[English] 日本語
Yorodumi
- EMDB-22530: The Cryo-EM structure of the Catalase-peroxidase from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22530
TitleThe Cryo-EM structure of the Catalase-peroxidase from Escherichia coli
Map data
Sample
  • Complex: KatG
    • Protein or peptide: Catalase-peroxidase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: water
Keywordscatalase-peroxidase / OXIDOREDUCTASE
Function / homology
Function and homology information


catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding
Similarity search - Function
Catalase-peroxidase haem / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsSu C-C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Methods / Year: 2021
Title: A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins.
Authors: Chih-Chia Su / Meinan Lyu / Christopher E Morgan / Jani Reddy Bolla / Carol V Robinson / Edward W Yu /
Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein ...Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (<100 kDa) and less abundant (<10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics.
History
DepositionSep 1, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jz6
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22530.png

Downloads & links

-
Map

FileDownload / File: emd_22530.map.gz / Format: CCP4 / Size: 7.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 139 pix.
= 150.12 Å		1.08 Å/pix.
x 109 pix.
= 117.72 Å		1.08 Å/pix.
x 133 pix.
= 143.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-3.1397276 - 4.6875
Average (Standard dev.)-0.000000000003159 (±0.36039728)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin121109106
Dimensions109133139
Spacing133109139
CellA: 143.64 Å / B: 117.72 Å / C: 150.12001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z133109139
origin x/y/z0.0000.0000.000
length x/y/z143.640117.720150.120
α/β/γ90.00090.00090.000
start NX/NY/NZ107101134
NX/NY/NZ14113986
MAP C/R/S123
start NC/NR/NS109121106
NC/NR/NS133109139
D min/max/mean-3.1404.688-0.000

-
Supplemental data

-
Sample components

-
Entire : KatG

EntireName: KatG
Components
  • Complex: KatG
    • Protein or peptide: Catalase-peroxidase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: water

-
Supramolecule #1: KatG

SupramoleculeName: KatG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Catalase-peroxidase

MacromoleculeName: Catalase-peroxidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: catalase-peroxidase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 80.112586 KDa
SequenceString: MSTSDDIHNT TATGKCPFHQ GGHDQSAGAG TTTRDWWPNQ LRVDLLNQHS NRSNPLGEDF DYRKEFSKLD YYGLKKDLKA LLTESQPWW PADWGSYAGL FIRMAWHGAG TYRSIDGRGG AGRGQQRFAP LNSWPDNVSL DKARRLLWPI KQKYGQKISW A DLFILAGN ...String:
MSTSDDIHNT TATGKCPFHQ GGHDQSAGAG TTTRDWWPNQ LRVDLLNQHS NRSNPLGEDF DYRKEFSKLD YYGLKKDLKA LLTESQPWW PADWGSYAGL FIRMAWHGAG TYRSIDGRGG AGRGQQRFAP LNSWPDNVSL DKARRLLWPI KQKYGQKISW A DLFILAGN VALENSGFRT FGFGAGREDV WEPDLDVNWG DEKAWLTHRH PEALAKAPLG ATEMGLIYVN PEGPDHSGEP LS AAAAIRA TFGNMGMNDE ETVALIAGGH TLGKTHGAGP TSNVGPDPEA APIEEQGLGW ASTYGSGVGA DAITSGLEVV WTQ TPTQWS NYFFENLFKY EWVQTRSPAG AIQFEAVDAP EIIPDPFDPS KKRKPTMLVT DLTLRFDPEF EKISRRFLND PQAF NEAFA RAWFKLTHRD MGPKSRYIGP EVPKEDLIWQ DPLPQPIYNP TEQDIIDLKF AIADSGLSVS ELVSVAWASA STFRG GDKR GGANGARLAL MPQRDWDVNA AAVRALPVLE KIQKESGKAS LADIIVLAGV VGVEKAASAA GLSIHVPFAP GRVDAR QDQ TDIEMFELLE PIADGFRNYR ARLDVSTTES LLIDKAQQLT LTAPEMTALV GGMRVLGANF DGSKNGVFTD RVGVLSN DF FVNLLDMRYE WKATDESKEL FEGRDRETGE VKFTASRADL VFGSNSVLRA VAEVYASSDA HEKFVKDFVA AWVKVMNL D RFDLL

UniProtKB: Catalase-peroxidase

-
Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 18 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 1.4) / Number images used: 123643
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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