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- EMDB-64931: Cryo-EM map of glycogen phosphorylase from Dorea longicatena (mon... -

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Basic information

Entry
Database: EMDB / ID: EMD-64931
TitleCryo-EM map of glycogen phosphorylase from Dorea longicatena (monomer form with extra density)
Map datasharp map
Sample
  • Complex: Dimeric structure of DlGP
    • Protein or peptide: Glycogen phosphorylase
Keywordsglycogen phosphorylase / TRANSFERASE
Biological speciesDorea longicatena (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsTakai M / Tanino H / Shobu K / Fukuda Y / Inoue T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Structural and mechanistic diversity of glycogen phosphorylases from gut bacteria
Authors: Shobu K / Takai M / Tanino H / Fukuda Y / Inoue T
History
DepositionJun 4, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64931.png

Downloads & links

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Map

FileDownload / File: emd_64931.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.156
Minimum - Maximum-1.0662415 - 1.5797206
Average (Standard dev.)0.0006808262 (±0.02545357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64931_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_64931_msk_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Mask #3

Fileemd_64931_msk_3.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: half map A

Fileemd_64931_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_64931_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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Sample components

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Entire : Dimeric structure of DlGP

EntireName: Dimeric structure of DlGP
Components
  • Complex: Dimeric structure of DlGP
    • Protein or peptide: Glycogen phosphorylase

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Supramolecule #1: Dimeric structure of DlGP

SupramoleculeName: Dimeric structure of DlGP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Dorea longicatena (bacteria)

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Macromolecule #1: Glycogen phosphorylase

MacromoleculeName: Glycogen phosphorylase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Dorea longicatena (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH ENLYFQGMNA PFTYSSPTLS VEALKHSIAY KLMFTIGKDP VVANKHEWLN ATLFAVRDRL VERWLRSNRA QLSQETRQVY YLSMEFLIGR TLSNAMLSLG IYEDVQGALE AMGLNLEELI DEENDPGLGN GGLGRLAACF LDSLATLGLP GRGYGIRYDY ...String:
MGSSHHHHHH ENLYFQGMNA PFTYSSPTLS VEALKHSIAY KLMFTIGKDP VVANKHEWLN ATLFAVRDRL VERWLRSNRA QLSQETRQVY YLSMEFLIGR TLSNAMLSLG IYEDVQGALE AMGLNLEELI DEENDPGLGN GGLGRLAACF LDSLATLGLP GRGYGIRYDY GMFKQNIVNG SQKESPDYWL EYGNPWEFKR HNTRYKVRFG GRIQQEGKKT RWIETEEILG VAYDQIIPGY DTDATNTLRL WSAQASSEIN LGKFNQGDYF AAVEDKNHSE NVSRVLYPDD STYSGRELRL RQEYFLVSST IQDILSRHYQ LHKTYDNLAD KIAIHLNDTH PVLSIPEMMR LLIDEHQFSW DDAFEVCCQV FSYTNHTLMS EALETWPVDM LGKILPRHLQ IIFEINDYFL KTLQEQYPND TDLLGRASII DESNGRRVRM AWLAVVVSHK VNGVSELHSN LMVQSLFADF AKIFPGRFTN VTNGVTPRRW LAVANPSLSA VLDEHLGRNW RTDLSLLNEL QQHCDFPMVN HAVHQAKLEN KKRLAEYIAQ QLNVVVNPKA LFDVQIKRIH EYKRQLMNVL HVITRYNRIK ADPDAKWVPR VNIFGGKAAS AYYMAKHIIH LINDVAKVIN NDPQIGDKLK VVFIPNYSVS LAQLIIPAAD LSEQISLAGT EASGTSNMKF ALNGALTIGT LDGANVEMLD HVGADNIFIF GNTAEEVEEL RRQGYKPREY YEKDEELHQV LTQIGSGVFS PEDPGRYRDL VDSLINFGDH YQVLADYRSY VDCQDKVDEL YELQEEWTAK AMLNIANMGY FSSDRTIKEY ADHIWHIDPV RL

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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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
150.0 mMsodium chlorideNaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: 3 microliters droplet, 0 seconds delay before blotting, 1.5 seconds blot, 0 second delay before plunging..

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6822 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

Particle selectionNumber selected: 1476535
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: NONE
Startup modelType of model: INSILICO MODEL / Details: Predicted by ColabFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 332779
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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