2026-10-07 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2026-09-15 2026-10-07 2026-10-07 2026-10-07 Other government United States Other private United States Cryo-EM structure of Sr01-080, a denovo designed borneol dehydrogenase Miles U McShan A McManus C Kamerlin SCL Di Geronimo Quintero B Dehydrogenase, De novo designed protein, borneol dehydrogenase, oxidoreductase Miles U McShan A McManus C Kamerlin SCL Di Geronimo Quintero B Full-Atom MPNN Based Redesign of Plant Dehydrogenase Enables Thermostability Enhancement Without Loss of Stereoselectivity To Be Published 0353 38rr FULLOVERLAP EMDB EMD-79087 associated EM volume
Cryo-EM structure of Sr01-080, a de novo designed borneol dehydrogenase
 01_80 01_80 0 1
Tetrameric complex of 4 01_80 units
synthetic construct Sr01-080 synthetic construct 0.02821609 4 Escherichia coli LEVO MGHHHHHHGRLEGKVAIVTGGASGIGRSTVELFHEEGAKVVIADIREEEGQALAEKLGDDVTFQHCDVTDEEQVKALVEA TVERWGGVDIMFSNAGIVEGPNSIADVDKADFERLMGINLVGAFLTAKYAAEVMKPQKSGVIIFTASACTEIAGIAGFAY TASKYGVVGLMKELAFELGKYGIRANAVSPFLVLTGIPPGGSKGVEEFAKLYEKVGTLKGKILTADDVAKTVLYLASDEA SFVSGVNLLVDGGYTVVNPTFVNVVNA singleParticle particle 5 8.0 125.0 NaCl Sodium Chloride 20.0 C4H11NO3 Tris
125 mM NaCl, 10 mM Tris HCl (pH = 8.0)
 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE OTHER ETHANE 100 283 FEI VITROBOT MARK III
This samples was monodisperse
 TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 0.6 2.0 100000.0 NITROGEN FEI FALCON IV (4k x 4k) 4096 4096 1 2564 8.0 52.88
Images were collected as movies with 80 images collected per movie at 100 ms of exposure for a total of 8.0 sec of exposure per micrograph
 1 3922227
Particles were picked using Blob Picker in CryoSPARC with min particle diameter 80 A, max particle diameter 120 A, and min separation distance 40 A. 5974094 picks were reduced with an Inspect Picks Job to 4494189, and an Extract Mics. (G) job reduced picks further to 3922227.
 PHASE FLIPPING AND AMPLITUDE CORRECTION
Ab-initio model generated in CryoSPARC
 1 D2 BACK PROJECTION 3.17 FSC 0.143 CUT-OFF cryoSPARC
Non-uniform refinement in CryosPARC with D2 symmetry and refinement mask excluding neighboring particles in psuedo-filaments present in micrographs.
743562 MAXIMUM LIKELIHOOD
Ab-initio model generated in CryoSPARC
 MAXIMUM LIKELIHOOD
Non-uniform refinement in CryoSPARC
 5 156481.0
Classes 0-4 contained 44.9%, 14.2%, 36.3%, 0.0%, and 4.6% of 782,408 particles. Classes 0-2 were retained for downstream processing.
 emd_79087.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 294.144 294.144 294.144 90.0 90.0 90.0 X Y Z -9.00569 9.286241 0.0014572679 0.1175112 1.149 1.149 1.149 0.278 AUTHOR EM half map of the 01_80 tetramer complex AlphaFold in silico model OTHER
Initial fitting was done in chimeraX, and refined through sequential Real space refinement protocol in PHENIX and manual refinement with ISOLDE
REAL emd_79087_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 295.168 295.168 295.168 90.0 90.0 90.0 X Y Z -0.43669543 1.1752977 0.0014542032 0.03568232 1.153 1.153 1.153 EMDB None emd_79087_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 295.168 295.168 295.168 90.0 90.0 90.0 X Y Z -0.47908187 1.1823884 0.0014796385 0.035586346 1.153 1.153 1.153 AUTHOR EM half map of the 01_80 tetramer complex