HEADER VIRAL PROTEIN 15-DEC-21 7WB5 TITLE LOCAL STRUCTURE OF HU33 AND SPIKE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HU33 HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HU33 LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SURFACE GLYCOPROTEIN; COMPND 11 CHAIN: R; COMPND 12 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 2; SOURCE 14 ORGANISM_TAXID: 2697049; SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS COMPLEX, SPIKE, ANTIBODY, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR L.PULAN REVDAT 1 26-OCT-22 7WB5 0 JRNL AUTH X.DUAN,R.SHI,P.LIU,Q.HUANG,F.WANG,X.CHEN,H.FENG,W.HUANG, JRNL AUTH 2 J.XIAO,J.YAN JRNL TITL A NON-ACE2-BLOCKING NEUTRALIZING ANTIBODY AGAINST JRNL TITL 2 OMICRON-INCLUDED SARS-COV-2 VARIANTS. JRNL REF SIGNAL TRANSDUCT TARGET THER V. 7 23 2022 JRNL REFN ESSN 2059-3635 JRNL PMID 35078968 JRNL DOI 10.1038/S41392-022-00879-2 REMARK 2 REMARK 2 RESOLUTION. 3.70 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) : 3.700 REMARK 3 NUMBER OF PARTICLES : 222776 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 7WB5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1300026371. 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 R33 AND 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 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) : 1500.00 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) : 5000.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN 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, 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 O ILE L 21 OG1 THR L 72 2.19 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 PRO L 80 CA - N - CD ANGL. DEV. = -12.6 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 PRO H 14 86.11 -65.33 REMARK 500 SER H 25 149.19 -174.28 REMARK 500 MET H 34 57.31 -142.62 REMARK 500 ASN H 35 151.04 -43.65 REMARK 500 PHE H 64 57.56 -92.08 REMARK 500 SER H 75 -9.28 70.38 REMARK 500 ALA H 79 47.29 -142.24 REMARK 500 ALA H 97 108.46 -162.93 REMARK 500 ARG H 98 99.32 -68.65 REMARK 500 SER L 30 -55.04 -29.89 REMARK 500 PRO L 44 170.70 -53.22 REMARK 500 ALA L 51 -8.83 72.89 REMARK 500 SER L 52 -53.20 -121.43 REMARK 500 SER L 60 49.27 -80.28 REMARK 500 ASP L 82 -68.49 -90.26 REMARK 500 PHE L 83 46.16 33.44 REMARK 500 ALA R 352 53.09 -112.34 REMARK 500 LEU R 368 -71.00 -53.03 REMARK 500 SER R 375 10.25 -149.75 REMARK 500 THR R 376 49.62 -156.95 REMARK 500 LYS R 378 94.23 6.79 REMARK 500 THR R 385 -79.46 -57.76 REMARK 500 LEU R 387 -20.61 -141.55 REMARK 500 ILE R 410 66.28 -100.28 REMARK 500 TYR R 421 49.52 -109.68 REMARK 500 ASN R 422 -89.62 -167.74 REMARK 500 ASP R 428 55.78 -114.04 REMARK 500 VAL R 433 60.53 -115.61 REMARK 500 ALA R 435 131.99 -171.19 REMARK 500 VAL R 445 95.71 -62.31 REMARK 500 LEU R 455 -106.13 -112.57 REMARK 500 LYS R 458 37.83 -92.86 REMARK 500 SER R 459 105.38 -165.29 REMARK 500 ASN R 460 108.93 -57.41 REMARK 500 PRO R 463 129.46 -30.34 REMARK 500 PHE R 464 71.64 49.87 REMARK 500 ALA R 475 -51.87 -130.46 REMARK 500 SER R 477 -91.17 -163.63 REMARK 500 THR R 478 110.13 -38.46 REMARK 500 ASN R 481 93.80 62.64 REMARK 500 PRO R 491 -72.58 -65.69 REMARK 500 LEU R 492 94.62 -49.75 REMARK 500 TYR R 501 146.58 -38.13 REMARK 500 VAL R 503 6.15 -68.57 REMARK 500 LEU R 513 75.60 -103.12 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 PHE H 106 ASP H 107 -146.68 REMARK 500 VAL L 29 SER L 30 -139.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32395 RELATED DB: EMDB REMARK 900 LOCAL STRUCTURE OF R33 AND SPIKE DBREF 7WB5 H 1 118 PDB 7WB5 7WB5 1 118 DBREF 7WB5 L 1 107 PDB 7WB5 7WB5 1 107 DBREF1 7WB5 R 334 516 UNP A0A7U3CI26_SARS2 DBREF2 7WB5 R A0A7U3CI26 11 193 SEQRES 1 H 118 GLN VAL GLN LEU VAL GLN SER GLY SER GLU LEU LYS LYS SEQRES 2 H 118 PRO GLY ALA SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 H 118 TYR THR PHE THR ASP TYR GLY MET ASN TRP VAL ARG GLN SEQRES 4 H 118 ALA PRO GLY GLN GLY LEU GLU TRP MET GLY TRP ILE ASN SEQRES 5 H 118 THR TYR SER GLY GLU PRO THR TYR ALA ASP ASP PHE ARG SEQRES 6 H 118 GLY ARG PHE VAL PHE SER LEU ASP THR SER VAL SER THR SEQRES 7 H 118 ALA TYR LEU GLN ILE CYS SER LEU LYS ALA GLU ASP THR SEQRES 8 H 118 ALA VAL TYR TYR CYS ALA ARG GLY GLY ASN TRP ASP TRP SEQRES 9 H 118 TYR PHE ASP VAL TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 10 H 118 SER SEQRES 1 L 107 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 107 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 107 GLN SER VAL SER ASN PHE LEU HIS TRP TYR GLN GLN LYS SEQRES 4 L 107 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR TYR ALA SER SEQRES 5 L 107 GLN SER ILE SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 107 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 107 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SER SEQRES 8 L 107 ASN THR TRP PRO LEU THR PHE GLY GLN GLY THR LYS LEU SEQRES 9 L 107 GLU ILE LYS 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 ASN 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 LEU 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 THR PRO CYS ASN GLY VAL LYS GLY PHE ASN CYS TYR SEQRES 13 R 183 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR TYR GLY SEQRES 14 R 183 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 R 183 GLU HET NAG A 1 14 HET NAG A 2 14 HET BMA A 3 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 4 BMA C6 H12 O6 HELIX 1 AA1 SER R 349 TRP R 353 5 5 HELIX 2 AA2 ASP R 364 ASN R 370 1 7 HELIX 3 AA3 GLY R 416 TYR R 421 1 6 SHEET 1 AA1 2 VAL H 5 GLN H 6 0 SHEET 2 AA1 2 CYS H 22 LYS H 23 -1 O LYS H 23 N VAL H 5 SHEET 1 AA2 2 LEU H 11 LYS H 12 0 SHEET 2 AA2 2 THR H 116 VAL H 117 1 O THR H 116 N LYS H 12 SHEET 1 AA3 4 GLU H 46 TRP H 47 0 SHEET 2 AA3 4 ASN H 35 GLN H 39 -1 N ARG H 38 O GLU H 46 SHEET 3 AA3 4 VAL H 93 ALA H 97 -1 O TYR H 95 N VAL H 37 SHEET 4 AA3 4 THR H 113 LEU H 114 -1 O THR H 113 N TYR H 94 SHEET 1 AA4 2 GLY H 49 ILE H 51 0 SHEET 2 AA4 2 PRO H 58 TYR H 60 -1 O THR H 59 N TRP H 50 SHEET 1 AA5 2 PHE H 68 PHE H 70 0 SHEET 2 AA5 2 LEU H 81 ILE H 83 -1 O GLN H 82 N VAL H 69 SHEET 1 AA6 4 MET L 4 SER L 7 0 SHEET 2 AA6 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AA6 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 AA6 4 PHE L 62 SER L 67 -1 N SER L 67 O ASP L 70 SHEET 1 AA7 2 SER L 10 ALA L 13 0 SHEET 2 AA7 2 LYS L 103 ILE L 106 1 O GLU L 105 N ALA L 13 SHEET 1 AA8 4 GLN L 53 SER L 54 0 SHEET 2 AA8 4 LYS L 45 TYR L 49 -1 N TYR L 49 O GLN L 53 SHEET 3 AA8 4 LEU L 33 GLN L 37 -1 N TRP L 35 O ILE L 48 SHEET 4 AA8 4 TYR L 87 GLN L 90 -1 O TYR L 87 N TYR L 36 SHEET 1 AA9 5 ASN R 354 ILE R 358 0 SHEET 2 AA9 5 VAL R 395 SER R 399 -1 O VAL R 395 N ILE R 358 SHEET 3 AA9 5 PRO R 507 SER R 514 -1 O SER R 514 N TYR R 396 SHEET 4 AA9 5 GLY R 431 TRP R 436 -1 N ILE R 434 O VAL R 511 SHEET 5 AA9 5 CYS R 379 TYR R 380 -1 N TYR R 380 O GLY R 431 SHEET 1 AB1 4 ASN R 354 ILE R 358 0 SHEET 2 AB1 4 VAL R 395 SER R 399 -1 O VAL R 395 N ILE R 358 SHEET 3 AB1 4 PRO R 507 SER R 514 -1 O SER R 514 N TYR R 396 SHEET 4 AB1 4 ILE R 402 ARG R 403 -1 N ILE R 402 O TYR R 508 SHEET 1 AB2 2 LEU R 452 ARG R 454 0 SHEET 2 AB2 2 LEU R 492 SER R 494 -1 O GLN R 493 N TYR R 453 SHEET 1 AB3 2 TYR R 473 GLN R 474 0 SHEET 2 AB3 2 CYS R 488 TYR R 489 -1 O TYR R 489 N TYR R 473 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 2 CYS L 23 CYS L 88 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 2.04 SSBOND 5 CYS R 480 CYS R 488 1555 1555 2.02 LINK ND2 ASN R 343 C1 NAG A 1 1555 1555 1.41 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.44 LINK O4 NAG A 2 C1 BMA A 3 1555 1555 1.43 CISPEP 1 SER L 7 PRO L 8 0 -1.77 CISPEP 2 TRP L 94 PRO L 95 0 -7.34 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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