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- EMDB-22530: The Cryo-EM structure of the Catalase-peroxidase from Escherichia coli -

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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 / cellular response to hydrogen peroxide / heme binding / metal ion binding / cytosol
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

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Structure visualization

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

emd_22530.png

Downloads & links

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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

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Supplemental data

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Sample components

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Entire : KatG

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

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Supramolecule #1: KatG

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

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

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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

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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

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