HEADER VIRAL PROTEIN/IMMUNE SYSTEM 27-JAN-22 7WRO TITLE LOCAL STRUCTURE OF BD55-3372 AND DELTA SPIKE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3372H; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 3372L; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: R; COMPND 12 FRAGMENT: RBD; COMPND 13 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS; SOURCE 13 ORGANISM_COMMON: 2019-NCOV,SARS-COV-2; SOURCE 14 ORGANISM_TAXID: 2901879; SOURCE 15 VARIANT: DELTA; SOURCE 16 GENE: S, 2; SOURCE 17 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS COMPLEX, SARS-COV-2, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM KEYWDS 2 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR P.L.LIU REVDAT 3 31-AUG-22 7WRO 1 JRNL REVDAT 2 13-JUL-22 7WRO 1 JRNL REVDAT 1 22-JUN-22 7WRO 0 JRNL AUTH Y.CAO,A.YISIMAYI,F.JIAN,W.SONG,T.XIAO,L.WANG,S.DU,J.WANG, JRNL AUTH 2 Q.LI,X.CHEN,Y.YU,P.WANG,Z.ZHANG,P.LIU,R.AN,X.HAO,Y.WANG, JRNL AUTH 3 J.WANG,R.FENG,H.SUN,L.ZHAO,W.ZHANG,D.ZHAO,J.ZHENG,L.YU,C.LI, JRNL AUTH 4 N.ZHANG,R.WANG,X.NIU,S.YANG,X.SONG,Y.CHAI,Y.HU,Y.SHI, JRNL AUTH 5 L.ZHENG,Z.LI,Q.GU,F.SHAO,W.HUANG,R.JIN,Z.SHEN,Y.WANG,X.WANG, JRNL AUTH 6 J.XIAO,X.S.XIE JRNL TITL BA.2.12.1, BA.4 AND BA.5 ESCAPE ANTIBODIES ELICITED BY JRNL TITL 2 OMICRON INFECTION. JRNL REF NATURE V. 608 593 2022 JRNL REFN ESSN 1476-4687 JRNL PMID 35714668 JRNL DOI 10.1038/S41586-022-04980-Y REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL 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 : 343297 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 7WRO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1300027302. 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 : LOCAL STRUCTURE OF BD55-3372 REMARK 245 AND DELTA RBD; BD55-3372; DELTA REMARK 245 RBD REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.20 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5800.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL 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: H, L, R 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: 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 ARG H 57 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 LEU R 368 CA - CB - CG ANGL. DEV. = 14.3 DEGREES REMARK 500 CYS R 379 CA - CB - SG ANGL. DEV. = 11.2 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 H 123 16.45 52.59 REMARK 500 SER L 70 -151.04 -140.08 REMARK 500 SER L 73 28.35 -142.46 REMARK 500 ASP L 103 55.91 -95.29 REMARK 500 SER L 111 -158.96 -152.25 REMARK 500 GLU R 406 45.24 -85.25 REMARK 500 PHE R 515 -166.38 -119.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY L 71 ASN L 72 -148.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32734 RELATED DB: EMDB REMARK 900 LOCAL STRUCTURE OF BD55-3372 AND DELTA SPIKE DBREF 7WRO H 20 137 PDB 7WRO 7WRO 20 137 DBREF 7WRO L 21 131 PDB 7WRO 7WRO 21 131 DBREF 7WRO R 334 516 UNP P0DTC2 SPIKE_SARS2 334 516 SEQADV 7WRO ARG R 452 UNP P0DTC2 LEU 452 VARIANT SEQADV 7WRO LYS R 478 UNP P0DTC2 THR 478 VARIANT SEQRES 1 H 118 GLU VAL HIS LEU VAL GLU SER GLY GLY GLY LEU VAL LYS SEQRES 2 H 118 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 118 PHE THR PHE SER ASN TYR ALA MET ASN TRP VAL ARG GLN SEQRES 4 H 118 ALA PRO GLY LYS GLY LEU GLN TRP VAL SER SER ILE THR SEQRES 5 H 118 GLY SER SER SER PHE ILE PHE TYR ALA ASP SER VAL LYS SEQRES 6 H 118 GLY ARG PHE THR ILE VAL ARG ASP ASN ALA GLN ASN SER SEQRES 7 H 118 LEU TYR LEU GLN MET ASN SER LEU ARG ASP GLU ASP THR SEQRES 8 H 118 ALA VAL TYR TYR CYS ALA ARG GLU ARG ASP ASP TYR ASP SEQRES 9 H 118 THR ARG LEU ASP TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 10 H 118 SER SEQRES 1 L 111 PRO MET LEU THR GLN PRO PRO SER VAL SER GLY ALA PRO SEQRES 2 L 111 GLY GLN THR VAL THR ILE SER CYS VAL GLY SER SER SER SEQRES 3 L 111 ASN ILE GLY ALA GLY TYR GLU VAL HIS TRP TYR GLN GLN SEQRES 4 L 111 LEU PRO GLY THR ALA PRO LYS ARG LEU LEU SER GLY ASN SEQRES 5 L 111 SER ASP ARG PRO SER GLY VAL PRO ASP ARG PHE SER GLY SEQRES 6 L 111 SER LYS SER GLY THR SER ALA SER LEU ALA ILE THR GLY SEQRES 7 L 111 LEU GLN ALA ASP ASP GLU ALA ASP TYR TYR CYS GLN SER SEQRES 8 L 111 TYR ASP SER SER LEU SER LEU SER ALA VAL VAL PHE GLY SEQRES 9 L 111 GLY GLY THR LYS LEU THR VAL SEQRES 1 R 183 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 2 R 183 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 R 183 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 R 183 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 R 183 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 R 183 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 R 183 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 8 R 183 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 R 183 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 R 183 TYR ARG TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 R 183 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 R 183 SER LYS PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 R 183 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 R 183 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 R 183 GLU HELIX 1 AA1 ASP H 81 LYS H 84 5 4 HELIX 2 AA2 ARG H 106 THR H 110 5 5 HELIX 3 AA3 TYR R 365 ASN R 370 1 6 HELIX 4 AA4 SER R 383 LEU R 390 5 8 HELIX 5 AA5 GLY R 404 ARG R 408 5 5 HELIX 6 AA6 LYS R 417 ASN R 422 1 6 HELIX 7 AA7 SER R 438 SER R 443 1 6 SHEET 1 AA1 4 HIS H 22 SER H 26 0 SHEET 2 AA1 4 SER H 36 SER H 44 -1 O ALA H 42 N VAL H 24 SHEET 3 AA1 4 SER H 97 ASN H 103 -1 O MET H 102 N LEU H 37 SHEET 4 AA1 4 THR H 88 ASP H 92 -1 N VAL H 90 O TYR H 99 SHEET 1 AA2 5 ILE H 77 TYR H 79 0 SHEET 2 AA2 5 LEU H 64 ILE H 70 -1 N SER H 69 O PHE H 78 SHEET 3 AA2 5 MET H 53 GLN H 58 -1 N MET H 53 O ILE H 70 SHEET 4 AA2 5 ALA H 111 ARG H 117 -1 O ALA H 116 N ASN H 54 SHEET 5 AA2 5 THR H 132 VAL H 134 -1 O VAL H 134 N ALA H 111 SHEET 1 AA3 2 THR L 36 VAL L 37 0 SHEET 2 AA3 2 ILE L 96 THR L 97 -1 O ILE L 96 N VAL L 37 SHEET 1 AA4 4 LYS L 66 ARG L 67 0 SHEET 2 AA4 4 TYR L 57 GLN L 59 -1 N GLN L 58 O LYS L 66 SHEET 3 AA4 4 ALA L 105 TYR L 108 -1 O ASP L 106 N GLN L 59 SHEET 4 AA4 4 THR L 127 LEU L 129 -1 O THR L 127 N TYR L 107 SHEET 1 AA5 2 SER L 86 SER L 88 0 SHEET 2 AA5 2 SER L 91 SER L 93 -1 O SER L 91 N SER L 88 SHEET 1 AA6 2 GLN L 110 ASP L 113 0 SHEET 2 AA6 2 ALA L 120 PHE L 123 -1 O ALA L 120 N ASP L 113 SHEET 1 AA7 3 TYR R 396 ILE R 402 0 SHEET 2 AA7 3 TYR R 508 SER R 514 -1 O TYR R 508 N ILE R 402 SHEET 3 AA7 3 VAL R 433 ASN R 437 -1 N TRP R 436 O ARG R 509 SHEET 1 AA8 2 ARG R 452 ARG R 454 0 SHEET 2 AA8 2 LEU R 492 SER R 494 -1 O GLN R 493 N TYR R 453 SHEET 1 AA9 2 TYR R 473 GLN R 474 0 SHEET 2 AA9 2 CYS R 488 TYR R 489 -1 O TYR R 489 N TYR R 473 SSBOND 1 CYS H 41 CYS H 115 1555 1555 2.03 SSBOND 2 CYS L 41 CYS L 109 1555 1555 2.03 SSBOND 3 CYS R 336 CYS R 361 1555 1555 2.03 SSBOND 4 CYS R 379 CYS R 432 1555 1555 2.05 SSBOND 5 CYS R 480 CYS R 488 1555 1555 2.03 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