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- EMDB-53306: GH161 phosphorylase in complex with beta-1,3 glucooligosaccharide -

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Basic information

Entry
Database: EMDB / ID: EMD-53306
TitleGH161 phosphorylase in complex with beta-1,3 glucooligosaccharide
Map data
Sample
  • Complex: gh161 phosphorylase
    • Protein or peptide: gh161 phosphorylase
Keywordsphosphorylase / gh161 / laminarin / CYTOSOLIC PROTEIN
Biological speciesuncultured bacterium (environmental samples) / gut metagenome (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsCooper N / Cioci G / Ladeveze S / Potocki-Veronese G / Moulis C / Remaud-Simeon M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2025
Title: Structural and Functional Dissection of GH161 beta-Glucan Phosphorylases: Molecular Specificities and Dynamics of Catalysis of Dimeric GH-Q Enzymes
Authors: Cooper NJ / Ladeveze S / Li A / Shayan R / Faure R / Ropartz D / Terrapon N / Lombard V / Henrissat B / Remaud-Simeon M / Potocki-Veronese G / Moulis C / Cioci G
History
DepositionApr 1, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53306.png

Downloads & links

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Map

FileDownload / File: emd_53306.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 300 pix.
= 288. Å		0.96 Å/pix.
x 300 pix.
= 288. Å		0.96 Å/pix.
x 300 pix.
= 288. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3120219 - 0.70308745
Average (Standard dev.)-0.0004020573 (±0.02399481)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53306_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53306_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 : gh161 phosphorylase

EntireName: gh161 phosphorylase
Components
  • Complex: gh161 phosphorylase
    • Protein or peptide: gh161 phosphorylase

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Supramolecule #1: gh161 phosphorylase

SupramoleculeName: gh161 phosphorylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: uncultured bacterium (environmental samples)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: gh161 phosphorylase

MacromoleculeName: gh161 phosphorylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: gut metagenome (others)
Molecular weightTheoretical: 119.868008 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTGKNETFVM DDYGKKSTFA SFLPGIAGIR GIPIWCYYVN RGQCVVSFGV DNKDHAIMEF YPAHQAYQNV KTTGFRTFLK KNGTVFEPF SDENITHRMQ IHMNGLAIEE QNRSSGMDTK VVYYTLPGEN VGALVRVVSV TNQSGEPIEL ELIDGMPAVI P YGVSMDSM ...String:
MTGKNETFVM DDYGKKSTFA SFLPGIAGIR GIPIWCYYVN RGQCVVSFGV DNKDHAIMEF YPAHQAYQNV KTTGFRTFLK KNGTVFEPF SDENITHRMQ IHMNGLAIEE QNRSSGMDTK VVYYTLPGEN VGALVRVVSV TNQSGEPIEL ELIDGMPAVI P YGVSMDSM KNMGQTAKAW MQVEDLSEGL PYYRVRASMD DTAAVRRIDG GNFSACCEAD GRRLQPIVDP SLIFSYDLSL KR PVGFEER PLKELLLEEQ MTQNLLPCSF YGITRTLAPG GSVTLYELIG QVENKQLLKE YFAEKKDAAY FEAKKREADE LAE ALTDGI RTRTASAAFD AYCRYTYMDN VLRGGYPMQL GNNKIFYVYS RKHGDLERDY NYFSMLPEFY SQGNGNFRDV NQNR RCDTF FAPFVGRKNI QEFYSLIQLD GYNPLGVEKL TYRLSKERAK KLLTDVKEEQ RSALIDFATK PFTPGALCRK FGEVF GDTW DETLFIRVID FAEEMVNGSF GEGYWSDHWT YNLDLILDYL SVFPEQEKEM LYEEVYTTFL SRINVNRRFR RYVETE NGL RQYRALNEAS RRADLGEKLV RTEYGSGDVL TMTLMEKLIL LGAVKFATLD AYGMGIEMEG GKPGWYDALN GMPGLFG SS MAETYELARM LSYTIEALKQ YPGEVALIEE LGCFLDELNL ITRLEHDNIM RDEELLSFWN RINDAKEIYR DKTYQGVS G KKMVYHTEQL AAILEGFLEI VTCGIKKARR ISGEICPTYF TYEVPEYEKL KDGGIRPLKF VPQNMPYFLE GPVRYLKLP VEQGEKRALY EAVKESDLYD GELSMYKVNA SLADSSFELG RARAFTPGWL ENESIWLHME YKYLLELLRS GLYEEFFADF KKAAIPFQN PEIYGRSIYE NSSFIASSRN PNPSCRGRGF VARLSGSTIE FISMWKEMMF GAHPFRTEQE ELVFSLAPAI P AYLIPEDG RLSAAFMSKT TVCYEFGGHR DYVPGTYRIR HMVFFYENGS QATVEGEKVS GKLAEDIRAG RVRKMEVAVD LE HHHHHH

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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

Concentration0.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5242 / Average exposure time: 5.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 150000

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Image processing

Particle selectionNumber selected: 81913
CTF correctionSoftware - Name: RELION (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 22729
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 1

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Atomic model buiding 1

Initial modelPDB ID:

9h2r
PDB Unreleased entry


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9qqk:
GH161 phosphorylase in complex with beta-1,3 glucooligosaccharide

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