2026-08-12 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update _pdbx_entry_details.has_protein_modification RCSB RCSB 2025-06-12 2025-11-12 2025-11-12 2026-08-12 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-71045 consensus EM volume EMD-71151 focused EM volume EMD-71152 focused EM volume 9p2r FULLOVERLAP EMDB EMD-71045 consensus EM volume EMDB EMD-71151 focused EM volume EMDB EMD-71152 focused EM volume EMDB EMD-71204 associated EM volume

Extended, CYR715-bound state of Manduca sexta soluble guanylate cyclase mutant beta C122S

PDB 9OXN unspecified

ligand-free Manduca sexta soluble guanylate cyclase mutant beta C122S in the contracted conformation

Ligand-free Manduca sexta soluble guanylase cyclase variant Ligand-free Manduca sexta soluble guanylase cyclase variant 0 1 2

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

Manduca sexta .147 Soluble guanylyl cyclase alpha-1 subunit Manduca sexta 0.078598727 1 Spodoptera aff. frugiperda 2 RZ-2014 LEVO MTCPFRRASSQHQFANGGSSAPKKPEFRSRTSSVHLTGPEEEDGERNTLTLKHMSEALQLLTAPSNECLHAAVTSLTKNQ SDHYHKYNCLRRLPDDVKTCRNYAYLQEIYDAVRATDSVNTKDFMAKLGEYLILTAFSHNCRLERAFKCLGTNLTEFLTT LDSVHDVLHDQDTPLKDETMEYEANFVCTTSQEGKIQLHLTTESEPVAYLLVGSLKAIAKRLYDTQTDIRLRSYTNDPRR FRYEINAVPLHQKSKEDSCELVNEAASVATSTKVTDLKIGVASFCKAFPWHFITDKRLELVQLGAGFMRLFGTHLATHGS SLGTYFRLLRPRGVPLDFREILKRVNTPFMFCLKMPGSTALAEGLEIKGQMVFCAESDSLLFVGSPFLDGLEGLTGRGLF ISDIPLHDATRDVILVGEQARAQDGLRRRMDKLKNSIEEASKAVDKEREKNVSLLHLIFPPHIAKRLWLGEKIEAKSHDD VTMLFSDIVGFTSICATATPMMVIAMLEDLYSVFDIFCEELDVYKVETIGDAYCVASGLHRKVETHAPQIAWMALRMVET CAQHLTHEGNPIKMRIGLHTGTVLAGVVGKTMLKYCLFGHNVTLANKFESGSEPLKINVSPTTYEWLIKFPGFDMEPRDR SCLPNSFPKDIHGTCYFLHKYTHPGTDPGEPQVKHIREALKDYGIGQANSTDVDTEEPT O77105 Guanylate cyclase soluble subunit beta-1 Manduca sexta 0.06816592999999999 1 Spodoptera aff. frugiperda 2 RZ-2014 LEVO MYGFVNYALELLVMKTFDEETWETIKKKADVAMEGSFLVRQIYEDEITYNLITAAVEVLQIPADAILELFGKTFFEFCQD SGYDKILQVLGATPRDFLQNLDGLHDHLGTLYPGMRSPSFRSTERPEDGALVLHYYSDRPGLEHIVIGIVKTVASKLHNT EVKVEILKTKEECDHVQFLITETSTTGRVSAPEIAEIETLSLEPKVSPATFCRVFPFHLMFDRDLNIVQAGRTVSRLLPR VTRPGCKITDVLDTVRPHLEMTFANVLAHINTVYVLKTKPEEMSVTDPHEEIASLRLKGQMLYIPETDVVVFQCYPSVTN LDDLTRRGLCIADIPLHDATRDLVLMSEQFEADYKLTQNLEVLTDKLQQTFRELELEKQKTDRLLYSVLPISVATELRHR RPVPARRYDTVTLLFSGIVGFANYCARNSDHKGAMKIVRMLNDLYTAFDVLTDPKRNPNVYKVETVGDKYMAVSGLPEYE VAHAKHISLLALDMMDLSQTVTVDGEPVGITIGIHSGEVVTGVIGHRMPRYCLFGNTVNLTSRCETTGVPGTINVSEDTY NYLMREDNHDEQFELTYRGHVTMKGKAEPMQTWFLTRKIH O77106 4.6.1.2 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER 0.0005212079999999999 1 G2P PROTOPORPHYRIN IX CONTAINING FE 0.000616487 1 HEM (2S,3R)-1-{5-fluoro-2-[(5P)-1-[(2-fluorophenyl)methyl]-5-(1,2-oxazol-3-yl)-1H-pyrazol-3-yl]pyrimidin-4-yl}-3-methylpiperidine-2-carboxylic acid 0.00048046699999999994 1 A1CGK 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. Additionally, 250 uM CYR715 (stimulator) and 1 mM GpCpp (non-hydrolyzable substrate-analog) were added to the sample before freezing.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.5 1.5 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K3 (6k x 4k) 1 8433 0.0354 1.25 1 1226641

Autopicking was used to produce a stack of 2,299,895 particles. Particles showing poor alignment or broken complexes were removed using a series of 2D classification steps, leaving a particle stack of 902,997 particles that resembled sGC dimers.

cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION The initial model of Ms sGC BC122S was built using SwissModel and Alphafold predicted structures of BC122S based on homology with solved structures of human sGC in the extended state. 3.6 FSC 0.143 CUT-OFF cryoSPARC

Non-Uniform (NU) refinement was performed on the higher resolution 3D class. The resulting 3.6 A consensus density resembled previous sGC structures in the extended, NO-bound state. Other refinement strategies were attempted, but did not lead to higher resolution global map densities. To improve local resolution of the domains of CYR715-bound sGC, local refinement was also performed. Separate masks were created for each domain, and local refinement as implemented in cryoSPARC was used to improve the resolution of the catalytic and H-NOX domains of the global map. The subsequent local refinement resulted in 3.5 A and 3.4 A maps for the H-NOX and catalytic domains respectively. These maps were then combined with the consensus map to create the composite map herein.

598571 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC 2 200000.0 cryoSPARC

The stack was subjected to 2-class ab initio refinement followed by heterogeneous refinement in cryoSPARC. 598,571 particles sorted into a higher resolution 3D class.

SwissModel in silico model

Structure best matched homology and shape with 8HBF.

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