Glycogen phosphorylase from Segatella copri decamer in complex with AMP

2026-04-01 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.page_first _citation.page_last _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.page_first _citation.page_last _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID _em_admin.last_update PDBj PDBj 2025-05-03 2026-02-18 2026-02-18 2026-04-01 Japan Society for the Promotion of Science (JSPS) Japan Glycogen phosphorylase from Segatella copri decamer in complex with AMP Shobu K Fukuda Y Inoue T glycogen metabolism, cryo-EM, gut bacteria, STRUCTURAL PROTEIN Shobu K Takai M Tanino H Fukuda Y Inoue T Structural and mechanistic diversity of glycogen phosphorylases from gut bacteria. Proc.Natl.Acad.Sci.USA US 123 e2518513123 e2518513123 2026 41662519 doi:10.1073/pnas.2518513123 1091-6490 0040 PNASA6 9utg FULLOVERLAP EMDB EMD-64491 associated EM volume

glycogen phosphorylase glycogen phosphorylase 0 1 Segatella copri Alpha-glucan family phosphorylase Segatella copri Segatella copri 0.09879593799999999

Sequence refers to WP_218459193.1 in NCBI

5 Escherichia coli BL21(DE3) LEVO MKIKADYANAPQWKETTIKSSLPKELKCLDEIAHNMWWAWNYEGRDLFKSLDPDLYEKCNANPVLLLERLSYDRKEAIVK DKETMAKVKNVYKMFREYMDVKPNAKRPSVAYFCMEYGINQVVKIYSGGLGMLAGDYLKEASDSNVDMCAVGFLYRYGYF KQSLSMDGQQIANYDAQNFNSLPIERVYDENGNPLVVDVPYTNYQVHAYVWQMNVGRIKLYLLDTDNDMNSEFDRPITYS LYGGDWENRLKQEILLGIGGILTLKKLGIKKEIYHCNEGHAALCNLQRLCDYIEEDGLNFNQALELVRASSLYTVHTPVP AGHDYFDEALFGKYMGGYPQRLGISWDEFIGMGRENADDHNERFCLSTFACNTCQEVNGVSKLHGWVSQQMFSNIWKGYF PEENHVGYVTNGVHFPTWTATEWRKLYDTYFDKNFMNDQSNEEIWHAIYKVSDAEIWNTRMTLKKKLVAYIREKFTQTWL KNQGDPARVVSLLERINPNALMIGFCRRFATYKRAHLLFTDLERLSKIVNDPEHPVLFFFSGKAHPADGAGQGLIKKIFE ISQRPEFLGKIIFLEDYDMTLARRLVSGVDIWMNTPTRPLEASGTSGE(LLP)AEMNGVVNLSVLDGWWVEGYREGAGWA LPEKRTYQNQGYQDQLDAATIYNLLENDIIPMYYNKNKEGFSKEWIQVVKNSIATIAPHYTMKRQLDDYYDKFYNKEAAR FKKLSANDNALAKEIALWKESVAERWDGIHVVSKDDCMLMAAETGQKIKVQYVIDEQGLNDAVGLELVVLKEQPEDGKQV YAVYPFKMVGHEGNNFTFEAEIEPINAGSFKTGVRMYPKNDKLPHRQDFCYVKWLN A0AA93BMC9 ADENOSINE MONOPHOSPHATE 0.000347221 8 AMP singleParticle particle 4.58 8.0 100.0 NaCl sodium chloride 20.0 Tris 5.0 AMP adenosine monophosphate Quantifoil R1.2/1.3 COPPER 200 GLOW DISCHARGE 20 AIR 0.007

10 mA current

ETHANE 100 281 FEI VITROBOT MARK IV

3 microliters droplet, 5 seconds delay before blotting, 3 seconds blot, 0 second delay before plunging..

JEOL CRYO ARM 200 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 0.7000000000000001 2.2 SerialEM GATAN K3 (6k x 4k) 1 6271 40.0 1 cryoSPARC NONE 9L6I C2 3.58 FSC 0.143 CUT-OFF cryoSPARC 30003 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC emd_64491.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.2710642 0.5928283 0.008464639 0.042972222 0.83 0.83 0.83 0.117 AUTHOR ::::EMDATABANK.org::::EMD-64491:::: UCSF ChimeraX emd_64491_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.77112573 0.9445161 0.008473301 0.11270627 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-64491:::: emd_64491_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.74012256 0.9243537 0.008480316 0.11301184 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-64491::::