[English] 日本語
Yorodumi
- EMDB-17962: Structure of catalase determined by cryoEM at 100 keV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17962
TitleStructure of catalase determined by cryoEM at 100 keV
Map data
Sample
  • Complex: Catalase from human erythrocytes
    • Protein or peptide: Catalase
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to L-ascorbic acid / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to light intensity ...response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to L-ascorbic acid / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to light intensity / catalase / UV protection / response to fatty acid / response to vitamin A / catalase activity / triglyceride metabolic process / peroxisomal membrane / ureteric bud development / antioxidant activity / Detoxification of Reactive Oxygen Species / peroxisomal matrix / positive regulation of cell division / response to hyperoxia / response to vitamin E / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / aerobic respiration / cholesterol metabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / response to activity / Peroxisomal protein import / response to lead ion / response to insulin / response to hydrogen peroxide / cellular response to growth factor stimulus / osteoblast differentiation / peroxisome / response to estradiol / NADP binding / response to ethanol / secretory granule lumen / ficolin-1-rich granule lumen / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to xenobiotic stimulus / focal adhesion / intracellular membrane-bounded organelle / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / extracellular region / membrane / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain ...Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMcMullan G / Naydenova K / Mihaylov D / Peet MJ / Wilson H / Yamashita K / Dickerson JL / Chen S / Cannone G / Lee Y ...McMullan G / Naydenova K / Mihaylov D / Peet MJ / Wilson H / Yamashita K / Dickerson JL / Chen S / Cannone G / Lee Y / Hutchings KA / Gittins O / Sobhy M / Wells T / El-Gomati MM / Dalby J / Meffert M / Schulze-Briese C / Henderson R / Russo CJ
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC UP 120117 United Kingdom
Medical Research Council (MRC, United Kingdom)MC U105184322 United Kingdom
Wellcome Trust220526/B/20/Z United Kingdom
Engineering and Physical Sciences Research CouncilR122522 United Kingdom
Innovate UK103806 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T003677/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure determination by cryoEM at 100 keV.
Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A ...Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A Hutchings / Olivia Gittins / Mohamed A Sobhy / Torquil Wells / Mohamed M El-Gomati / Jason Dalby / Matthias Meffert / Clemens Schulze-Briese / Richard Henderson / Christopher J Russo /
Abstract: Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose- ...Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems.
History
DepositionJul 17, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17962.png

Downloads & links

-
Map

FileDownload / File: emd_17962.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8255 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.105123855 - 0.1860316
Average (Standard dev.)0.00069783104 (±0.007246366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.328 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_17962_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_17962_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_17962_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Catalase from human erythrocytes

EntireName: Catalase from human erythrocytes
Components
  • Complex: Catalase from human erythrocytes
    • Protein or peptide: Catalase
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

-
Supramolecule #1: Catalase from human erythrocytes

SupramoleculeName: Catalase from human erythrocytes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human) / Tissue: human erythrocytes

-
Macromolecule #1: Catalase

MacromoleculeName: Catalase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: catalase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.836996 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADSRDPASD QMQHWKEQRA AQKADVLTTG AGNPVGDKLN VITVGPRGPL LVQDVVFTDE MAHFDRERIP ERVVHAKGAG AFGYFEVTH DITKYSKAKV FEHIGKKTPI AVRFSTVAGE SGSADTVRDP RGFAVKFYTE DGNWDLVGNN TPIFFIRDPI L FPSFIHSQ ...String:
MADSRDPASD QMQHWKEQRA AQKADVLTTG AGNPVGDKLN VITVGPRGPL LVQDVVFTDE MAHFDRERIP ERVVHAKGAG AFGYFEVTH DITKYSKAKV FEHIGKKTPI AVRFSTVAGE SGSADTVRDP RGFAVKFYTE DGNWDLVGNN TPIFFIRDPI L FPSFIHSQ KRNPQTHLKD PDMVWDFWSL RPESLHQVSF LFSDRGIPDG HRHMNGYGSH TFKLVNANGE AVYCKFHYKT DQ GIKNLSV EDAARLSQED PDYGIRDLFN AIATGKYPSW TFYIQVMTFN QAETFPFNPF DLTKVWPHKD YPLIPVGKLV LNR NPVNYF AEVEQIAFDP SNMPPGIEAS PDKMLQGRLF AYPDTHRHRL GPNYLHIPVN CPYRARVANY QRDGPMCMQD NQGG APNYY PNSFGAPEQQ PSALEHSIQY SGEVRRFNTA NDDNVTQVRA FYVNVLNEEQ RKRLCENIAG HLKDAQIFIQ KKAVK NFTE VHPDYGSHIQ ALLDKYNAEK PKNAIHTFVQ SGSHLAAREK ANL

UniProtKB: Catalase

-
Macromolecule #2: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 2 / Number of copies: 1 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

-
Macromolecule #3: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 3 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL 1400/HR + YPS FEG
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: DECTRIS SINGLA (1k x 1k) / Digitization - Dimensions - Width: 1030 pixel / Digitization - Dimensions - Height: 1066 pixel / Average electron dose: 40.0 e/Å2

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27165
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7p8w


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL
Output model

PDB-8pvd:
Structure of catalase determined by cryoEM at 100 keV

+
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