HEADER MEMBRANE PROTEIN 10-SEP-25 9Y7F TITLE CRYSTAL STRUCTURE OF NANOBODY R3D8 IN COMPLEX WITH HUMAN VOLTAGE-GATED TITLE 2 SODIUM CHANNEL NAV1.7 P-LOOP 1. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY R3D8; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SODIUM CHANNEL PROTEIN TYPE 9 SUBUNIT ALPHA; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: NEUROENDOCRINE SODIUM CHANNEL,HNE-NA,PERIPHERAL SODIUM COMPND 9 CHANNEL 1,PN1,SODIUM CHANNEL PROTEIN TYPE IX SUBUNIT ALPHA,VOLTAGE- COMPND 10 GATED SODIUM CHANNEL SUBUNIT ALPHA NAV1.7; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES; COMPND 13 OTHER_DETAILS: Y304C AND Y305 MUTATIONS TO GENERATE DISULFIDE BOND COMPND 14 STABILIZED P-LOOP1. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 3 ORGANISM_COMMON: ALPACA; SOURCE 4 ORGANISM_TAXID: 30538; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: SCN9A, NENA; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VOLTAGE-GATED SODIUM CHANNEL, NAV1.7, NANOBODY, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.-E.CHEN,J.LIU,M.MOBLI,B.M.COLLINS REVDAT 1 16-SEP-26 9Y7F 0 JRNL AUTH J.LIU,W.CHEN,B.CRISTOFORI-ARMSTRONG,T.CRAWFORD,K.E.CHEN, JRNL AUTH 2 P.XIE,R.W.B.CHAN,Y.ZHU,M.GOLDER,A.PEREIRA SCHMIDT, JRNL AUTH 3 J.D.NAUGHTON,N.D.CONDON,A.ANDERSSON,F.DEHKHODA,K.L.MCMAHON, JRNL AUTH 4 T.KLASFAUSEWEH,A.THAPA,H.TRAN,P.TRAN,S.JAMI,L.RAGNARSSON, JRNL AUTH 5 S.G.B.FURNESS,J.R.DEUIS,B.M.COLLINS,W.H.THAM,I.PRASADAM, JRNL AUTH 6 I.VETTER,M.MOBLI JRNL TITL ANTIGEN-DETECTED NMR FOR MINIMAL EPITOPE ENGINEERING AND JRNL TITL 2 STRUCTURE-GUIDED SELECTION OF A NA V 1.7-SELECTIVE NANOBODY. JRNL REF ADV SCI 77611 2026 JRNL REFN ESSN 2198-3844 JRNL PMID 42702812 JRNL DOI 10.1002/ADVS.77611 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 14825 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1482 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 36.9600 - 3.7800 1.00 1266 141 0.1649 0.2005 REMARK 3 2 3.7800 - 3.0000 1.00 1225 136 0.1829 0.2275 REMARK 3 3 3.0000 - 2.6200 1.00 1226 137 0.2062 0.2525 REMARK 3 4 2.6200 - 2.3800 1.00 1232 137 0.2142 0.2246 REMARK 3 5 2.3800 - 2.2100 1.00 1225 136 0.1974 0.2808 REMARK 3 6 2.2100 - 2.0800 1.00 1211 134 0.2066 0.2525 REMARK 3 7 2.0800 - 1.9800 1.00 1214 135 0.2049 0.2536 REMARK 3 8 1.9800 - 1.8900 0.99 1213 135 0.2252 0.2927 REMARK 3 9 1.8900 - 1.8200 0.99 1210 134 0.2893 0.2954 REMARK 3 10 1.8200 - 1.7600 0.99 1196 132 0.3633 0.3824 REMARK 3 11 1.7500 - 1.7000 0.93 1125 125 0.5112 0.4905 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 1227 REMARK 3 ANGLE : 1.056 1656 REMARK 3 CHIRALITY : 0.062 173 REMARK 3 PLANARITY : 0.009 219 REMARK 3 DIHEDRAL : 5.134 169 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 10.4527 1.5278 4.8528 REMARK 3 T TENSOR REMARK 3 T11: 0.1675 T22: 0.1408 REMARK 3 T33: 0.1509 T12: 0.0007 REMARK 3 T13: -0.0042 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 1.0454 L22: 0.7449 REMARK 3 L33: 0.7257 L12: 0.3548 REMARK 3 L13: 0.4233 L23: 0.1522 REMARK 3 S TENSOR REMARK 3 S11: 0.0626 S12: 0.0403 S13: -0.1297 REMARK 3 S21: -0.0323 S22: 0.0383 S23: 0.0294 REMARK 3 S31: 0.0348 S32: 0.0626 S33: 0.0003 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9Y7F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000299944. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14888 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 43.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.93800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: LONG PLATE SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12 %W/V PEG 8000, 50 MM SODIUM REMARK 280 CACODYLATE PH 6.5, 90 MM NH4SO4., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 21.81800 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS A 125 REMARK 465 HIS A 126 REMARK 465 HIS A 127 REMARK 465 ASN B 278 REMARK 465 SER B 279 REMARK 465 LEU B 280 REMARK 465 GLU B 281 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 29 -160.51 -109.43 REMARK 500 ALA A 75 30.00 -142.34 REMARK 500 ALA A 92 161.14 176.90 REMARK 500 ASN B 283 -11.60 78.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 418 DISTANCE = 5.86 ANGSTROMS DBREF 9Y7F A 1 127 PDB 9Y7F 9Y7F 1 127 DBREF 9Y7F B 275 305 UNP Q15858 SCN9A_HUMAN 275 305 SEQADV 9Y7F CYS B 304 UNP Q15858 TYR 304 ENGINEERED MUTATION SEQADV 9Y7F SER B 305 UNP Q15858 TYR 305 ENGINEERED MUTATION SEQRES 1 A 127 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 127 ASP GLY GLY SER LEU ARG LEU SER CYS VAL ALA SER GLY SEQRES 3 A 127 PHE ILE PHE ASP ASP TYR ALA ILE GLY TRP PHE ARG GLN SEQRES 4 A 127 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ALA ILE SER SEQRES 5 A 127 TRP ASN GLY LEU SER THR ARG TYR ALA ASP SER VAL LYS SEQRES 6 A 127 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ILE ALA SEQRES 7 A 127 VAL TYR LEU GLN MET ASP ASN LEU THR PRO ASP ASP THR SEQRES 8 A 127 ALA ARG TYR TYR CYS THR MET ARG ALA TRP SER GLU ASN SEQRES 9 A 127 THR GLY ASN PHE ALA SER ARG GLY GLN GLY THR GLN VAL SEQRES 10 A 127 THR VAL SER SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 31 CYS PHE ARG ASN SER LEU GLU ASN ASN GLU THR LEU GLU SEQRES 2 B 31 SER ILE MET ASN THR LEU GLU SER GLU GLU ASP PHE ARG SEQRES 3 B 31 LYS TYR PHE CYS SER FORMUL 3 HOH *82(H2 O) HELIX 1 AA1 THR A 87 THR A 91 5 5 HELIX 2 AA2 THR B 285 ASN B 291 1 7 HELIX 3 AA3 SER B 295 CYS B 304 1 10 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 25 N GLN A 3 SHEET 3 AA1 4 ALA A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 AA1 4 PHE A 68 ARG A 72 -1 N THR A 69 O GLN A 82 SHEET 1 AA2 6 GLY A 10 GLN A 13 0 SHEET 2 AA2 6 THR A 115 SER A 120 1 O THR A 118 N VAL A 12 SHEET 3 AA2 6 ALA A 92 SER A 102 -1 N TYR A 94 O THR A 115 SHEET 4 AA2 6 TYR A 32 GLN A 39 -1 N PHE A 37 O TYR A 95 SHEET 5 AA2 6 GLU A 46 SER A 52 -1 O ALA A 49 N TRP A 36 SHEET 6 AA2 6 THR A 58 TYR A 60 -1 O ARG A 59 N ALA A 50 SHEET 1 AA3 4 GLY A 10 GLN A 13 0 SHEET 2 AA3 4 THR A 115 SER A 120 1 O THR A 118 N VAL A 12 SHEET 3 AA3 4 ALA A 92 SER A 102 -1 N TYR A 94 O THR A 115 SHEET 4 AA3 4 GLY A 106 ARG A 111 -1 O PHE A 108 N ALA A 100 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.22 SSBOND 2 CYS B 275 CYS B 304 1555 1555 2.22 CRYST1 38.829 43.636 42.325 90.00 107.84 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.025754 0.000000 0.008289 0.00000 SCALE2 0.000000 0.022917 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024820 0.00000 CONECT 157 757 CONECT 757 157 CONECT 983 1200 CONECT 1200 983 MASTER 258 0 0 3 14 0 0 6 1276 2 4 13 END