HEADER VIRAL PROTEIN 29-JAN-25 9N2L TITLE CRYO-EM STRUCTURE OF LOCALLY REFINED UP CONFORMATION OF SARS-COV-2 TITLE 2 SPIKE PROTEIN RECEPTOR BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: F; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS; SOURCE 3 ORGANISM_TAXID: 2901879; SOURCE 4 GENE: S, 2; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2 SPIKE PROTEIN, RECEPTOR BINDING DOMAIN, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.SINGH,S.S.HASAN REVDAT 2 19-MAR-25 9N2L 1 JRNL REVDAT 1 05-MAR-25 9N2L 0 JRNL AUTH S.SINGH,Y.LIU,M.BURKE,V.RAYAPROLU,S.E.STEIN,S.S.HASAN JRNL TITL PRODUCTION AND CRYO-ELECTRON MICROSCOPY STRUCTURE OF AN JRNL TITL 2 INTERNALLY TAGGED SARS-COV-2 SPIKE ECTO-DOMAIN CONSTRUCT. JRNL REF J STRUCT BIOL X V. 11 00123 2025 JRNL REFN ESSN 2590-1524 JRNL PMID 40046771 JRNL DOI 10.1016/J.YJSBX.2025.100123 REMARK 2 REMARK 2 RESOLUTION. 2.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, UCSF CHIMERA, PHENIX, COOT REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 9CSS REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE 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) : 2.990 REMARK 3 NUMBER OF PARTICLES : 326639 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 9N2L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000292268. 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 PROTEIN REMARK 245 ECTODOMAIN WITH INTERNAL TAG REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.50 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : TFS FALCON 4I (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 4397.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 16500 REMARK 245 CALIBRATED MAGNIFICATION : 191780 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: F 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 ARG F 319 REMARK 465 VAL F 320 REMARK 465 GLN F 321 REMARK 465 PRO F 322 REMARK 465 THR F 323 REMARK 465 GLU F 324 REMARK 465 SER F 325 REMARK 465 ILE F 326 REMARK 465 VAL F 327 REMARK 465 ARG F 328 REMARK 465 PHE F 329 REMARK 465 PRO F 330 REMARK 465 ASN F 331 REMARK 465 ILE F 332 REMARK 465 ARG F 457 REMARK 465 LYS F 458 REMARK 465 SER F 459 REMARK 465 ASN F 460 REMARK 465 THR F 470 REMARK 465 GLU F 471 REMARK 465 ILE F 472 REMARK 465 TYR F 473 REMARK 465 GLN F 474 REMARK 465 ALA F 475 REMARK 465 GLY F 476 REMARK 465 SER F 477 REMARK 465 THR F 478 REMARK 465 PRO F 479 REMARK 465 CYS F 480 REMARK 465 ASN F 481 REMARK 465 GLY F 482 REMARK 465 VAL F 483 REMARK 465 GLU F 484 REMARK 465 GLY F 485 REMARK 465 PHE F 486 REMARK 465 ASN F 487 REMARK 465 PRO F 527 REMARK 465 LYS F 528 REMARK 465 LYS F 529 REMARK 465 SER F 530 REMARK 465 THR F 531 REMARK 465 ASN F 532 REMARK 465 LEU F 533 REMARK 465 VAL F 534 REMARK 465 LYS F 535 REMARK 465 ASN F 536 REMARK 465 LYS F 537 REMARK 465 CYS F 538 REMARK 465 VAL F 539 REMARK 465 ASN F 540 REMARK 465 PHE F 541 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 GLN F 498 C - N - CA ANGL. DEV. = 17.7 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 ASN F 343 37.96 -94.68 REMARK 500 ASN F 360 52.09 39.62 REMARK 500 ASP F 389 46.75 -96.51 REMARK 500 ASP F 428 47.36 -86.36 REMARK 500 SER F 438 44.63 -141.14 REMARK 500 LEU F 518 -169.04 -125.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-48839 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF LOCALLY REFINED UP CONFORMATION OF SARS-COV-2 REMARK 900 SPIKE PROTEIN RECEPTOR BINDING DOMAIN DBREF 9N2L F 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 SEQRES 1 F 223 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 F 223 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 F 223 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 F 223 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 F 223 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 F 223 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 F 223 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 F 223 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 F 223 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 F 223 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 F 223 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 F 223 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 F 223 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 F 223 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 F 223 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 F 223 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 F 223 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL SEQRES 18 F 223 ASN PHE HELIX 1 AA1 PHE F 338 ASN F 343 1 6 HELIX 2 AA2 SER F 349 TRP F 353 5 5 HELIX 3 AA3 TYR F 365 ASN F 370 1 6 HELIX 4 AA4 THR F 385 LEU F 390 5 6 HELIX 5 AA5 GLY F 404 ILE F 410 5 7 HELIX 6 AA6 GLY F 416 ASN F 422 1 7 HELIX 7 AA7 SER F 438 SER F 443 1 6 SHEET 1 AA1 5 ASN F 354 ILE F 358 0 SHEET 2 AA1 5 ASN F 394 ILE F 402 -1 O ALA F 397 N LYS F 356 SHEET 3 AA1 5 TYR F 508 GLU F 516 -1 O TYR F 508 N ILE F 402 SHEET 4 AA1 5 CYS F 432 ASN F 437 -1 N CYS F 432 O LEU F 513 SHEET 5 AA1 5 THR F 376 CYS F 379 -1 N LYS F 378 O VAL F 433 SHEET 1 AA2 2 LEU F 452 ARG F 454 0 SHEET 2 AA2 2 LEU F 492 SER F 494 -1 O GLN F 493 N TYR F 453 SSBOND 1 CYS F 336 CYS F 361 1555 1555 2.02 SSBOND 2 CYS F 379 CYS F 432 1555 1555 2.03 SSBOND 3 CYS F 391 CYS F 525 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