CryoEM structure of AdhE spirosome from Clostridium thermocellum uncovered by visual proteomics.

2026-09-16 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY COORDINATE_REPLACEMENT AUTHOR Model orientation/position

Refined ligand to remove bond outliers, improved overall model statistics

STRUCTURE_SUMMARY atom_site audit_author citation_author em_admin em_ctf_correction em_final_classification em_image_scans em_imaging em_particle_selection em_software pdbx_audit_support pdbx_contact_author pdbx_entity_instance_feature pdbx_entry_details pdbx_struct_conn_angle pdbx_struct_sheet_hbond pdbx_validate_torsion refine refine_ls_restr struct struct_conf struct_conn struct_keywords struct_sheet struct_sheet_order struct_sheet_range _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _em_admin.last_update _em_ctf_correction.details _em_ctf_correction.type _em_image_scans.dimension_height _em_image_scans.sampling_size _em_imaging.nominal_defocus_max _em_imaging.nominal_defocus_min _pdbx_entry_details.has_ligand_of_interest _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct.title _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_keywords.pdbx_keywords _struct_keywords.text STRUCTURE_SUMMARY citation_author em_admin em_ctf_correction em_final_classification em_image_scans em_imaging em_particle_selection em_software struct_keywords _em_admin.last_update _em_ctf_correction.details _em_ctf_correction.type _em_image_scans.dimension_height _em_image_scans.sampling_size _em_imaging.nominal_defocus_max _em_imaging.nominal_defocus_min _struct_keywords.pdbx_keywords _struct_keywords.text RCSB RCSB 2026-05-06 2026-06-24 2026-06-24 2026-09-16 Department of Energy (DOE, United States) DE-FC02-02ER63421 United States National Science Foundation (NSF, United States) DMR-1548924 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM128867 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM145286 United States Department of Energy (DOE, United States) KP1607011 United States CryoEM structure of AdhE spirosome from Clostridium thermocellum uncovered by visual proteomics. Agdanowski MP Rodriguez JA Moser T Evans JE Dehydrogenase, Filament, Ethanol Production, PROTEIN FIBRIL Agdanowski MP Kensil MJ Moser TH Humm E Guandique YI Mason-Chalmers K Pia VG Al-Set T Ogorzalek Loo RR Evans JE Gunsalus RP Loo JA Rodriguez JA Visual exoproteomics of Clostridium thermocellum during anaerobic biomass-degradation identifies functional spirosomes. Biorxiv US 2026 42239438 doi:10.64898/2026.05.21.726627 2692-8205 13he FULLOVERLAP EMDB EMD-77065 associated EM volume

AdhE spirosome AdhE spirosome 0 1 Acetivibrio thermocellus DSM 1313 Aldehyde-alcohol dehydrogenase Acetivibrio thermocellus DSM 1313 0.094788023 6 LEVO EVIDNVEKLEKALKRLREAQSVYATYTQEQVDKIFFEAAMAANKMRIPLAKMAVEETGMGVVEDKVIKNHYASEYIYNAY KNTKTCGVIEEDPAFGIKKIAEPLGVIAAVIPTTNPTSTAIFKTLIALKTRNAIIISPHPRAKNSTIEAAKIVLEAAVKA GAPEGIIGWIDVPSLELTNLVMREADVILATGGPGLVKAAYSSGKPAIGVGAGNTPAIIDDSADIVLAVNSIIHSKTFDN GMICASEQSVIVLDGVYKEVKKEFEKRGCYFLNEDETEKVRKTIIINGALNAKIVGQKAHTIANLAGFEVPETTKILIGE VTSVDISEEFAHEKLCPVLAMYRAKDFDDALDKAERLVADGGFGHTSSLYIDTVTQKEKLQKFSERMKTCRILVNTPSSQ GGIGDLYNFKLAPSLTLGCGSWGGNSVSDNVGVKHLLNIKTVAERRENMLWFRTPEKIYIKRGCLPVALDELKNVMGKKK AFIVTDNFLYNNGYTKPITDKLDEMGIVHKTFFDVSPDPSLASAKAGAAEMLAFQPDTIIAVGGGSAMDAAKIMWVMYEH PEVDFMDMAMRFMDIRKRVYTFPKMGQKAYFIAIPTSAGTGSEVTPFAVITDEKTGIKYPLADYELLPDMAIVDADMMMN APKGLTAASGIDALTHALEAYVSMLATDYTDSLALRAIKMIFEYLPRAYENGASDPVAREKMANAATIAGMAFANAFLGV CHSMAHKLGAFYHLPHGVANALMINEVIRFNSSEAPTKMGTFPQYDHPRTLERYAEIADYIGLKGKNNEEKVENLIKAID ELKEKVGIRKTIKDYDIDEKEFLDRLDEMVEQAFDDQCTGTNPRYPLMNEIRQMYLNAYYG A0A0H3W5U9 FE (III) ION 5.5845e-05 6 FE NICOTINAMIDE-ADENINE-DINUCLEOTIDE 0.0006634249999999999 6 NAD helical filament 3 8.0 20.0 Tris Tris 150.0 NaCl sodium chloride 2.0 CaCl2 calcium chloride

20mM Tris pH 8.0, 150mM NaCl, 2mM CaCl2

EMS Formvar Carbon COPPER 300 CARBON HOLEY 20.0 GLOW DISCHARGE 20

CFlat 1.2/1.3 300 mesh holey carbon Cu support grids were negatively glow discharged for 20 seconds on the sample side.

ETHANE 100 285.15 FEI VITROBOT MARK IV

Vitification was performed on CFlat 1.2/1.3 300 mesh holey carbon grids with copper support..

Sample was obtained from partially-purified extracellular media and contained an array of unidentified species.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.5 2.5 130000.0 GIF Bioquantum 20 GATAN K3 (6k x 4k) 11520 8184 1 4863 1.03 48.0

Images were recorded as movies consisting of 50 frames over an exposure time of 1.03 seconds, with a total accumulated dose of 48 electrons per Angstrom

1 65 60.06 -166.03 C1 FOURIER SPACE 4.07 FSC 0.143 CUT-OFF cryoSPARC 4.7.0 Helical Refinement with parameters imposed

Overall resolution 4.07 angstrom as estimated by the masked gold-standard FSC = 0.143 criterion in cryoSPARC. Unmasked FSC values are lower, consistent with expected effects of masking." in the details field.

95407 cryoSPARC 4.7 CTF Estimation

Patch CTF was used on micrographs, final volume had global and local CTF estimation jobs performed on it.

PHASE FLIPPING AND AMPLITUDE CORRECTION 94278 cryoSPARC 4.7.0 Filament Tracer

94,278 particles were used in final reconstruction. Particles were picked using cryoSPARC's automated filament tracer with particle diameter of 70Ang and spacing of 0.2

Initial model was generated by running an Ab Initio model job on particles from the selected 2D classes

NOT APPLICABLE cryoSPARC 4.7.0 Helical Refinement with parameters imposed

Final particle orientations were refined during cryoSPARC helical refinement. Initial helical refinement was performed without imposed helical parameters. Helical symmetry was subsequently estimated using cryoSPARC Helical Symmetry Search and refined in later helical refinement jobs with rise and twist allowed to optimize.

emd_77065.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 348.16 348.16 348.16 90.0 90.0 90.0 X Y Z -0.081321776 0.18744588 0.00064235827 0.008742937 0.68 0.68 0.68 0.04 AUTHOR ::::EMDATABANK.org::::EMD-77065:::: Sharpened cryoEM map of Ct spirosome obtained by helical refinement in cryoSPARC 8UHW A 11-869 PDB experimental model

published structure was fast relaxed and then used as an initial model for model building and refinement

RIGID BODY FIT Coot 0.9.8.96

A existing structure's (PDB:8UHW) coordinates were relaxed using the Rosetta Fast Relax algorithm and refined against the EM density from cryoSPARC using Phenix and Coot. Histidine residues coordinate the iron ion; short distances flagged as clashes correspond to metal coordination geometry.

emd_77065_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 348.16 348.16 348.16 90.0 90.0 90.0 X Y Z -0.045598704 0.12674133 0.0006423583 0.0071379817 0.68 0.68 0.68 AUTHOR ::::EMDATABANK.org::::EMD-77065:::: Unsharpened cryoEM map of Ct spirosome obtained by helical refinement in cryoSPARC emd_77065_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 348.16 348.16 348.16 90.0 90.0 90.0 X Y Z -1.3192139 1.414088 0.000040898045 0.16458593 0.68 0.68 0.68 AUTHOR ::::EMDATABANK.org::::EMD-77065:::: Half Map B of helical Ct Spirosome emd_77065_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 348.16 348.16 348.16 90.0 90.0 90.0 X Y Z -1.377627 1.3900203 0.000020571786 0.16561049 0.68 0.68 0.68 AUTHOR ::::EMDATABANK.org::::EMD-77065:::: Half Map A of helical Ct Spirosome