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- EMDB-44453: MicroED structure of bovine liver catalase with missing cone solv... -

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Basic information

Entry
Database: EMDB / ID: EMD-44453
TitleMicroED structure of bovine liver catalase with missing cone solved by suspended drop
Map data
Sample
  • Complex: Bovine liver catalase
    • Protein or peptide: Catalase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
KeywordsHeme-containing enzyme / OXIDOREDUCTASE
Function / homology
Function and homology information


catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / positive regulation of cell division / peroxisomal matrix / hydrogen peroxide catabolic process ...catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / positive regulation of cell division / peroxisomal matrix / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / heme binding / enzyme binding / mitochondrion / metal ion binding / 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 speciesBos taurus (cattle)
Methodelectron crystallography / cryo EM / Resolution: 4.0 Å
AuthorsGillman C / Bu G / Gonen T
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM136508 United States
Department of Defense (DOD, United States)HDTRA1-21-1-0004 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J Struct Biol X / Year: 2024
Title: Eliminating the missing cone challenge through innovative approaches.
Authors: Cody Gillman / Guanhong Bu / Emma Danelius / Johan Hattne / Brent L Nannenga / Tamir Gonen /
Abstract: Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle ...Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle arises with plate-like crystals that consistently orient themselves flat on the electron microscopy grid. If the normal of the plate correlates with the axes of the crystal lattice, the crystal orientations accessible for measurement are restricted because the crystal cannot be arbitrarily rotated. This limits the information that can be acquired, resulting in a missing cone of information. We recently introduced a novel crystallization strategy called suspended drop crystallization and proposed that crystals in a suspended drop could effectively address the challenge of preferred crystal orientation. Here we demonstrate the success of the suspended drop approach in eliminating the missing cone in two samples that crystallize as thin plates: bovine liver catalase and the SARS‑CoV‑2 main protease (Mpro). This innovative solution proves indispensable for crystals exhibiting systematic preferred orientations, unlocking new possibilities for structure determination by MicroED.
History
DepositionApr 11, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44453.png

Downloads & links

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Map

FileDownload / File: emd_44453.map.gz / Format: CCP4 / Size: 2.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.31 Å/pix.
x 91 pix.
= 182.7 Å		1.32 Å/pix.
x 75 pix.
= 68.64 Å		1.31 Å/pix.
x 82 pix.
= 173.316 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 1.32 Å / Y: 1.313 Å / Z: 1.305 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.10239
Minimum - Maximum-0.29993725 - 0.36236355
Average (Standard dev.)-0.000092148126 (±0.068261355)
SymmetrySpace group: 19
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-62-35-71
Dimensions758291
Spacing52132140
CellA: 68.64 Å / B: 173.316 Å / C: 182.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Bovine liver catalase

EntireName: Bovine liver catalase
Components
  • Complex: Bovine liver catalase
    • Protein or peptide: Catalase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Supramolecule #1: Bovine liver catalase

SupramoleculeName: Bovine liver catalase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (cattle)

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Macromolecule #1: Catalase

MacromoleculeName: Catalase / type: protein_or_peptide / ID: 1 / Details: from bovine liver / Number of copies: 4 / Enantiomer: LEVO / EC number: catalase
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 59.99916 KDa
SequenceString: MADNRDPASD QMKHWKEQRA AQKPDVLTTG GGNPVGDKLN SLTVGPRGPL LVQDVVFTDE MAHFDRERIP ERVVHAKGAG AFGYFEVTH DITRYSKAKV FEHIGKRTPI AVRFSTVAGE SGSADTVRDP RGFAVKFYTE DGNWDLVGNN TPIFFIRDAL L FPSFIHSQ ...String:
MADNRDPASD QMKHWKEQRA AQKPDVLTTG GGNPVGDKLN SLTVGPRGPL LVQDVVFTDE MAHFDRERIP ERVVHAKGAG AFGYFEVTH DITRYSKAKV FEHIGKRTPI AVRFSTVAGE SGSADTVRDP RGFAVKFYTE DGNWDLVGNN TPIFFIRDAL L FPSFIHSQ KRNPQTHLKD PDMVWDFWSL RPESLHQVSF LFSDRGIPDG HRHMNGYGSH TFKLVNANGE AVYCKFHYKT DQ GIKNLSV EDAARLAHED PDYGLRDLFN AIATGNYPSW TLYIQVMTFS EAEIFPFNPF DLTKVWPHGD YPLIPVGKLV LNR NPVNYF AEVEQLAFDP SNMPPGIEPS PDKMLQGRLF AYPDTHRHRL GPNYLQIPVN CPYRARVANY QRDGPMCMMD NQGG APNYY PNSFSAPEHQ PSALEHRTHF SGDVQRFNSA NDDNVTQVRT FYLKVLNEEQ RKRLCENIAG HLKDAQLFIQ KKAVK NFSD VHPEYGSRIQ ALLDKYNEEK PKNAVHTYVQ HGSHLSAREK ANL

UniProtKB: Catalase

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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: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 3 / Number of copies: 4 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

BufferpH: 6.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 0.0025 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm / Camera length: 2941 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Molecular replacementSoftware - Name: MOLREP
Crystallography statisticsNumber intensities measured: 89263 / Number structure factors: 18157 / Fourier space coverage: 94.859 / R merge: 65.2 / Overall phase residual: 0 / Phase error rejection criteria: Rfree / High resolution: 4.0 Å
Shell:
Shell IDHigh resolutionLow resolutionNumber structure factorsPhase residualFourier space coverageMultiplicity
17.26 Å44.109 Å289648.29999999999999791.2000000000000034.44
25.77 Å7.26 Å293243.78999999999999995.4000000000000064.89
35.04 Å5.77 Å289034.14000000000000195.7999999999999975.0
44.58 Å5.04 Å284929.37999999999999995.7999999999999975.06
54.25 Å4.58 Å287933.95000000000000395.9000000000000065.06
64.0 Å4.25 Å284942.21999999999999996.0999999999999945.07

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-9bdj:
MicroED structure of bovine liver catalase with missing cone eliminated by suspended drop

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