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- EMDB-55403: Catalase CryoEM Structure from Human erythrocyte at 1.87A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-55403
TitleCatalase CryoEM Structure from Human erythrocyte at 1.87A resolution
Map data
Sample
  • Organelle or cellular component: Catalase with cofactor NADPH
    • Protein or peptide: Catalase
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: water
KeywordsCatalase / NADPH / Heme B / Protoporphyrin IX with Fe / OXIDOREDUCTASE
Function / homology
Function and homology information


response to amitrole / response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to L-ascorbic acid ...response to amitrole / response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to L-ascorbic acid / catalase / response to fatty acid / UV protection / response to light intensity / catalase activity / response to vitamin A / peroxisomal membrane / ureteric bud development / triglyceride metabolic process / response to vitamin E / Detoxification of Reactive Oxygen Species / antioxidant activity / peroxisomal matrix / positive regulation of cell division / response to hyperoxia / Mitochondrial unfolded protein response (UPRmt) / response to cadmium ion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cholesterol metabolic process / aerobic respiration / response to reactive oxygen species / response to activity / hydrogen peroxide catabolic process / Peroxisomal protein import / response to hydrogen peroxide / response to insulin / cellular response to growth factor stimulus / response to lead ion / 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 / metal ion binding / identical protein binding / membrane / cytoplasm / cytosol
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 immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / 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 immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / 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: 1.87 Å
AuthorsLi J / Henderson R / Russo CJ / Wilson H / Chen S
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_120117 United Kingdom
CitationJournal: To Be Published
Title: Comparison of human and bacterial monofunctional catalase structures obtained by electron cryomicroscopy
Authors: Slowik D / Li J / Wilson H / Shtyrov A / Chen S / McMullan G / Russo CJ / Murshudov G / Henderson R
History
DepositionOct 17, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55403.png

Downloads & links

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Map

FileDownload / File: emd_55403.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 512 pix.
= 409.6 Å		0.8 Å/pix.
x 512 pix.
= 409.6 Å		0.8 Å/pix.
x 512 pix.
= 409.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0646354 - 0.23304915
Average (Standard dev.)0.00003497954 (±0.0016143428)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 409.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55403_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55403_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55403_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Catalase with cofactor NADPH

EntireName: Catalase with cofactor NADPH
Components
  • Organelle or cellular component: Catalase with cofactor NADPH
    • Protein or peptide: Catalase
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: water

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Supramolecule #1: Catalase with cofactor NADPH

SupramoleculeName: Catalase with cofactor NADPH / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human) / Tissue: Erythrocyte / Location in cell: cytoplasm
Molecular weightTheoretical: 240 KDa

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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) / Tissue: Blood
Molecular weightTheoretical: 59.836996 KDa
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

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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

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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

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 397 / 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

Concentration25 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
154.0 mMNaClsodium chloride
10.0 mMNaH2PO4-Na2HPO4sodium phosphate
0.2 mMC21H30N7O17P3Nicotinamide adenine diphosphate
5.0 mMC32H58N2O8SCHAPSO
GridModel: HexAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 45 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 75 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.003 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 80.0 K / Max: 80.0 K
Alignment procedureComa free - Residual tilt: 0.08 mrad
DetailsThere was 1 optical group with AFIS up to 3 microns.
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 27080 / Average exposure time: 3.0 sec. / Average electron dose: 50.4 e/Å2
Details: Images were collected using AFIS with maximum image shift of 3 microns.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.23 µm / Calibrated defocus min: 1.7 µm / Calibrated magnification: 273437 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.23 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 155000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2187875
Details: 1676 particles picked manually for Topaz training set.
CTF correctionSoftware - Name: RELION (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

13256

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 1070801
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 14 / Avg.num./class: 76500 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7p8w


Chain - Residue range: 4-505 / Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: All 4 chains of entry 7P8W were used
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9t0k:
Catalase CryoEM Structure from Human erythrocyte at 1.87A resolution

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