HEADER ANTIVIRAL PROTEIN 09-SEP-25 9WPP TITLE CRYSTAL STRUCTURE OF THE SARS-COV-2 SPIKE PROTEIN HR1 IN COMPLEX WITH TITLE 2 A DESIGNED PEPTIDE INHIBITOR DP-S2FI-0087 AT 3.1 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S2'; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HR1; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DP-S2FI-0087; COMPND 8 CHAIN: B, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS-COV-2 PSEUDOVIRUS; SOURCE 3 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 4 ORGANISM_TAXID: 3092168; SOURCE 5 GENE: S, 2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, COMPLEX, FUSION CORE, ANTIVIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.WANG,Z.LYU,S.YE REVDAT 1 16-SEP-26 9WPP 0 JRNL AUTH K.WANG,Z.LYU,S.YE JRNL TITL CRYSTAL STRUCTURE OF THE SARS-COV-2 SPIKE PROTEIN HR1 IN JRNL TITL 2 COMPLEX WITH A DESIGNED PEPTIDE INHIBITOR DP-S2FI-0087 AT JRNL TITL 3 3.1 ANGSTROM RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 4428 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.301 REMARK 3 R VALUE (WORKING SET) : 0.298 REMARK 3 FREE R VALUE : 0.353 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 222 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 35.4700 - 3.9100 0.98 2085 108 0.2895 0.3621 REMARK 3 2 3.9100 - 3.1000 0.99 2121 114 0.3146 0.3359 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) : 0.324 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.897 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.43 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 : 0.001 1596 REMARK 3 ANGLE : 0.345 2160 REMARK 3 CHIRALITY : 0.031 280 REMARK 3 PLANARITY : 0.001 280 REMARK 3 DIHEDRAL : 3.131 218 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 9WPP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 12-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1300063327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU AFC-6R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5983 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 55.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.88 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.53000 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 (%): 53.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES MONOHYDRATE PH 6.5,POLYETHYLENE REMARK 280 GLYCOL 20,000,GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.03650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.30013 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 103.27233 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 23.03650 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 13.30013 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 103.27233 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 23.03650 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 13.30013 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 103.27233 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.60026 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 206.54467 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 26.60026 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 206.54467 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 26.60026 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 206.54467 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -164.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -161.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 46.07300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 23.03650 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 39.90039 REMARK 350 BIOMT3 3 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 THR A 912 REMARK 465 GLN A 913 REMARK 465 ILE B 1167 REMARK 465 GLY B 1168 REMARK 465 GLY B 1201 REMARK 465 LYS B 1202 REMARK 465 THR C 912 REMARK 465 GLN C 913 REMARK 465 ILE D 1167 REMARK 465 GLY D 1168 REMARK 465 GLY D 1201 REMARK 465 LYS D 1202 DBREF 9WPP A 912 988 UNP P0DTC2 SPIKE_SARS2 912 988 DBREF 9WPP B 1167 1202 PDB 9WPP 9WPP 1167 1202 DBREF 9WPP C 912 988 UNP P0DTC2 SPIKE_SARS2 912 988 DBREF 9WPP D 1167 1202 PDB 9WPP 9WPP 1167 1202 SEQRES 1 A 77 THR GLN ASN VAL LEU TYR GLU ASN GLN LYS LEU ILE ALA SEQRES 2 A 77 ASN GLN PHE ASN SER ALA ILE GLY LYS ILE GLN ASP SER SEQRES 3 A 77 LEU SER SER THR ALA SER ALA LEU GLY LYS LEU GLN ASP SEQRES 4 A 77 VAL VAL ASN GLN ASN ALA GLN ALA LEU ASN THR LEU VAL SEQRES 5 A 77 LYS GLN LEU SER SER ASN PHE GLY ALA ILE SER SER VAL SEQRES 6 A 77 LEU ASN ASP ILE LEU SER ARG LEU ASP LYS VAL GLU SEQRES 1 B 36 ILE GLY ILE SER GLY ILE ASN ALA SER VAL ILE ASN ILE SEQRES 2 B 36 ARG ALA GLN ILE ALA ALA ILE GLN THR LEU ALA ALA ALA SEQRES 3 B 36 LEU GLU GLU SER LEU ILE ASP LEU GLY LYS SEQRES 1 C 77 THR GLN ASN VAL LEU TYR GLU ASN GLN LYS LEU ILE ALA SEQRES 2 C 77 ASN GLN PHE ASN SER ALA ILE GLY LYS ILE GLN ASP SER SEQRES 3 C 77 LEU SER SER THR ALA SER ALA LEU GLY LYS LEU GLN ASP SEQRES 4 C 77 VAL VAL ASN GLN ASN ALA GLN ALA LEU ASN THR LEU VAL SEQRES 5 C 77 LYS GLN LEU SER SER ASN PHE GLY ALA ILE SER SER VAL SEQRES 6 C 77 LEU ASN ASP ILE LEU SER ARG LEU ASP LYS VAL GLU SEQRES 1 D 36 ILE GLY ILE SER GLY ILE ASN ALA SER VAL ILE ASN ILE SEQRES 2 D 36 ARG ALA GLN ILE ALA ALA ILE GLN THR LEU ALA ALA ALA SEQRES 3 D 36 LEU GLU GLU SER LEU ILE ASP LEU GLY LYS FORMUL 5 HOH *8(H2 O) HELIX 1 AA1 ASN A 914 GLU A 988 1 75 HELIX 2 AA2 ILE B 1179 LEU B 1193 1 15 HELIX 3 AA3 GLU B 1194 LEU B 1197 5 4 HELIX 4 AA4 VAL C 915 GLU C 988 1 74 HELIX 5 AA5 ILE D 1179 LEU D 1193 1 15 HELIX 6 AA6 GLU D 1194 LEU D 1197 5 4 CRYST1 46.073 46.073 309.817 90.00 90.00 120.00 H 3 18 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 0.021705 0.012531 0.000000 0.00000 SCALE2 0.000000 0.025062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003228 0.00000 MASTER 257 0 0 6 0 0 0 6 1602 4 0 18 END