2025-11-26 REL RCSB RCSB RCSB 2025-06-04 2025-11-12 2025-11-12 2025-11-26 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 5F32 GM149060-02 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) U24 GM129541-02 United States Thomas WC Houghton KA Cyclase, NO, SIGNALING PROTEIN Houghton KA Thomas WC Marletta MA Biochemistry US 64 4529 4541 2025 41146038 doi:10.1021/acs.biochem.5c00424 0006-2960 0033 BICHAW EMD-70990 other EM volume

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EMDB EMD-71030 associated EM volume EMDB EMD-70990 other EM volume

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Ligand-free Manduca sexta soluble guanylase cyclase variant Ligand-free Manduca sexta soluble guanylase cyclase variant 0 1

Heterodimeric sGC molecule in the ligand-free, compact state. Beta-C122S mutant variant.

Manduca sexta .147 Soluble guanylate cyclase (H-NOX domain) Manduca sexta

N-terminal domain focused refinement of a heterodimeric complex

Spodoptera aff. frugiperda 2 RZ-2014 LEVO MTCPFRRASSQHQFANGGSSAPKKPEFRSRTSSVHLTGPEEEDGERNTLTLKHMSEALQLLTAPSNECLHAAVTSLTKNQSDHYHKYNCLRRLPDDVKTCRNYAYLQEIYDAVRATDSVNTKDFMAKLGEYLILTAFSHNCRLERAFKCLGTNLTEFLTTLDSVHDVLHDQDTPLKDETMEYEANFVCTTSQEGKIQLHLTTESEPVAYLLVGSLKAIAKRLYDTQTDIRLRSYTNDPRRFRYEINAVPLHQKSKEDSCELVNEAASVATSTKVTDLKIGVASFCKAFPWHFITDKRLELVQLGAGFMRLFGTHLATHGSSLGTYFRLLRPRGVPLDFREILKRVNTPFMFCLKMPGSTALAEGLEIKGQMVFCAESDSLLFVGSPFLDGLEGLTGRGLFISDIPLHDATRDVILVGEQARAQDGLRRRMDKLKNSIEEASKAVDKEREKNVSLLHLIFPPHIAKRLWLGEKIEAKSHDDVTMLFSDIVGFTSICATATPMMVIAMLEDLYSVFDIFCEELDVYKVETIGDAYCVASGLHRKVETHAPQIAWMALRMVETCAQHLTHEGNPIKMRIGLHTGTVLAGVVGKTMLKYCLFGHNVTLANKFESGSEPLKINVSPTTYEWLIKFPGFDMEPRDRSCLPNSFPKDIHGTCYFLHKYTHPGTDPGEPQVKHIREALKDYGIGQANSTDVDTEEPT MYGFVNYALELLVMKTFDEETWETIKKKADVAMEGSFLVRQIYEDEITYNLITAAVEVLQIPADAILELFGKTFFEFCQDSGYDKILQVLGATPRDFLQNLDGLHDHLGTLYPGMRSPSFRSTERPEDGALVLHYYSDRPGLEHIVIGIVKTVASKLHNTEVKVEILKTKEECDHVQFLITETSTTGRVSAPEIAEIETLSLEPKVSPATFCRVFPFHLMFDRDLNIVQAGRTVSRLLPRVTRPGCKITDVLDTVRPHLEMTFANVLAHINTVYVLKTKPEEMSVTDPHEEIASLRLKGQMLYIPETDVVVFQCYPSVTNLDDLTRRGLCIADIPLHDATRDLVLMSEQFEADYKLTQNLEVLTDKLQQTFRELELEKQKTDRLLYSVLPISVATELRHRRPVPARRYDTVTLLFSGIVGFANYCARNSDHKGAMKIVRMLNDLYTAFDVLTDPKRNPNVYKVETVGDKYMAVSGLPEYEVAHAKHISLLALDMMDLSQTVTVDGEPVGITIGIHSGEVVTGVIGHRMPRYCLFGNTVNLTSRCETTGVPGTINVSEDTYNYLMREDNHDEQFELTYRGHVTMKGKAEPMQTWFLTRKIH singleParticle particle 1.5 7.5 25.0 C6H15NO3 Triethanolamine (TEA) 25.0 NaCl Sodium chloride 5.0 C4H10O2S2 Dithiothreitol (DTT) 5.0 MgCl2 Magnesium chloride 0.5 C20H25F13O11 Fluorinated Octyl Maltoside Quantifoil R1.2/1.3 CARBON ETHANE 100 277 FEI VITROBOT MARK IV

Cryo-EM samples were prepared by applying 3 ul to a glow-discharged Quantifoil R1.2/1.3 holey-carbon cryo-EM grid. The grid was blotted for 4 s with Whatman #1 filter paper and then plunge-frozen in liquid ethane with a Mark IV Vitrobot (ThermoFisher) at 4 C and 100% humidity..

Samples were prepared in a Coy anaerobic chamber at RT. Protein was thawed at 4 C, reduced with 10 mM Na2S2O4 for 15 minutes at RT, and desalted using a Zeba spin column equilibrated with Buffer, 0.22 um filtered. Protein samples were then diluted to 10 uM in equivalent buffer but with addition of 0.5 mM FOM.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.5 1.5 FEI TITAN KRIOS AUTOGRID HOLDER FEI FALCON I (4k x 4k) 1 11872 0.2195 1.25 1 1226641

Autopicking was used to produce a stack of 1,226,641 particles. Particles showing poor alignment or broken complexes were removed using a series of 2D classification steps, leaving a particle stack of 368,563 particles that resembled sGC dimers.

cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION The initial model of Ms sGC BC122S was built using ModelAngelo in known sequence mode and with a sharpened global 3.3 A map as a starting point. 3.0 FSC 0.143 CUT-OFF cryoSPARC

During refinement it became clear that there was minor interdomain flexibility within the 264,227 particles. In particular, the catalytic domain was at lower resolution and had considerable missing density. Separate masks were created for each domain, and local refinement as implemented in cryoSPARC was used to improve the resolution of the separate catalytic and H-NOX domains of the global map. The subsequent local refinement resulted in 3.0 A and 3.4 A maps for the H-NOX and catalytic domains respectively. Both have improved density for outer regions of the map and improved local resolution

264227 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC 2 200000.0 cryoSPARC

After 2D classification for intact dimers, the particle stack was subjected to 2-class ab initio refinement followed by heterogeneous refinement in cryoSPARC. 264,227 particles sorted into a higher resolution 3D class, on which Non-Uniform (NU) refinement was performed. The resulting 3.3 A global map strongly resembled previous sGC structures in the ligand-free, contracted state, and the map was used for initial model building. Other refinement strategies were attempted, but did not lead to higher resolution global map densities.

AlphaFold in silico model

ModelAngelo and Alphafold

FLEXIBLE FIT

Refinement was performed using iterative rounds of Phenix real space refinement and manual modeling in Coot. Phenix refinement was performed for separate domains of the model using the higher-resolution local maps of those domains.

REAL emd_71030_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 305.28 305.28 305.28 90.0 90.0 90.0 X Y Z -0.80916166 2.7341666 0.0030769538 0.06862876 0.954 0.954 0.954 AUTHOR ::::EMDATABANK.org::::EMD-71030:::: Half-map A of local (focused) map of H-NOX domain of ligand-free, compact M. sexta sGC C122S emd_71030_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 305.28 305.28 305.28 90.0 90.0 90.0 X Y Z -0.72209835 2.7818863 0.0030908678 0.06849889 0.954 0.954 0.954 AUTHOR ::::EMDATABANK.org::::EMD-71030:::: Half-map A of local (focused) map of H-NOX domain of ligand-free, compact M. sexta sGC C122S