HEADER VIRAL PROTEIN 25-JAN-22 7TPK TITLE SARS-COV-2 E406W MUTANT RBD - LOCAL REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: E; COMPND 4 FRAGMENT: RECEPTOR-BINDING DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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 KEYWDS VIRAL ENTRY PROTEIN, VIRAL GLYCOPROTEIN, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.ADDETIA,D.VEESLER REVDAT 3 06-NOV-24 7TPK 1 REMARK REVDAT 2 02-OCT-24 7TPK 1 REMARK HELIX SHEET SSBOND REVDAT 2 2 1 LINK ATOM REVDAT 1 08-FEB-23 7TPK 0 JRNL AUTH A.ADDETIA,D.VEESLER JRNL TITL SARS-COV-2 E406W MUTANT RBD - LOCAL REFINEMENT JRNL REF TO BE PUBLISHED JRNL REFN 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 : 113154 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 7TPK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000262714. 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 : RECEPTOR BINDING DOMAIN OF THE REMARK 245 SARS-COV-2 SPIKE PROTEIN 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 : 8.00 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) : 0.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2600.00 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) : 6300.00 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU E 340 CG CD OE1 OE2 REMARK 470 SER E 359 OG REMARK 470 SER E 366 OG REMARK 470 SER E 373 OG REMARK 470 SER E 375 OG REMARK 470 THR E 376 OG1 CG2 REMARK 470 LYS E 378 CG CD CE NZ REMARK 470 SER E 383 OG REMARK 470 THR E 385 OG1 CG2 REMARK 470 THR E 393 OG1 CG2 REMARK 470 ASN E 394 CG OD1 ND2 REMARK 470 THR E 415 OG1 CG2 REMARK 470 ASP E 420 CG OD1 OD2 REMARK 470 ASP E 427 CG OD1 OD2 REMARK 470 ASP E 428 CG OD1 OD2 REMARK 470 SER E 438 OG REMARK 470 ASN E 439 CG OD1 ND2 REMARK 470 ASN E 440 CG OD1 ND2 REMARK 470 LEU E 441 CG CD1 CD2 REMARK 470 ASP E 442 CG OD1 OD2 REMARK 470 SER E 443 OG REMARK 470 LYS E 444 CG CD CE NZ REMARK 470 VAL E 445 CG1 CG2 REMARK 470 ASN E 448 CG OD1 ND2 REMARK 470 ASN E 450 CG OD1 ND2 REMARK 470 SER E 459 OG REMARK 470 SER E 469 OG REMARK 470 SER E 477 OG REMARK 470 THR E 478 OG1 CG2 REMARK 470 ASN E 481 CG OD1 ND2 REMARK 470 VAL E 483 CG1 CG2 REMARK 470 PHE E 486 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN E 487 CG OD1 ND2 REMARK 470 SER E 494 OG REMARK 470 GLN E 498 CG CD OE1 NE2 REMARK 470 THR E 500 OG1 CG2 REMARK 470 ASN E 501 CG OD1 ND2 REMARK 470 VAL E 503 CG1 CG2 REMARK 470 GLN E 506 CG CD OE1 NE2 REMARK 470 SER E 514 OG REMARK 470 GLU E 516 CG CD OE1 OE2 REMARK 470 LEU E 518 CG CD1 CD2 REMARK 470 HIS E 519 CG ND1 CD2 CE1 NE2 REMARK 470 THR E 523 OG1 CG2 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 E 346 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG E 403 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG E 408 NE - CZ - NH2 ANGL. DEV. = 3.1 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 E 337 44.00 -75.91 REMARK 500 PHE E 464 16.02 55.33 REMARK 500 ALA E 475 42.73 -142.06 REMARK 500 THR E 478 146.21 66.67 REMARK 500 VAL E 503 -61.90 -158.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE E 377 0.07 SIDE CHAIN REMARK 500 TYR E 495 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-26058 RELATED DB: EMDB REMARK 900 SARS-COV-2 E406W MUTANT RBD - LOCAL REFINEMENT DBREF 7TPK E 333 526 UNP P0DTC2 SPIKE_SARS2 333 526 SEQADV 7TPK TRP E 406 UNP P0DTC2 GLU 406 ENGINEERED MUTATION SEQRES 1 E 194 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 E 194 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 E 194 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 E 194 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 E 194 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 E 194 ASP SER PHE VAL ILE ARG GLY ASP TRP VAL ARG GLN ILE SEQRES 7 E 194 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 E 194 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 E 194 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 E 194 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 E 194 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 E 194 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 E 194 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 E 194 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 E 194 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY HET NAG E 601 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 2 NAG C8 H15 N O6 HELIX 1 AA1 PRO E 337 ASN E 343 1 7 HELIX 2 AA2 TYR E 365 ASN E 370 1 6 HELIX 3 AA3 SER E 383 ASP E 389 5 7 HELIX 4 AA4 TRP E 406 ILE E 410 5 5 HELIX 5 AA5 GLY E 416 ASN E 422 1 7 SHEET 1 AA1 5 ASN E 354 ILE E 358 0 SHEET 2 AA1 5 VAL E 395 ARG E 403 -1 O VAL E 395 N ILE E 358 SHEET 3 AA1 5 PRO E 507 PHE E 515 -1 O TYR E 508 N ILE E 402 SHEET 4 AA1 5 GLY E 431 ASN E 437 -1 N CYS E 432 O LEU E 513 SHEET 5 AA1 5 THR E 376 TYR E 380 -1 N TYR E 380 O GLY E 431 SHEET 1 AA2 3 CYS E 361 VAL E 362 0 SHEET 2 AA2 3 VAL E 524 CYS E 525 1 O CYS E 525 N CYS E 361 SHEET 3 AA2 3 CYS E 391 PHE E 392 -1 N PHE E 392 O VAL E 524 SHEET 1 AA3 2 LEU E 452 ARG E 454 0 SHEET 2 AA3 2 LEU E 492 SER E 494 -1 O GLN E 493 N TYR E 453 SHEET 1 AA4 2 TYR E 473 GLN E 474 0 SHEET 2 AA4 2 CYS E 488 TYR E 489 -1 O TYR E 489 N TYR E 473 SSBOND 1 CYS E 336 CYS E 361 1555 1555 2.03 SSBOND 2 CYS E 379 CYS E 432 1555 1555 2.04 SSBOND 3 CYS E 391 CYS E 525 1555 1555 2.04 SSBOND 4 CYS E 480 CYS E 488 1555 1555 2.03 LINK ND2 ASN E 343 C1 NAG E 601 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