2025-03-05 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 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 _citation_author.identifier_ORCID _citation_author.name _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 _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update RCSB RCSB 2024-10-15 2024-10-30 2024-10-30 2025-03-05 Bill & Melinda Gates Foundation United States Catalytic domain of Dihydrolipoamide Succinytransferase Carr KD Borst AJ Weidle C E2, 2-oxoglutarate dehydrogenase complex, catalytic domain, tricarboxylic acid cycle, TRANSFERASE Carr KD Zambrano DED Weidle C Goodson A Eisenach HE Pyles H Courbet A King NP Borst AJ Protein identification using Cryo-EM and artificial intelligence guides improved sample purification. J Struct Biol X NE 11 100120 100120 2025 39958810 doi:10.1016/j.yjsbx.2025.100120 2590-1524 9dz8 FULLOVERLAP Dihydrolipoamide Succinyltransferase Dihydrolipoamide Succinyltransferase 0 1
This protein was observed as contaminant in a sample of a two component nanoparticle assembly.
Escherichia coli BL21(DE3) 1.056 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex Escherichia coli BL21(DE3) 0.026107419999999996 24 LEVO ARSEKRVPMTRLRKRVAERLLEAKNSTAMLTTFNEVNMKPIMDLRKQYGEAFEKRHGIRLGFMSFYVKAVVEALKRYPEV NASIDGDDVVYHNYFDVSMAVSTPRGLVTPVLRDVDTLGMADIEKKIKELAVKGRDGKLTVEDLTGGNFTITNGGVFGSL MSTPIINPPQSAILGMHAIKDRPMAVNGQVEILPMMYLALSYDHRLIDGRESVGFLVTIKELLEDPTRLLLDV A0A140NDX4 2.3.1.61 water 1.8015e-05 2088 HOH singleParticle particle 0.3 8.0 Quantifoil R2/2 COPPER 300 CARBON HOLEY 40.0 GLOW DISCHARGE ETHANE 100 295.15 FEI VITROBOT MARK IV
Wait time: 7.5 seconds Blot time: 0.5 seconds Blot force: 0 seconds.
This sample was heterogeneous and contamined both DLST and the designed nanoparticle assembly.
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 1.8 GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 1 4264 5.0 47.0
6211 movies were collected, the best 4264 were used for particle picking and further processing.
 1
ab-initio
 76 O 2.51 FSC 0.143 CUT-OFF cryoSPARC 4.4.1 19033 MAXIMUM LIKELIHOOD cryoSPARC 4.4.1 MAXIMUM LIKELIHOOD cryoSPARC 4.4.1 76 250.0 cryoSPARC 4.4.1 emd_47326.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 503.99997 503.99997 503.99997 90.0 90.0 90.0 X Y Z -0.028140226 1.6010301 0.00071355194 0.018694753 0.84 0.84 0.84 0.1 AUTHOR Sharpened map using DeepEMhancer Other in silico model
ModelAngelo
 OTHER
The final model was built to density using the UniProt sequence in ModelAngelo. Further refinement of the model to the density was performed using ISOLDE in ChimeraX, Coot, Phenix. Waters were built to one chain and then that chain and water network were rebuilt in ChimeraX using symmetry.
Cross-correlation coefficient REAL 69.900000000000006 emd_47326_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 503.99997 503.99997 503.99997 90.0 90.0 90.0 X Y Z -0.22639729 0.48300368 0.00012883026 0.0114713 0.84 0.84 0.84 AUTHOR Sharpened map emd_47326_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 503.99997 503.99997 503.99997 90.0 90.0 90.0 X Y Z -0.048001297 0.1633293 0.00012883026 0.00392705 0.84 0.84 0.84 AUTHOR Unsharpened map emd_47326_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 503.99997 503.99997 503.99997 90.0 90.0 90.0 X Y Z -0.16151297 0.20577239 0.00015345594 0.018386403 0.84 0.84 0.84 AUTHOR Half map A emd_47326_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 503.99997 503.99997 503.99997 90.0 90.0 90.0 X Y Z -0.16699524 0.2808454 0.00015480681 0.018540625 0.84 0.84 0.84 AUTHOR Half map B