HEADER IMMUNE SYSTEM 07-OCT-22 8EQF TITLE CRYOEM STRUCTURE OF A BROADLY NEUTRALIZING ANTI-SARS-COV-2 ANTIBODY TITLE 2 STI-9167 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: FAB LIGHT CHAIN; COMPND 11 CHAIN: L; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: S, 2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; 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: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS ANTIBODY, SARS-COV-2, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR G.BAJIC REVDAT 4 16-OCT-24 8EQF 1 JRNL REVDAT 3 09-OCT-24 8EQF 1 REMARK REVDAT 2 24-APR-24 8EQF 1 JRNL REVDAT 1 11-OCT-23 8EQF 0 JRNL AUTH K.E.ATANASOFF,L.BRAMBILLA,D.C.ADELSBERG,S.KOWDLE, JRNL AUTH 2 C.S.STEVENS,S.SLAMANIG,C.T.HUNG,Y.FU,R.LIM,L.TRAN,R.ALLEN, JRNL AUTH 3 W.SUN,J.A.DUTY,G.BAJIC,B.LEE,D.TORTORELLA JRNL TITL AN IN VITRO EXPERIMENTAL PIPELINE TO CHARACTERIZE THE JRNL TITL 2 EPITOPE OF A SARS-COV-2 NEUTRALIZING ANTIBODY. JRNL REF MBIO V. 15 47723 2024 JRNL REFN ESSN 2150-7511 JRNL PMID 38054729 JRNL DOI 10.1128/MBIO.02477-23 REMARK 2 REMARK 2 RESOLUTION. 3.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : LEGINON 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) : 3.160 REMARK 3 NUMBER OF PARTICLES : 320574 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 8EQF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1000269132. 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 RBD IN COMPLEX REMARK 245 WITH 10A3 FAB REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 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 : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5892.00 REMARK 245 ILLUMINATION MODE : OTHER 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: A, H, L, 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 GLN H 1 REMARK 465 LYS L 107 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 O4 NAG B 1 O6 NAG B 2 2.00 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 TYR A 358 48.35 -87.77 REMARK 500 ASP A 421 52.81 -95.97 REMARK 500 SER A 431 34.48 -143.01 REMARK 500 LEU A 434 -3.20 80.90 REMARK 500 ASP A 435 16.62 -145.50 REMARK 500 SER H 30 38.95 -82.42 REMARK 500 SER H 63 -2.45 75.96 REMARK 500 LYS H 103 -3.17 69.26 REMARK 500 HIS L 30 -130.00 62.65 REMARK 500 ALA L 51 -11.23 75.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-28537 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF A BROADLY NEUTRALIZING ANTI-SARS-COV-2 ANTIBODY REMARK 900 10A3 REMARK 900 RELATED ID: EMD-29227 RELATED DB: EMDB REMARK 900 GLOBAL MAPS DBREF 8EQF A 326 519 UNP P0DTC2 SPIKE_SARS2 333 526 DBREF 8EQF H 1 123 PDB 8EQF 8EQF 1 123 DBREF 8EQF L 1 107 PDB 8EQF 8EQF 1 107 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 SEQRES 1 H 123 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 H 123 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 123 PHE THR PHE SER SER TYR GLY MET ASN TRP VAL ARG GLN SEQRES 4 H 123 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA ILE ILE TRP SEQRES 5 H 123 TYR ASP GLY ASN ASN LYS TYR TYR VAL ASP SER VAL LYS SEQRES 6 H 123 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 H 123 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 123 ALA VAL TYR TYR CYS ALA ARG LYS ASP TYR SER LYS THR SEQRES 9 H 123 TYR TYR GLY TYR TYR PHE ASP TYR TRP GLY GLN GLY THR SEQRES 10 H 123 LEU VAL THR VAL SER 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 ILE HIS SER PHE LEU ASN TRP TYR GLN GLN LYS SEQRES 4 L 107 PRO GLY LYS PRO PRO ASN LEU LEU ILE TYR ALA ALA SER SEQRES 5 L 107 SER LEU GLN SER GLY LEU 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 TYR ILE THR PRO PRO THR PHE GLY HIS GLY THR LYS VAL SEQRES 9 L 107 GLU ILE LYS HET NAG B 1 14 HET NAG B 2 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 2(C8 H15 N O6) HELIX 1 AA1 PRO A 330 ASN A 336 1 7 HELIX 2 AA2 SER A 342 TRP A 346 5 5 HELIX 3 AA3 ASP A 398 ILE A 403 5 6 HELIX 4 AA4 GLY A 409 ASN A 415 1 7 HELIX 5 AA5 THR H 28 TYR H 32 5 5 HELIX 6 AA6 ARG H 87 THR H 91 5 5 HELIX 7 AA7 GLN L 79 PHE L 83 5 5 SHEET 1 AA1 5 ASN A 347 ILE A 351 0 SHEET 2 AA1 5 ASN A 387 ARG A 396 -1 O ALA A 390 N LYS A 349 SHEET 3 AA1 5 PRO A 500 GLU A 509 -1 O TYR A 501 N ILE A 395 SHEET 4 AA1 5 GLY A 424 ASN A 430 -1 N ILE A 427 O VAL A 504 SHEET 5 AA1 5 THR A 369 CYS A 372 -1 N THR A 369 O ALA A 428 SHEET 1 AA2 2 CYS A 354 VAL A 355 0 SHEET 2 AA2 2 VAL A 517 CYS A 518 1 O CYS A 518 N CYS A 354 SHEET 1 AA3 2 LEU A 445 ARG A 447 0 SHEET 2 AA3 2 LEU A 485 SER A 487 -1 O GLN A 486 N TYR A 446 SHEET 1 AA4 2 TYR A 466 GLN A 467 0 SHEET 2 AA4 2 CYS A 481 TYR A 482 -1 O TYR A 482 N TYR A 466 SHEET 1 AA5 4 GLN H 3 SER H 7 0 SHEET 2 AA5 4 LEU H 18 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 AA5 4 THR H 78 MET H 83 -1 O LEU H 81 N LEU H 20 SHEET 4 AA5 4 PHE H 68 ASP H 73 -1 N THR H 69 O GLN H 82 SHEET 1 AA6 6 GLY H 10 VAL H 11 0 SHEET 2 AA6 6 THR H 117 THR H 120 1 O THR H 120 N GLY H 10 SHEET 3 AA6 6 ALA H 92 ARG H 98 -1 N TYR H 94 O THR H 117 SHEET 4 AA6 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 AA6 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA6 6 LYS H 58 TYR H 60 -1 O TYR H 59 N ILE H 50 SHEET 1 AA7 4 MET L 4 SER L 7 0 SHEET 2 AA7 4 VAL L 19 ALA L 25 -1 O THR L 22 N SER L 7 SHEET 3 AA7 4 ASP L 70 ILE L 75 -1 O ILE L 75 N VAL L 19 SHEET 4 AA7 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 AA8 6 SER L 10 SER L 12 0 SHEET 2 AA8 6 THR L 102 GLU L 105 1 O GLU L 105 N LEU L 11 SHEET 3 AA8 6 THR L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AA8 6 LEU L 33 GLN L 38 -1 N GLN L 38 O THR L 85 SHEET 5 AA8 6 ASN L 45 TYR L 49 -1 O ASN L 45 N GLN L 37 SHEET 6 AA8 6 SER L 53 LEU L 54 -1 O SER L 53 N TYR L 49 SSBOND 1 CYS A 329 CYS A 354 1555 1555 2.03 SSBOND 2 CYS A 372 CYS A 425 1555 1555 2.03 SSBOND 3 CYS A 384 CYS A 518 1555 1555 2.03 SSBOND 4 CYS A 473 CYS A 481 1555 1555 2.03 SSBOND 5 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 6 CYS L 23 CYS L 88 1555 1555 2.03 LINK ND2 ASN A 336 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 CISPEP 1 SER L 7 PRO L 8 0 -3.15 CISPEP 2 THR L 94 PRO L 95 0 3.30 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