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- EMDB-55127: Catalytically active GH161A phosphorylase refined in C1 -

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Basic information

Entry
Database: EMDB / ID: EMD-55127
TitleCatalytically active GH161A phosphorylase refined in C1
Map data
Sample
  • Complex: GH161A Phosphorylase
    • Protein or peptide: GH161A
  • Ligand: PHOSPHATE ION
  • Ligand: beta-D-glucopyranose
KeywordsGH161 / phosphorylase / HYDROLASE
Biological speciesgut metagenome (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsCooper N / Cioci G / Ladeveze S / Potocki-Veronese G / Moulis C
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
DepositionSep 23, 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_55127.png

Downloads & links

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Map

FileDownload / File: emd_55127.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: 0.117
Minimum - Maximum-0.46042553 - 0.94648546
Average (Standard dev.)0.00012392402 (±0.02749389)
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: #2

Fileemd_55127_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_55127_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 : GH161A Phosphorylase

EntireName: GH161A Phosphorylase
Components
  • Complex: GH161A Phosphorylase
    • Protein or peptide: GH161A
  • Ligand: PHOSPHATE ION
  • Ligand: beta-D-glucopyranose

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Supramolecule #1: GH161A Phosphorylase

SupramoleculeName: GH161A Phosphorylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: gut metagenome (others)

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Macromolecule #1: GH161A

MacromoleculeName: GH161A / 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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Macromolecule #3: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #4: beta-D-glucopyranose

MacromoleculeName: beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / Formula: BGC
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BGC:
beta-D-glucopyranose

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 39.54 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9h2r
PDB Unreleased entry

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 179478
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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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-9sr2:
Catalytically active GH161A phosphorylase refined in C1

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