HEADER VIRAL PROTEIN/PROEIN BINDING 20-JAN-24 8XZ4 TITLE SARS-COV-2 S AND RADIXIN COMPLEX STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RADIXIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FERM DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SPIKE PROTEIN S2'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RDX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 11 2; SOURCE 12 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 13 ORGANISM_TAXID: 2697049 KEYWDS SARS-COV-2, S, EZRIN-RADIXIN-MOESIN, CYTOSKELETON, ASSEMBLY, KEYWDS 2 VIRAL/PROTEIN BINDING, VIRAL PROTEIN-PROEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.M.WANG,W.F.MA REVDAT 1 08-OCT-25 8XZ4 0 JRNL AUTH J.M.WANG,W.F.MA JRNL TITL SARS-COV-2 S AND RADIXIN COMPLEX STRUCTURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.16_3549: ???) 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) : 2.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 19283 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1942 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 38.6880 - 5.1286 1.00 1287 151 0.1889 0.2242 REMARK 3 2 5.1286 - 4.0721 1.00 1270 139 0.1794 0.2332 REMARK 3 3 4.0721 - 3.5578 0.85 1069 119 0.1945 0.2845 REMARK 3 4 3.5578 - 3.2327 1.00 1250 145 0.2221 0.2559 REMARK 3 5 3.2327 - 3.0011 1.00 1261 138 0.2506 0.2979 REMARK 3 6 3.0011 - 2.8242 1.00 1248 137 0.2519 0.3166 REMARK 3 7 2.8242 - 2.6828 1.00 1247 140 0.2464 0.2960 REMARK 3 8 2.6828 - 2.5660 1.00 1265 145 0.2587 0.3145 REMARK 3 9 2.5660 - 2.4673 1.00 1219 137 0.2555 0.2623 REMARK 3 10 2.4673 - 2.3821 1.00 1261 138 0.2496 0.3541 REMARK 3 11 2.3821 - 2.3077 1.00 1228 138 0.2641 0.2948 REMARK 3 12 2.3077 - 2.2417 1.00 1249 137 0.2360 0.2786 REMARK 3 13 2.2417 - 2.1827 1.00 1233 141 0.2518 0.2664 REMARK 3 14 2.1827 - 2.1295 1.00 1254 137 0.2754 0.2936 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.120 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 : 0.004 2594 REMARK 3 ANGLE : 0.647 3509 REMARK 3 CHIRALITY : 0.044 375 REMARK 3 PLANARITY : 0.004 453 REMARK 3 DIHEDRAL : 5.494 1561 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8XZ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 26-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300044536. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NFPSS REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19283 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 75 MM SODIUM ACETATE, 0.1 M TRIS-HCL, REMARK 280 PH 7.4, 5.5% PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.22200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.83300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.61100 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: 1210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 MET A 1 REMARK 465 PRO A 2 REMARK 465 LYS A 3 REMARK 465 THR B 1273 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 23 CG OD1 ND2 REMARK 470 LYS A 53 CG CD CE NZ REMARK 470 LYS A 63 CG CD CE NZ REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 LYS A 71 CG CD CE NZ REMARK 470 LYS A 72 CG CD CE NZ REMARK 470 LYS A 262 CG CD CE NZ REMARK 470 LYS A 263 CG CD CE NZ 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 ASP A 13 21.21 -140.96 REMARK 500 ASP A 51 -169.91 -106.29 REMARK 500 HIS A 142 72.46 -118.66 REMARK 500 PRO A 144 121.83 -37.21 REMARK 500 HIS A 161 51.07 -93.07 REMARK 500 ASP A 252 -113.51 52.58 REMARK 500 LYS A 262 -29.65 92.63 REMARK 500 SER B1261 36.36 72.26 REMARK 500 REMARK 500 REMARK: NULL DBREF 8XZ4 A 1 296 UNP P35241 RADI_HUMAN 1 296 DBREF 8XZ4 B 1260 1273 UNP P0DTC2 SPIKE_SARS2 1260 1273 SEQRES 1 A 296 MET PRO LYS PRO ILE ASN VAL ARG VAL THR THR MET ASP SEQRES 2 A 296 ALA GLU LEU GLU PHE ALA ILE GLN PRO ASN THR THR GLY SEQRES 3 A 296 LYS GLN LEU PHE ASP GLN VAL VAL LYS THR VAL GLY LEU SEQRES 4 A 296 ARG GLU VAL TRP PHE PHE GLY LEU GLN TYR VAL ASP SER SEQRES 5 A 296 LYS GLY TYR SER THR TRP LEU LYS LEU ASN LYS LYS VAL SEQRES 6 A 296 THR GLN GLN ASP VAL LYS LYS GLU ASN PRO LEU GLN PHE SEQRES 7 A 296 LYS PHE ARG ALA LYS PHE PHE PRO GLU ASP VAL SER GLU SEQRES 8 A 296 GLU LEU ILE GLN GLU ILE THR GLN ARG LEU PHE PHE LEU SEQRES 9 A 296 GLN VAL LYS GLU ALA ILE LEU ASN ASP GLU ILE TYR CYS SEQRES 10 A 296 PRO PRO GLU THR ALA VAL LEU LEU ALA SER TYR ALA VAL SEQRES 11 A 296 GLN ALA LYS TYR GLY ASP TYR ASN LYS GLU ILE HIS LYS SEQRES 12 A 296 PRO GLY TYR LEU ALA ASN ASP ARG LEU LEU PRO GLN ARG SEQRES 13 A 296 VAL LEU GLU GLN HIS LYS LEU THR LYS GLU GLN TRP GLU SEQRES 14 A 296 GLU ARG ILE GLN ASN TRP HIS GLU GLU HIS ARG GLY MET SEQRES 15 A 296 LEU ARG GLU ASP SER MET MET GLU TYR LEU LYS ILE ALA SEQRES 16 A 296 GLN ASP LEU GLU MET TYR GLY VAL ASN TYR PHE GLU ILE SEQRES 17 A 296 LYS ASN LYS LYS GLY THR GLU LEU TRP LEU GLY VAL ASP SEQRES 18 A 296 ALA LEU GLY LEU ASN ILE TYR GLU HIS ASP ASP LYS LEU SEQRES 19 A 296 THR PRO LYS ILE GLY PHE PRO TRP SER GLU ILE ARG ASN SEQRES 20 A 296 ILE SER PHE ASN ASP LYS LYS PHE VAL ILE LYS PRO ILE SEQRES 21 A 296 ASP LYS LYS ALA PRO ASP PHE VAL PHE TYR ALA PRO ARG SEQRES 22 A 296 LEU ARG ILE ASN LYS ARG ILE LEU ALA LEU CYS MET GLY SEQRES 23 A 296 ASN HIS GLU LEU TYR MET ARG ARG ARG LYS SEQRES 1 B 14 ASP SER GLU PRO VAL LEU LYS GLY VAL LYS LEU HIS TYR SEQRES 2 B 14 THR FORMUL 3 HOH *105(H2 O) HELIX 1 AA1 THR A 25 GLY A 38 1 14 HELIX 2 AA2 GLU A 41 TRP A 43 5 3 HELIX 3 AA3 LYS A 64 GLN A 68 5 5 HELIX 4 AA4 ASP A 88 LEU A 93 1 6 HELIX 5 AA5 GLN A 95 ASN A 112 1 18 HELIX 6 AA6 PRO A 118 GLY A 135 1 18 HELIX 7 AA7 PRO A 154 GLN A 160 1 7 HELIX 8 AA8 THR A 164 GLU A 178 1 15 HELIX 9 AA9 LEU A 183 GLN A 196 1 14 HELIX 10 AB1 ARG A 273 ARG A 294 1 22 SHEET 1 AA1 6 SER A 56 TRP A 58 0 SHEET 2 AA1 6 PHE A 45 VAL A 50 -1 N TYR A 49 O THR A 57 SHEET 3 AA1 6 LEU A 76 ALA A 82 -1 O LYS A 79 N GLN A 48 SHEET 4 AA1 6 ILE A 5 THR A 10 1 N ARG A 8 O PHE A 78 SHEET 5 AA1 6 ALA A 14 ILE A 20 -1 O LEU A 16 N VAL A 9 SHEET 6 AA1 6 VAL B1264 LEU B1270 -1 O LYS B1266 N GLU A 17 SHEET 1 AA2 7 ILE A 238 PRO A 241 0 SHEET 2 AA2 7 GLY A 224 GLU A 229 -1 N LEU A 225 O PHE A 240 SHEET 3 AA2 7 GLU A 215 ASP A 221 -1 N GLY A 219 O ASN A 226 SHEET 4 AA2 7 ASN A 204 ASN A 210 -1 N ILE A 208 O LEU A 216 SHEET 5 AA2 7 PHE A 267 TYR A 270 -1 O TYR A 270 N LYS A 209 SHEET 6 AA2 7 LYS A 254 PRO A 259 -1 N PHE A 255 O PHE A 269 SHEET 7 AA2 7 ILE A 245 ASN A 251 -1 N ARG A 246 O LYS A 258 CRYST1 77.375 77.375 58.444 90.00 90.00 90.00 P 43 4 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 0.012924 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017110 0.00000 MASTER 256 0 0 10 13 0 0 6 2634 2 0 25 END