HEADER ANTIVIRAL PROTEIN 06-MAY-22 7ZSD TITLE CRYO-EM STRUCTURE OF OMICRON SPIKE IN COMPLEX WITH DE NOVO DESIGNED TITLE 2 BINDER, LOCAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: M; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DE NOVO DESIGNED BINDER; COMPND 8 CHAIN: P; COMPND 9 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: DROSOPHILA MELANOGASTER; SOURCE 10 ORGANISM_COMMON: FRUIT FLY; SOURCE 11 ORGANISM_TAXID: 7227; SOURCE 12 GENE: L(2)GD1, LGD, CG4713; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV2, DE NOVO, DESIGN BINDER, SPIKE, RBD, RECEPTOR BINDING KEYWDS 2 DOMAIN, ANTIVIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR G.PABLO,W.SARAH,V.H.ALEXANDRA,M.ANTHONY,S.ANDREAS,H.ZANDER, AUTHOR 2 N.DONGCHUN,T.SHUGUANG,S.FREYR,G.CASPER,T.PRISCILLA,T.ALEXANDRA, AUTHOR 3 R.STEPHANE,G.SANDRINE,M.JANE,P.AARON,X.ZEPENG,C.YAN,H.PU,G.GEORGE, AUTHOR 4 O.ELISA,F.BEAT,T.DIDIER,S.HENNING,B.MICHAEL,E.C.BRUNO REVDAT 5 24-MAY-23 7ZSD 1 JRNL REVDAT 4 17-MAY-23 7ZSD 1 JRNL REVDAT 3 10-MAY-23 7ZSD 1 JRNL REVDAT 2 26-APR-23 7ZSD 1 JRNL REVDAT 1 01-MAR-23 7ZSD 0 JRNL AUTH P.GAINZA,S.WEHRLE,A.VAN HALL-BEAUVAIS,A.MARCHAND,A.SCHECK, JRNL AUTH 2 Z.HARTEVELD,S.BUCKLEY,D.NI,S.TAN,F.SVERRISSON,C.GOVERDE, JRNL AUTH 3 P.TURELLI,C.RACLOT,A.TESLENKO,M.PACESA,S.ROSSET,S.GEORGEON, JRNL AUTH 4 J.MARSDEN,A.PETRUZZELLA,K.LIU,Z.XU,Y.CHAI,P.HAN,G.F.GAO, JRNL AUTH 5 E.ORICCHIO,B.FIERZ,D.TRONO,H.STAHLBERG,M.BRONSTEIN, JRNL AUTH 6 B.E.CORREIA JRNL TITL DE NOVO DESIGN OF PROTEIN INTERACTIONS WITH LEARNED SURFACE JRNL TITL 2 FINGERPRINTS. JRNL REF NATURE V. 617 176 2023 JRNL REFN ESSN 1476-4687 JRNL PMID 37100904 JRNL DOI 10.1038/S41586-023-05993-X REMARK 2 REMARK 2 RESOLUTION. 3.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERA, COOT, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7QO7 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 33.800 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) : 3.290 REMARK 3 NUMBER OF PARTICLES : 50758 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7ZSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1292122855. 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 : OMICRON SPIKE IN COMPLEX WITH REMARK 245 DE NOVO DESIGNED BINDER; REMARK 245 OMICRON SPIKE; DE NOVO DESIGNED REMARK 245 BINDER 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 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) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: M, P, 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 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 GLU P -5 REMARK 465 THR P -4 REMARK 465 GLY P -3 REMARK 465 ALA P -2 REMARK 465 SER P -1 REMARK 465 SER P 0 REMARK 465 GLY P 66 REMARK 465 SER P 67 REMARK 465 GLU P 68 REMARK 465 ASN P 69 REMARK 465 LEU P 70 REMARK 465 TYR P 71 REMARK 465 PHE P 72 REMARK 465 GLN P 73 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 M 337 49.11 -81.23 REMARK 500 ALA M 372 75.22 53.52 REMARK 500 ALA M 411 149.15 -171.17 REMARK 500 PHE M 486 -175.57 -67.57 REMARK 500 ASN M 487 65.36 -69.67 REMARK 500 TYR M 489 163.96 65.41 REMARK 500 ASN P 2 -135.80 39.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-14922 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-14930 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF OMICRON SPIKE IN COMPLEX WITH DE NOVO DESIGNED REMARK 900 BINDER, LOCAL DBREF 7ZSD M 332 527 UNP P0DTC2 SPIKE_SARS2 332 527 DBREF 7ZSD P 1 65 UNP Q9VKJ9 C2D1_DROME 359 423 SEQADV 7ZSD ASP M 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 7ZSD LEU M 371 UNP P0DTC2 SER 371 VARIANT SEQADV 7ZSD PRO M 373 UNP P0DTC2 SER 373 VARIANT SEQADV 7ZSD PHE M 375 UNP P0DTC2 SER 375 VARIANT SEQADV 7ZSD ASN M 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 7ZSD LYS M 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 7ZSD SER M 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 7ZSD ASN M 477 UNP P0DTC2 SER 477 VARIANT SEQADV 7ZSD LYS M 478 UNP P0DTC2 THR 478 VARIANT SEQADV 7ZSD ALA M 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7ZSD ARG M 493 UNP P0DTC2 GLN 493 ENGINEERED MUTATION SEQADV 7ZSD SER M 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 7ZSD ARG M 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 7ZSD TYR M 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 7ZSD HIS M 505 UNP P0DTC2 TYR 505 VARIANT SEQADV 7ZSD GLU P -5 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD THR P -4 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD GLY P -3 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD ALA P -2 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD SER P -1 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD SER P 0 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD GLN P 12 UNP Q9VKJ9 GLU 370 ENGINEERED MUTATION SEQADV 7ZSD PHE P 13 UNP Q9VKJ9 LYS 371 ENGINEERED MUTATION SEQADV 7ZSD HIS P 15 UNP Q9VKJ9 GLN 373 ENGINEERED MUTATION SEQADV 7ZSD GLY P 16 UNP Q9VKJ9 SER 374 ENGINEERED MUTATION SEQADV 7ZSD GLN P 17 UNP Q9VKJ9 VAL 375 ENGINEERED MUTATION SEQADV 7ZSD VAL P 18 UNP Q9VKJ9 GLU 376 ENGINEERED MUTATION SEQADV 7ZSD ARG P 20 UNP Q9VKJ9 ALA 378 ENGINEERED MUTATION SEQADV 7ZSD ALA P 22 UNP Q9VKJ9 LYS 380 ENGINEERED MUTATION SEQADV 7ZSD LEU P 23 UNP Q9VKJ9 ALA 381 ENGINEERED MUTATION SEQADV 7ZSD GLY P 66 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD SER P 67 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD GLU P 68 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD ASN P 69 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD LEU P 70 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD TYR P 71 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD PHE P 72 UNP Q9VKJ9 EXPRESSION TAG SEQADV 7ZSD GLN P 73 UNP Q9VKJ9 EXPRESSION TAG SEQRES 1 M 196 ILE THR ASN LEU CYS PRO PHE ASP GLU VAL PHE ASN ALA SEQRES 2 M 196 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 3 M 196 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 4 M 196 LEU ALA PRO PHE PHE THR PHE LYS CYS TYR GLY VAL SER SEQRES 5 M 196 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 6 M 196 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 7 M 196 ILE ALA PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN SEQRES 8 M 196 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 9 M 196 TRP ASN SER ASN LYS LEU ASP SER LYS VAL SER GLY ASN SEQRES 10 M 196 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 11 M 196 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 12 M 196 ALA GLY ASN LYS PRO CYS ASN GLY VAL ALA GLY PHE ASN SEQRES 13 M 196 CYS TYR PHE PRO LEU ARG SER TYR SER PHE ARG PRO THR SEQRES 14 M 196 TYR GLY VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 15 M 196 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 16 M 196 PRO SEQRES 1 P 79 GLU THR GLY ALA SER SER THR ASN MET LEU GLU ALA LEU SEQRES 2 P 79 GLN GLN ARG LEU GLN PHE TYR HIS GLY GLN VAL ALA ARG SEQRES 3 P 79 ALA ALA LEU GLU ASN ASN SER GLY LYS ALA ARG ARG PHE SEQRES 4 P 79 GLY ARG ILE VAL LYS GLN TYR GLU ASP ALA ILE LYS LEU SEQRES 5 P 79 TYR LYS ALA GLY LYS PRO VAL PRO TYR ASP GLU LEU PRO SEQRES 6 P 79 VAL PRO PRO GLY PHE GLY GLY SER GLU ASN LEU TYR PHE SEQRES 7 P 79 GLN HET NAG A 1 14 HET NAG A 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 3 NAG 2(C8 H15 N O6) HELIX 1 AA1 PRO M 337 ASN M 343 1 7 HELIX 2 AA2 SER M 349 TRP M 353 5 5 HELIX 3 AA3 TYR M 365 LEU M 371 1 7 HELIX 4 AA4 SER M 383 LEU M 390 1 8 HELIX 5 AA5 ASP M 405 ILE M 410 5 6 HELIX 6 AA6 GLY M 416 ASN M 422 1 7 HELIX 7 AA7 MET P 3 GLU P 24 1 22 HELIX 8 AA8 ASN P 26 ALA P 49 1 24 SHEET 1 AA1 5 ASN M 354 ILE M 358 0 SHEET 2 AA1 5 VAL M 395 ARG M 403 -1 O VAL M 395 N ILE M 358 SHEET 3 AA1 5 PRO M 507 SER M 514 -1 O VAL M 512 N ASP M 398 SHEET 4 AA1 5 GLY M 431 ASN M 437 -1 N ILE M 434 O VAL M 511 SHEET 5 AA1 5 CYS M 379 TYR M 380 -1 N TYR M 380 O GLY M 431 SHEET 1 AA2 2 LEU M 452 ARG M 454 0 SHEET 2 AA2 2 LEU M 492 SER M 494 -1 O ARG M 493 N TYR M 453 SSBOND 1 CYS M 336 CYS M 361 1555 1555 2.03 SSBOND 2 CYS M 379 CYS M 432 1555 1555 2.03 SSBOND 3 CYS M 391 CYS M 525 1555 1555 2.03 SSBOND 4 CYS M 480 CYS M 488 1555 1555 2.03 LINK ND2 ASN M 343 C1 NAG A 1 1555 1555 1.44 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.45 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