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- EMDB-34921: The cryo-EM structure of cellobiose phosphorylase from Clostridiu... -

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Basic information

Entry
Database: EMDB / ID: EMD-34921
TitleThe cryo-EM structure of cellobiose phosphorylase from Clostridium thermocellum
Map data
Sample
  • Organelle or cellular component: Cellobiose phosphorylase
    • Protein or peptide: Cellobiose phosphorylase
  • Ligand: water
KeywordsCellobiose phosphorylase / TRANSFERASE
Function / homology
Function and homology information


cellobiose phosphorylase / cellobiose phosphorylase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 65, C-terminal / Glycosyl hydrolase family 65, C-terminal domain / Cellobiose phosphorylase, N-terminal / Putative carbohydrate binding domain / Putative carbohydrate binding domain / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily ...Glycoside hydrolase family 65, C-terminal / Glycosyl hydrolase family 65, C-terminal domain / Cellobiose phosphorylase, N-terminal / Putative carbohydrate binding domain / Putative carbohydrate binding domain / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Cellobiose phosphorylase
Similarity search - Component
Biological speciesAcetivibrio thermocellus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsIriya S / Kuga T / Sunagawa N / Igarashi K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22J12566 Japan
CitationJournal: To Be Published
Title: The cryo-EM structure of cellobiose phosphorylase from Clostridium thermocellum
Authors: Iriya S / Kuga T / Sunagawa N / Igarashi K
History
DepositionDec 9, 2022-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34921.png

Downloads & links

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Map

FileDownload / File: emd_34921.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 12.0
Minimum - Maximum-34.455260000000003 - 48.916527000000002
Average (Standard dev.)-0.000000000003804 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34921_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34921_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34921_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 : Cellobiose phosphorylase

EntireName: Cellobiose phosphorylase
Components
  • Organelle or cellular component: Cellobiose phosphorylase
    • Protein or peptide: Cellobiose phosphorylase
  • Ligand: water

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Supramolecule #1: Cellobiose phosphorylase

SupramoleculeName: Cellobiose phosphorylase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acetivibrio thermocellus (bacteria) / Strain: YM4
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: Cellobiose phosphorylase

MacromoleculeName: Cellobiose phosphorylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cellobiose phosphorylase
Source (natural)Organism: Acetivibrio thermocellus (bacteria)
Molecular weightTheoretical: 93.872453 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEFGFFDDAN KEYVITVPRT PYPWINYLGT ENFFSLISNT AGGYCFYRDA RLRRITRYRY NNVPIDMGGR YFYIYDNGDF WSPGWSPVK RELESYECRH GLGYTKIAGK RNGIKAEVTF FVPLNYNGEV QKLILKNEGQ DKKKITLFSF IEFCLWNAYD D MTNFQRNF ...String:
MEFGFFDDAN KEYVITVPRT PYPWINYLGT ENFFSLISNT AGGYCFYRDA RLRRITRYRY NNVPIDMGGR YFYIYDNGDF WSPGWSPVK RELESYECRH GLGYTKIAGK RNGIKAEVTF FVPLNYNGEV QKLILKNEGQ DKKKITLFSF IEFCLWNAYD D MTNFQRNF STGEVEIEGS VIYHKTEYRE RRNHYAFYSV NAKISGFDSD RDSFIGLYNG FDAPQAVVNG KSNNSVADGW AP IASHSIE IELNPGEQKE YVFIIGYVEN KDEEKWESKG VINKKKAYEM IEQFNTVEKV DKAFEELKSY WNALLSKYFL ESH DEKLNR MVNIWNQYQC MVTFNMSRSA SYFESGIGRG MGFRDSNQDL LGFVHQIPER ARERLLDLAA TQLEDGSAYH QYQP LTKKG NNEIGSNFND DPLWLILATA AYIKETGDYS ILKEQVPFNN DPSKADTMFE HLTRSFYHVV NNLGPHGLPL IGRAD WNDC LNLNCFSTVP DESFQTTTSK DGKVAESVMI AGMFVFIGKD YVKLCEYMGL EEEARKAQQH IDAMKEAILK YGYDGE WFL RAYDDFGRKV GSKENEEGKI FIESQGFCVM AEIGLEDGKA LKALDSVKKY LDTPYGLVLQ NPAFTRYYIE YGEISTY PP GYKENAGIFC HNNAWIICAE TVVGRGDMAF DYYRKIAPAY IEDVSDIHKL EPYVYAQMVA GKDAKRHGEA KNSWLTGT A AWNFVAISQW ILGVKPDYDG LKIDPCIPKA WDGYKVTRYF RGSTYEITVK NPNHVSKGVA KITVDGNEIS GNILPVFND GKTHKVEVIL EHHHHHH

UniProtKB: Cellobiose phosphorylase

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 112 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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

Concentration3 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
20.0 mMC6H13NO4S2-(N-morpholino)ethanesulfonic acid
70.0 mMNaClSodium chloridesodium chloride

Details: 20 mM MES, 70 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrification carried out in nitrogen atmosphere..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 2907 / Average exposure time: 5.121 sec. / Average electron dose: 49.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1858960
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3qde

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 658438
FSC plot (resolution estimation)

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