2025-04-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION database_2 em_3d_fitting_list em_admin pdbx_initial_refinement_model _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_3d_fitting_list em_admin pdbx_entry_details pdbx_initial_refinement_model _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update PDBe PDBe 2018-12-13 2019-10-02 2020-02-12 2025-04-09 European Union 647784 France Grenoble Instruct-ERIC Center UMS 3518 CNRS-CEA-UJF-EMBL France French Infrastructure for Integrated Structural Biology ANR-10-INSB-05-02 France European Molecular Biology Organization ALTF441-2017 France Spiral structure of E. coli RavA in the RavA-LdcI cage-like complex Arragain B Felix J Complex, MoxR ATPase, Lysine decarboxylase, HYDROLASE Jessop M Arragain B Miras R Fraudeau A Huard K Bacia-Verloop M Catty P Felix J Malet H Gutsche I Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex. Commun Biol UK 3 46 46 2020 31992852 doi:10.1038/s42003-020-0772-0 2399-3642 EMD-2679 other EM volume EMD-4469 other EM volume 6q7m FULLOVERLAP Complex of the hexameric MoxR AAA+ ATPase RavA and the decameric lysine decarboxylase LdcI. Complex of the hexameric MoxR AAA+ ATPase RavA and the decameric lysine decarboxylase LdcI. 0 1 2 Escherichia coli 3.3 Inducible lysine decarboxylase Escherichia coli 0.081357008 20 Escherichia coli LEVO MNVIAILNHMGVYFKEEPIRELHRALERLNFQIVYPNDRDDLLKLIENNARLCGVIFDWDKYNLELCEEISKMNENLPLY AFANTYSTLDVSLNDLRLQISFFEYALGAAEDIANKIKQTTDEYINTILPPLTKALFKYVREGKYTFCTPGHMGGTAFQK SPVGSLFYDFFGPNTMKSDISISVSELGSLLDHSGPHKEAEQYIARVFNADRSYMVTNGTSTANKIVGMYSAPAGSTILI DRNCHKSLTHLMMMSDVTPIYFRPTRNAYGILGGIPQSEFQHATIAKRVKETPNATWPVHAVITNSTYDGLLYNTDFIKK TLDVKSIHFDSAWVPYTNFSPIYEGKCGMSGGRVEGKVIYETQSTHKLLAAFSQASMIHVKGDVNEETFNEAYMMHTTTS PHYGIVASTETAAAMMKGNAGKRLINGSIERAIKFRKEIKRLRTESDGWFFDVWQPDHIDTTECWPLRSDSTWHGFKNID NEHMYLDPIKVTLLTPGMEKDGTMSDFGIPASIVAKYLDEHGIVVEKTGPYNLLFLFSIGIDKTKALSLLRALTDFKRAF DLNLRVKNMLPSLYREDPEFYENMRIQELAQNIHKLIVHHNLPDLMYRAFEVLPTMVMTPYAAFQKELHGMTEEVYLDEM VGRINANMILPYPPGVPLVMPGEMITEESRPVLEFLQMLCEIGAHYPGFETDIHGAYRQADGRYTVKVLKEESKK P0A9H4 4.1.1.18 ATPase RavA Escherichia coli 0.056351445 6 Escherichia coli LEVO MAHPHLLAERISRLSSSLEKGLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPE EVFGPLSIQALKDEGRYERLTSGYLPEAEIVFLDEIWKAGPAILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELPEA DSSLEALYDRMLIRLWLDKVQDKANFRSMLTSQQDENDNPVPDALQVTDEEYERWQKEIGEITLPDHVFELIFMLRQQLD KLPDAPYVSDRRWKKAIRLLQASAFFSGRSAVAPVDLILLKDCLWYDAQSLNLIQQQIDVLMTGHAWQQQGMLTRLGAIV QRHLQLQQQQSDKTALTVIRLGGIFSRRQQYQLPVNVTASTLTLLLQKPLKLHDMEVVHISFERSALEQWLSKGGEIRGK LNGIGFAQKLNLEVDSAQHLVVRDVSLQGSTLALPGSSAEGLPGEIKQQLEELESDWRKQHALFSEQQKCLFIPGDWLGR IEASLQDVGAQIRQAQQ J7QAN2 3.6.3.- PYRIDOXAL-5'-PHOSPHATE 0.000247142 20 PLP ADENOSINE-5'-DIPHOSPHATE 0.000427201 5 ADP singleParticle particle 0.98 7.9
20 mM Tris pH 7.9, 300 mM NaCl, 2 mM ADP, 10 mM MgCl 2 , 0.1 mM PLP and 1 mM DTT
 ETHANE
Concentrations of LdcI and RavA were 0.38 mg/ml (4.67 microM) and 0.6 mg/ml (10.64 microM) respectively.
 FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 41270.0
Data collection was performed on an FEI Polara microscope operated at 300 kV. Movies of 40 frames were collected with a total exposure time of 8s and a total dose of 40e-/Angstrom^2 on a K2 summit direct electron detector (Gatan) at a magnification of 41270x, corresponding to 1.21 Angstrom/pixel at the specimen level.
GATAN K2 SUMMIT (4k x 4k) COUNTING 3-40 1819 8.0 40.0 1 18902
The cleanded dataset contains 11866 particles. Dataset expansion (C5) resulted in a dataset containing 59330 particles.
 The initial 3D model based on 2D class averages was calculated with sxviper (SPARX) (Hohn et al., 2007) imposing D5 symmetry. 1 C1 7.8 FSC 0.143 CUT-OFF RELION 2.0 16513 MAXIMUM LIKELIHOOD RELION 2.0 MAXIMUM LIKELIHOOD RELION 2.0 2 17867.0 RELION 2.0 emd_4470.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 484.0002 484.0002 484.002 90.0 90.0 90.0 X Y Z -0.101965666 0.19264637 0.00012397133 0.006753406 2.420001 2.420001 2.42001 0.02 AUTHOR Cryo-EM map of Class 2 of the E. coli RavA-LdcI cage-like complex after symmetry expansion and masked 3D classification. 3N75 PDB experimental model 3NBX PDB experimental model FLEXIBLE FIT
Local resolution estimation and subsequent filtering of maps were performed in Relion3.0. For fitting of atomic models in the resulting filtered maps, we used the previously-determined X-ray structures of LdcI (PDB ID: 3N75) (Kanjee et al., 2011) and RavA (PDB ID: 3NBX) (El Bakkouri et al., 2010). In each map, two decameric LdcI molecules extracted from PDB 3N75 and one spiral RavA hexamer extracted from a continuous RavA helix generated from PDB 3NBX were fitted separately using iMODFIT (Lopez-Blanco and Chacon, 2013), followed by a single round of B-factor (ADP) refinement in Phenix.
 emd_4470_msk_1.map emd_4470_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 484.0002 484.0002 484.002 90.0 90.0 90.0 X Y Z -0.053210165 0.06925123 -0.000007022791 0.005304998 2.420001 2.420001 2.42001 AUTHOR Unfiltered half-map 1. emd_4470_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 484.0002 484.0002 484.002 90.0 90.0 90.0 X Y Z -0.053777065 0.07123723 -0.000006485192 0.0051935352 2.420001 2.420001 2.42001 AUTHOR Unfiltered half-map 1.