HEADER VIRAL PROTEIN/IMMUNE SYSTEM 12-JUL-22 7YH6 TITLE STRUCTURE OF SARS-COV-2 SPIKE RBD IN COMPLEX WITH NEUTRALIZING TITLE 2 ANTIBODY NIV-8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NIV-8 FAB LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: H; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NIV-8 FAB HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: SPIKE PROTEIN S1; COMPND 12 CHAIN: A; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 15 2; SOURCE 16 ORGANISM_COMMON: 2019-NCOV,SARS-COV-2; SOURCE 17 ORGANISM_TAXID: 2697049; SOURCE 18 GENE: S, 2; SOURCE 19 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 7227 KEYWDS COMPLEX, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR S.MORIYAMA,Y.ANRAKU,S.MURANISHI,Y.ADACHI,D.KURODA,Y.HIGUCHI,R.KOTAKI, AUTHOR 2 K.TONOUCHI,K.YUMOTO,T.SUZUKI,S.KITA,H.FUKUHARA,Y.KURODA,T.YAMAMOTO, AUTHOR 3 T.ONODERA,S.FUKUSHI,K.MAEDA,F.NAKAMURA-UCHIYAMA,T.HASHIGUCHI, AUTHOR 4 A.HOSHINO,K.MAENAKA,Y.TAKAHASHI REVDAT 2 25-OCT-23 7YH6 1 JRNL REMARK REVDAT 1 19-JUL-23 7YH6 0 JRNL AUTH S.MORIYAMA,Y.ANRAKU,S.TAMINISHI,Y.ADACHI,D.KURODA,S.KITA, JRNL AUTH 2 Y.HIGUCHI,Y.KIRITA,R.KOTAKI,K.TONOUCHI,K.YUMOTO,T.SUZUKI, JRNL AUTH 3 T.SOMEYA,H.FUKUHARA,Y.KURODA,T.YAMAMOTO,T.ONODERA,S.FUKUSHI, JRNL AUTH 4 K.MAEDA,F.NAKAMURA-UCHIYAMA,T.HASHIGUCHI,A.HOSHINO, JRNL AUTH 5 K.MAENAKA,Y.TAKAHASHI JRNL TITL STRUCTURAL DELINEATION AND COMPUTATIONAL DESIGN OF JRNL TITL 2 SARS-COV-2-NEUTRALIZING ANTIBODIES AGAINST OMICRON JRNL TITL 3 SUBVARIANTS. JRNL REF NAT COMMUN V. 14 4198 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37452031 JRNL DOI 10.1038/S41467-023-39890-8 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERA, PHENIX, CRYOSPARC, CRYOSPARC, REMARK 3 RELION, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 6M0J REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.400 REMARK 3 NUMBER OF PARTICLES : 64245 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7YH6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030241. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : SARS-COV-2 SPIKE GLYCOPROTEIN REMARK 245 IN COMPLEX WITH NIV-8; SARS-COV- REMARK 245 2 SPIKE GLYCOPROTEIN; NIV-8 FAB REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 4.20 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOTTING TIME 5 S AND BLOTTING REMARK 245 FORCE 5. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 1986 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5700.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, A 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG1 THR A 393 OE2 GLU A 516 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 391 CA - CB - SG ANGL. DEV. = 10.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 L 52 173.14 62.84 REMARK 500 ASN L 54 -129.69 57.28 REMARK 500 GLU H 89 30.69 -98.49 REMARK 500 SER H 104 -113.45 59.84 REMARK 500 TYR H 106 174.27 59.23 REMARK 500 SER H 124 -169.62 -167.02 REMARK 500 ASN A 360 -132.02 57.12 REMARK 500 CYS A 361 -173.62 54.71 REMARK 500 ASN A 422 -53.87 -120.45 REMARK 500 HIS A 519 177.44 58.45 REMARK 500 ALA A 520 157.40 67.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33820 RELATED DB: EMDB REMARK 900 STRUCTURE OF SARS-COV-2 SPIKE RBD IN COMPLEX WITH NEUTRALIZING REMARK 900 ANTIBODY NIV-8 DBREF 7YH6 L 1 111 PDB 7YH6 7YH6 1 111 DBREF 7YH6 H 1 125 PDB 7YH6 7YH6 1 125 DBREF 7YH6 A 333 526 UNP P0DTC2 SPIKE_SARS2 333 526 SEQRES 1 L 111 GLN SER VAL LEU THR GLN PRO PRO SER VAL SER GLY ALA SEQRES 2 L 111 PRO GLY GLN ARG VAL THR ILE SER CYS THR GLY SER SER SEQRES 3 L 111 SER ASN ILE GLY ALA GLY TYR ASP VAL HIS TRP TYR GLN SEQRES 4 L 111 GLN LEU PRO GLY ARG ALA PRO LYS LEU LEU ILE PHE ASP SEQRES 5 L 111 ASN ASN ASN ARG PRO SER GLY VAL PRO ASP ARG PHE SER SEQRES 6 L 111 GLY SER LYS SER GLY THR SER ALA SER LEU ALA ILE THR SEQRES 7 L 111 GLY LEU GLN THR GLU ASP GLU ALA TYR TYR TYR CYS GLN SEQRES 8 L 111 SER TYR ASP ASN SER LEU ILE LEU ALA VAL PHE GLY GLY SEQRES 9 L 111 GLY THR LYS VAL THR VAL LEU SEQRES 1 H 125 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 H 125 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 125 PHE LYS PHE SER LYS PHE ALA MET HIS TRP VAL ARG GLN SEQRES 4 H 125 ALA PRO GLY LYS GLY PRO GLU TRP VAL ALA VAL ILE SER SEQRES 5 H 125 TYR ASP GLY ASN GLN TYR HIS SER ALA ASP SER VAL LYS SEQRES 6 H 125 GLY ARG PHE THR ILE SER ARG ASP ASN SER PHE ASN THR SEQRES 7 H 125 LEU TYR LEU GLN MET ASN SER LEU GLY PRO GLU ASP THR SEQRES 8 H 125 ALA VAL TYR TYR CYS ALA ARG ASP GLY PRO ASP THR SER SEQRES 9 H 125 GLY TYR TYR ALA ASN ILE TYR PHE ASP PHE TRP GLY GLN SEQRES 10 H 125 GLY THR LEU VAL THR VAL SER SER SEQRES 1 A 194 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 A 194 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 A 194 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 A 194 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 A 194 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 A 194 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 A 194 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 A 194 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 A 194 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 A 194 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 A 194 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 A 194 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 A 194 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 A 194 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 A 194 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY HET NAG A 601 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 NAG C8 H15 N O6 HELIX 1 AA1 GLN L 81 GLU L 85 5 5 HELIX 2 AA2 GLY H 87 THR H 91 5 5 HELIX 3 AA3 PHE A 338 ASN A 343 1 6 HELIX 4 AA4 SER A 349 TRP A 353 5 5 HELIX 5 AA5 TYR A 365 ASN A 370 1 6 HELIX 6 AA6 PRO A 384 ASP A 389 5 6 HELIX 7 AA7 GLU A 406 ILE A 410 5 5 HELIX 8 AA8 GLY A 416 ASN A 422 1 7 HELIX 9 AA9 SER A 438 SER A 443 1 6 SHEET 1 AA1 5 SER L 9 VAL L 10 0 SHEET 2 AA1 5 THR L 106 VAL L 108 1 O LYS L 107 N VAL L 10 SHEET 3 AA1 5 ALA L 86 ASP L 94 -1 N TYR L 88 O THR L 106 SHEET 4 AA1 5 HIS L 36 GLN L 40 -1 N HIS L 36 O GLN L 91 SHEET 5 AA1 5 LYS L 47 ILE L 50 -1 O LYS L 47 N GLN L 39 SHEET 1 AA2 4 SER L 9 VAL L 10 0 SHEET 2 AA2 4 THR L 106 VAL L 108 1 O LYS L 107 N VAL L 10 SHEET 3 AA2 4 ALA L 86 ASP L 94 -1 N TYR L 88 O THR L 106 SHEET 4 AA2 4 LEU L 99 PHE L 102 -1 O VAL L 101 N SER L 92 SHEET 1 AA3 3 VAL L 18 THR L 23 0 SHEET 2 AA3 3 SER L 72 ILE L 77 -1 O ALA L 73 N CYS L 22 SHEET 3 AA3 3 PHE L 64 SER L 69 -1 N SER L 65 O ALA L 76 SHEET 1 AA4 4 GLN H 3 SER H 7 0 SHEET 2 AA4 4 SER H 17 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 AA4 4 THR H 78 ASN H 84 -1 O MET H 83 N LEU H 18 SHEET 4 AA4 4 PHE H 68 ASP H 73 -1 N THR H 69 O GLN H 82 SHEET 1 AA5 6 VAL H 11 VAL H 12 0 SHEET 2 AA5 6 THR H 119 VAL H 123 1 O THR H 122 N VAL H 12 SHEET 3 AA5 6 ALA H 92 ASP H 99 -1 N ALA H 92 O VAL H 121 SHEET 4 AA5 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 AA5 6 PRO H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA5 6 TYR H 58 SER H 60 -1 O HIS H 59 N VAL H 50 SHEET 1 AA6 4 VAL H 11 VAL H 12 0 SHEET 2 AA6 4 THR H 119 VAL H 123 1 O THR H 122 N VAL H 12 SHEET 3 AA6 4 ALA H 92 ASP H 99 -1 N ALA H 92 O VAL H 121 SHEET 4 AA6 4 PHE H 112 TRP H 115 -1 O PHE H 114 N ARG H 98 SHEET 1 AA7 5 ASN A 354 ILE A 358 0 SHEET 2 AA7 5 VAL A 395 ILE A 402 -1 O ALA A 397 N LYS A 356 SHEET 3 AA7 5 TYR A 508 PHE A 515 -1 O VAL A 510 N PHE A 400 SHEET 4 AA7 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA7 5 THR A 376 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 1 AA8 2 LEU A 452 ARG A 454 0 SHEET 2 AA8 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SSBOND 1 CYS L 22 CYS L 90 1555 1555 2.04 SSBOND 2 CYS H 22 CYS H 96 1555 1555 2.04 SSBOND 3 CYS A 336 CYS A 361 1555 1555 2.04 SSBOND 4 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 5 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 6 CYS A 480 CYS A 488 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG A 601 1555 1555 1.44 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000