology:
Function and homology information
Biological speciesEscherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsIarocci J / Song M / Guo S
Funding support Canada, 2 items
OrganizationGrant numberCountry
Fonds de Recherche du Quebec - Sante (FRQS)359456 & 376506 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2024-04631 Canada
CitationJournal: To Be Published
Title: Adhesin-mediated co-purification of Escherichia coli HPII (KatE) Catalase revealed its cryo-EM structure
Authors: Iarocci J / Song M / Nadeau J / Wang M / Hancock M / Bui KH / Guo S
History
DepositionApr 27, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_76915.png

Downloads & links

-
Map

FileDownload / File: emd_76915.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the HPII Catalase from Escherichia coli
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 440 pix.
= 297. Å		0.68 Å/pix.
x 440 pix.
= 297. Å		0.68 Å/pix.
x 440 pix.
= 297. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.1555833 - 0.29700696
Average (Standard dev.)0.0008427935 (±0.009861416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map A

Fileemd_76915_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_76915_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HPII catalase

EntireName: HPII catalase
Components
  • Organelle or cellular component: HPII catalase
    • Protein or peptide: Catalase
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

-
Supramolecule #1: HPII catalase

SupramoleculeName: HPII catalase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

-
Macromolecule #1: Catalase

MacromoleculeName: Catalase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: catalase
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Molecular weightTheoretical: 79.615414 KDa
SequenceString: PPAQPTAPGS LKAPDTRNEK LNSLEDVRKG SENYALTTNQ GVRIADDQNS LRAGNRGPTL LEDFILREKI THFDHERIPE RIVHARGSA AHGYFQPYKS LSDITKADFL SDPNKITPVF VRFSTVQGGA GSADTVRDIR GFATKFYTEE GIFDLVGNNT P IFFIQDAH ...String:
PPAQPTAPGS LKAPDTRNEK LNSLEDVRKG SENYALTTNQ GVRIADDQNS LRAGNRGPTL LEDFILREKI THFDHERIPE RIVHARGSA AHGYFQPYKS LSDITKADFL SDPNKITPVF VRFSTVQGGA GSADTVRDIR GFATKFYTEE GIFDLVGNNT P IFFIQDAH KFPDFVHAVK PEPHWAIPQG QSAHDTFWDY VSLQPETLHN VMWAMSDRGI PRSYRTMEGF GIHTFRLINA EG KATFVRF HWKPLAGKAS LVWDEAQKLT GRDPDFHRRE LWEAIEAGDF PEYELGFQLI PEEDEFKFDF DLLDPTKLIP EEL VPVQRV GKMVLNRNPD NFFAENEQAA FHPGHIVPGL DFTNDPLLQG RLFSYTDTQI SRLGGPNFHE IPINRPTCPY HNFQ RDGMH RMGIDTNPAN YEPNSINDNW PRETPPGPKR GGFESYQERV EGNKVRERSP SFGEYYSHPR LFWLSQTPFE QRHIV DGFS FELSKVVRPY IRERVVDQLA HIDLTLAQAV AKNLGIELTD DQLNITPPPD VNGLKKDPSL SLYAIPDGDV KGRVVA ILL NDEVRSADLL AILKALKAKG VHAKLLYSRM GEVTADDGTV LPIAATFAGA PSLTVDAVIV P(OCS)GNIADIAD NGD ANYYLM EAYKHLKPIA LAGDARKFKA TIKIADQGEE GIVEADSADG SFMDELLTLM AAHRVWSRIP KIDKIPA

UniProtKB: UNIPROTKB: A0A061KVC0

-
Macromolecule #2: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

MacromoleculeName: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 2 / Number of copies: 4 / Formula: HDD
Molecular weightTheoretical: 632.487 Da
Chemical component information

ChemComp-HDD:
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 9
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 80.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 28000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
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