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- PDB-7p8w: Human erythrocyte catalase cryoEM -

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Basic information

Entry
Database: PDB / ID: 7p8w
TitleHuman erythrocyte catalase cryoEM
ComponentsCatalase
KeywordsOXIDOREDUCTASE / Human erythrocyte catalase cryoEM
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 / peroxisomal membrane / ureteric bud development / triglyceride metabolic process / Detoxification of Reactive Oxygen Species / antioxidant activity / peroxisomal matrix / positive regulation of cell division / response to vitamin E / response to hyperoxia / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / aerobic respiration / cholesterol metabolic process / response to activity / response to reactive oxygen species / hydrogen peroxide catabolic process / 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 / secretory granule lumen / response to ethanol / ficolin-1-rich granule lumen / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia / response to xenobiotic stimulus / intracellular membrane-bounded organelle / focal adhesion / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / 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 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / Catalase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsChen, S. / Li, J. / Vinothkumar, K.R. / Henderson, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105184322 United Kingdom
CitationJournal: Microscopy (Oxf) / Year: 2022
Title: Interaction of human erythrocyte catalase with air-water interface in cryoEM.
Authors: Shaoxia Chen / Jade Li / Kutti R Vinothkumar / Richard Henderson /
Abstract: One of the key goals in single-particle cryo-microscopy is to obtain a uniform distribution of particle orientations, so that the three-dimensional structure has isotropic resolution in Fourier space. ...One of the key goals in single-particle cryo-microscopy is to obtain a uniform distribution of particle orientations, so that the three-dimensional structure has isotropic resolution in Fourier space. A common problem arises from the interaction of protein molecules with the air-water interface that exists on both surfaces of the thin film of liquid that is formed prior to plunge-freezing into liquid ethane. Some proteins and other macromolecular complexes are disrupted by interaction with the air-water interface. Other proteins or macromolecules either become concentrated through their interaction with the interface or are excluded because they bind strongly to some other part of the grid or the filter paper used in blotting. In this paper, the interaction of human erythrocyte catalase with the air-water interface is investigated and minimized by the addition of certain detergents. Detergents can form an amphipathic monolayer at the air-water interface that creates a barrier and leaves the molecules free to adopt a variety of orientations, thus facilitating the 3D structure determination. These results suggest that further characterization and development of detergents for cryo-microscopy plunge-freezing would be useful.
History
DepositionJul 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jul 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _em_3d_fitting_list.accession_code ..._citation.country / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Catalase
B: Catalase
C: Catalase
D: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,79612
Polymers239,3484
Non-polymers5,4488
Water19,9971110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area53400 Å2
ΔGint-306 kcal/mol
Surface area58510 Å2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 4 - 505 / Label seq-ID: 4 - 505

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Catalase


Mass: 59836.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: erythrocyte / Gene: CAT / Cell (production host): Erythrocyte / Production host: Homo sapiens (human) / Tissue (production host): Blood / References: UniProt: P04040, catalase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human erythrocyte catalase with cofactors Heme and NADPH
Type: ORGANELLE OR CELLULAR COMPONENT / Details: Purified protein / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.24 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
10.15 MSodium chlorideNaCl1
210 mMTris ChlorideC4H11NO31
30.2 mMNADPHNADPH1
SpecimenConc.: 40 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Controlled environment plunge-freezer (Bellare et al, 1988; Technion University)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 0.25 mradians
Image recordingAverage exposure time: 59 sec. / Electron dose: 38 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 356
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

SoftwareName: REFMAC / Version: 5.8.0270 / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4RELION3.1CTF correction
7Coot9.03model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13REFMAC5.8model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 150000 / Details: Autopicked using RELION Laplacian operator
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119169 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 40 / Protocol: OTHER / Space: RECIPROCAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-IDPdb chain residue range
11F4J

1f4j

1F4J124-502
24BLC

4blc

4BLC25-23
RefinementResolution: 2.2→109.17 Å / Cor.coef. Fo:Fc: 0.854 / SU B: 5.34 / SU ML: 0.12 / ESU R: 0.224
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.25656 --
obs0.25656 183210 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 38.369 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å2-0 Å2
2---0.11 Å2-0 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Total: 17668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01317084
ELECTRON MICROSCOPYr_bond_other_d0.0010.01715364
ELECTRON MICROSCOPYr_angle_refined_deg1.4511.67423312
ELECTRON MICROSCOPYr_angle_other_deg1.2961.59435364
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.99352012
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.42222.361000
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.556152616
ELECTRON MICROSCOPYr_dihedral_angle_4_deg16.9815112
ELECTRON MICROSCOPYr_chiral_restr0.0730.22104
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0219900
ELECTRON MICROSCOPYr_gen_planes_other0.0030.024256
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it3.1193.7368048
ELECTRON MICROSCOPYr_mcbond_other3.1183.7348047
ELECTRON MICROSCOPYr_mcangle_it4.7915.61410060
ELECTRON MICROSCOPYr_mcangle_other4.7915.61610061
ELECTRON MICROSCOPYr_scbond_it4.3014.2159036
ELECTRON MICROSCOPYr_scbond_other4.3014.2169034
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other7.0176.10713252
ELECTRON MICROSCOPYr_long_range_B_refined9.51844.26619848
ELECTRON MICROSCOPYr_long_range_B_other9.50944.24519819
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A34244
12B34244
21A34238
22C34238
31A34240
32D34240
41B34238
42C34238
51B34240
52D34240
61C34238
62D34238
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.862 13532 -
obs--100 %

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