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- EMDB-34504: cryo-EM structure of cellodextrin phosphorylase from Clostridium ... -

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Basic information

Entry
Database: EMDB / ID: EMD-34504
Titlecryo-EM structure of cellodextrin phosphorylase from Clostridium thermocellum
Map data
Sample
  • Complex: Homodimeric structure of cellodextrin phosphorylase from Clostridium thermocellum (CtCDP)
    • Protein or peptide: Cellodextrin phosphorylase
  • Ligand: CHLORIDE IONChloride
Keywordscellulose / cellodextrin / phosphorolysis / synthesis / CARBOHYDRATE
Function / homology
Function and homology information


transferase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
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
Cellodextrin phosphorylase
Similarity search - Component
Biological speciesAcetivibrio thermocellus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsKuga T / Sunagawa N / Igarashi K
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22J12566 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)18H05494 Japan
CitationJournal: To Be Published
Title: structure and dynamics of cellodextrin phosphorylase from Clostridium thermocellum determine chain length and crystalline packing of highly ordered cellulose II synthesized in vitro
Authors: Kuga T / Sunagawa N / Igarashi K
History
DepositionOct 17, 2022-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34504.png

Downloads & links

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Map

FileDownload / File: emd_34504.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.575758 - 1.8362952
Average (Standard dev.)0.00047157847 (±0.03324383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34504_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_34504_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 : Homodimeric structure of cellodextrin phosphorylase from Clostrid...

EntireName: Homodimeric structure of cellodextrin phosphorylase from Clostridium thermocellum (CtCDP)
Components
  • Complex: Homodimeric structure of cellodextrin phosphorylase from Clostridium thermocellum (CtCDP)
    • Protein or peptide: Cellodextrin phosphorylase
  • Ligand: CHLORIDE IONChloride

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Supramolecule #1: Homodimeric structure of cellodextrin phosphorylase from Clostrid...

SupramoleculeName: Homodimeric structure of cellodextrin phosphorylase from Clostridium thermocellum (CtCDP)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acetivibrio thermocellus (bacteria) / Strain: YM4
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: Cellodextrin phosphorylase

MacromoleculeName: Cellodextrin phosphorylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetivibrio thermocellus (bacteria)
Molecular weightTheoretical: 112.599523 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVTKVTARNN KITPVELLNQ KFGNKINLGN FADAVFTDAA FKNVAGIANL PMKAPVMQVL MENCIVSKYL KQFVPDRSVC FVEEGQKFY IVLEDGQKIE VPEDVNKALK ATVSDVKHWA GYLTEDGEHV IDLLKPAPGP HFYVNLLIGN RLGFKRTLQT T PKSVVDRF ...String:
MVTKVTARNN KITPVELLNQ KFGNKINLGN FADAVFTDAA FKNVAGIANL PMKAPVMQVL MENCIVSKYL KQFVPDRSVC FVEEGQKFY IVLEDGQKIE VPEDVNKALK ATVSDVKHWA GYLTEDGEHV IDLLKPAPGP HFYVNLLIGN RLGFKRTLQT T PKSVVDRF GRGSFRSHAA TQVLATRFDM RQEENGFPAN RQFYLYEDGK QIFYSALIDD NIVEATCKHS CNRTVIKYKT AC NLEITRT IFLVPHKKGF PLATELQRIE IKNASDKARN LSITYTGMFG TGAVHAIFED VTYTNVIMQS AALYNDKGEF IGI TPDYYP EEFKQDTRFV TMIVRNGDEK SFPQSFCTDY NDFVGTGTLE HPAGGCNLNN KLNRKGPGFF ALGAPFTVEP GKTV IIDTF TGLSSSKDNE NYSDAVMLRE LDNLLRYFEK SESVEETLNE IINFHENYGK YFQFNTGNKL FDSGFNRNLA FQVLY QTFM SRSFGQTQKG YREIGFREIQ DLFASMYYFI NIGYQDFVKE LLFEWTANVY KMGYANHNFY WVGKQPGLYS DDSLWL LQA YYRYIIYTKD TSVLNEEVPV ADGNNEKRAV RETLKAIIQY SACISVGDHG LPLLDLADWN DCLKIDSNSI DGATKEK LY YEQLKKTNGK YGDRFMSDYS ESVMNAFLLK LAIDHLAEIA TLDNDTQLAQ QMSELSKEVT DRIQKHAWKE NFFARVLI N RYKDGSYTYL GAKGDKLSAD PNIDGVYFLN SFAWSVLSDV ATDEQIAIMV DVIKKHLLTP YGLRLVTPAD LNKIANDTA TGHYFFGDRE NGAVFKHASM MAVAALIKAA KKVKDNELAK EMARIAYFMI DLVLPYKNLE NPFQVAGNPR ICTQYINTDT GENIGPLLS GTATWLNLNL ISLAGIEYTR DGISFNPILR EEETQLNFTL KAPKCSYKFS ITKPVGFARM ESSEYELFVD G QKIDNTVI PMYTDEKEHI VTLKFKHHHH HH

UniProtKB: Cellodextrin phosphorylase

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Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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

Concentration3.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
120.0 mMNaClSodium chloridesodium chloride
20.0 mMC4H11NO3tris(hydroxymethyl)aminomethane
0.1 mMC4H10O2S2DTT

Details: 20 mM Tris-HCl, 120 mM NaCl, 0.1 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 280 K / Instrument: FEI VITROBOT MARK IV

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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 / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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: 3503460
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5nz7

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: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 604474
FSC plot (resolution estimation)

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