The ERAD misfolded glycoprotein checkpoint complex from Chaetomium thermophilum (EDEM:PDI heterodimer).

2026-07-01 OBS PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name EXPERIMENTAL_SUMMARY em_admin em_author_list _em_admin.last_update DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name STRUCTURE_SUMMARY audit_author em_admin em_author_list _em_admin.last_update OBSOLETE REPOSITORY OTHER em_admin em_author_list em_supersede pdbx_database_PDB_obs_spr pdbx_database_status _em_admin.current_status _em_admin.last_update _pdbx_database_status.status_code OBSOLETE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_author_list em_supersede pdbx_database_PDB_obs_spr _em_admin.current_status _em_admin.last_update PDBe PDBe 2023-06-27 2024-07-10 2024-07-10 2026-07-01 2026-07-01 2026-07-01 EMD-56105 Wellcome Trust 204801/Z/16/Z United Kingdom Wellcome Trust 214090/Z/18/Z United Kingdom Italian National Research Council (CNR) Plant_EDEM Italy The ERAD misfolded glycoprotein checkpoint complex from Chaetomium thermophilum (EDEM:PDI heterodimer). Roversi P Hitchman CJ Lia A Bayo Y Gooptu B mannosidase, disulfide isomerase, glycoprotein degradation, erad, misfolding, OXIDOREDUCTASE Roversi P Hitchman CJ Lia A Bayo Y The ERAD misfolded glycoprotein checkpoint complex from Chaetomium thermophilum (EDEM:PDI heterodimer). To Be Published 0353 8pko FULLOVERLAP EMDB EMD-17749 associated EM volume

Complex of Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM) and Endoplasmic reticulum degradation enhancing protein disulfide isomerase (CtPDI) Complex of Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM) and Endoplasmic reticulum degradation enhancing protein disulfide isomerase (CtPDI) 0 1 2

Coexpressed by transient co-transfection of two plasmids

Thermochaetoides thermophila 0.055 Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM) 1 1

CtEDEM expressed as a N-term GFP fusion, truncated at the N-term and with hexahistidine tag at the Cterm

Thermochaetoides thermophila ER Endoplasmic reticulum degradation enhancing protein disulfide isomerase (CtPDI) 1 2

CtPDI expressed as a Cterm truncation with no KDEL and a hexahistidine tag at the Cterm.

Thermochaetoides thermophila Green fluorescent protein,alpha-1,2-Mannosidase Thermochaetoides thermophila 0.142162812

Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM),Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM),Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM),Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM),Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM),Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM),Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM),Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM)

1 Homo sapiens LEVO MVSKGELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQ HDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNG IKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKLE VLFQGPDRVRALRRETVEMFYYGFDNYMKVAFPEDELRPVSCTPLTRDLKNPRNFELNDVLGNYSLTLIDSLSTLAILAS APAEDSGTGPKALRDFQDGVAALVEQYGDGRPGPSGVGRRARGFDLDSKVQVFETVIRGVGGLLSAHLFAIGALPITGYQ PLRQEDDLFNPPPIPWPNGFTYDGQLLRLALDLAQRLLPAFYTKTGLPYPRVNLRHGIPFYVNSPLHEDPPAKGTTEGPP EITETCSAGAGSLVLEFTVLSRLTGDPRFEQAAKRAFWAVWYRKSQIGLIGAGVDAEQGHWIGTYSVIGAGADSFFEYAL KSHILLSGHALPNQTHPSPLHKDVNWMDPNTLFEPLSDAENSAESFLEAWHHAHAAIKRHLYSEREHPHYDNVNLWTGSL VSHWVDSLGAYYSGLLVLAGEVDEAIETNLLYAAIWTRYAALPERWSLREKTVEGGLGWWPLRPEFIESTYHLYRATKDP WYLYVGEMVLRDITRRCWTPCGWAGLQNVLSGEKSDRMESFFLGETTKYMYLLFDDDHPLNKLDASFVFTTEGHPLILPK PKSARRSRNSPRSSQKALTVYQGEGFTNSCPPRPSITPLSGSVIAARDDIYHPARMVDLHLLTTSKHALDGGQMSGQHMA KSNYTLYPWTLPPELLPSNGTCAKVYQPHEVTLEFASNTQQVLGGSAFNFMLSGQNLERLSTDRIRVLSLSGLKITLQLV EEGEREWRVTKLNGIPLGRDEYVVINRAILGDVSDPRFNLVRDPVIAKLQQLHQVNLLDDTTTEEHPDNLDTLDTASAID LPQDQSSDSEVPDPANLSALLPDLSSFVKSLFARLSNLTSPSPDPSSNLPLNVVINQTAILPTGIGAAPLPPAASNSPSG APIPVFGPVPESLFPWKTIYAAGEACAGPLPDSAPRENQVILIRRGGCSFSDKLANIPAFTPSEESLQLVVVVSDDEHEG QSGLVRPLLDEIQHTPGGMPRRHPIAMVMVGGGETVYQQLSVASAIGIQRRYYIESSGVKVKNIIVDDGDGGVDGGTKHH HHHH P42212 G0SCX7 3.2.1.- Protein disulfide-isomerase Thermochaetoides thermophila 0.055841366999999996

Chaetomium thermophilum Endoplasmic reticulum degradation enhancing protein disulfide isomerase (CtPDI)

1 Homo sapiens LEVO ETGSDVIQLKKDTFDDFIKSNDLVLAEFFAPWCGHCKALAPEYEEAATNLKDKNIKLVKVDCTEETELCQEHGVEGYPTL KVFRGLDNVTPYKGQRKAAAITSYMIKQSLPAVSDVTKDTLEEFKKADKVVLVAYVDASDKASAEVFKKVAEKLRDNYPF GSSSDAELAEAEGVKAPAIVLYKDFDEGKAVFTEKFDEEAIQKWAKVAATPLIGEIGPETYGEYMAAGIPLAYIFAETPE ERKELSEKLKPIAEATRGKINFGTIDAKAYGAHAGNLNLKTDKFPAFAIQETTKNQKFPYDQDKEITHDSIKQFVDDYLA GKIEPSIKSEPIPEKQEGPVTVVVAKTYNDIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGRLYSNSEFKDRVVIAKID ATANDVPDDIMGFPTIKMYPAGAKDKPVTYSGNRSVEDMIKFVAENGKYKALISENEEENATAASSSSETSATPTSTAAS EETAASETASAEEGKETAGTKHHHHHH G0SGS2 5.3.4.1 CALCIUM ION 4.0078e-05 1 CA THIOSULFATE 0.000112128 1 THJ 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 2 NAG alpha-D-mannopyranose 0.000180156 1 MAN water 1.8015e-05 3 HOH singleParticle particle 0.02 7.0 150.0 NaCl sodium chloride 20.0 C6H13NO4S MES 1.0 CaCl2 calcium chloride

Micro SEC buffer: 150 mM NaCl, 20 mM MES pH 7.0, 1 mM CaCl2

Quantifoil R1.2/1.3 GOLD 300 GRAPHENE OXIDE HOLEY GLOW DISCHARGE 180 AIR 0.2

The Quantifoil Au300 R1.2/1.3 Holey Carbon grids were glow discharged using the EMS GloQube. For grids to be coated in GO, the Graphene Oxide setting was used (0.2m Bar, 40 mA for 180 seconds). For GO coating, graphene oxide solution (Sigma) at 0.2 mg/ml was spun at 300 g for 30 s to remove large aggregates. 3 uL was added to the grids for 1 minute, before blotting with Whatman No1 filter paper and washing three times with 20 uL drops of ultrapure water.

ETHANE 100 277 FEI VITROBOT MARK IV

Blotting time 3 s, waiting time 30 s Sample volume 3 uL, blot force 10.

40 uL of a protein sample with an OD_280 of 0.88 were injected onto a Cytiva Superdex 200 Increase 3.2/300 size-exclusion chromatography column, equilibrated in 150 mM NaCl, 20 mM MES pH 7.0, 1 mM CaCl2, collecting 50 uL fractions.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 2.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 4 C1 BACK PROJECTION 2.6 FSC 0.143 CUT-OFF cryoSPARC 1400000 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 4 150000.0 cryoSPARC emd_17749.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 250.5 250.5 250.5 90.0 90.0 90.0 X Y Z -0.30968925 0.64553756 0.0002195782 0.017497346 0.835 0.835 0.835 0.07 AUTHOR ::::EMDATABANK.org::::EMD-17749:::: Cryosparc class, 150,000 particles, iteration 4 emd_17749_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 250.5 250.5 250.5 90.0 90.0 90.0 X Y Z -0.7228094 0.7633535 0.00040772138 0.08530867 0.835 0.835 0.835 AUTHOR ::::EMDATABANK.org::::EMD-17749:::: Cryosparc class, 150,000 particles, iteration 3 emd_17749_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 250.5 250.5 250.5 90.0 90.0 90.0 X Y Z -0.8742642 0.8069648 0.00040091062 0.08536441 0.835 0.835 0.835 AUTHOR ::::EMDATABANK.org::::EMD-17749:::: Cryosparc class, 150,000 particles, iteration 3