HEADER ANTIVIRAL PROTEIN 21-NOV-23 8R68 TITLE ZORYA ANTI-BACTERIOPHAGE DEFENSE SYSTEM ZORC WT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZORYA PROTEIN ZORC EH DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: BF481_003651; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS ANTIVIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.HU,N.M.I.TAYLOR REVDAT 3 09-APR-25 8R68 1 JRNL REVDAT 2 12-FEB-25 8R68 1 JRNL REVDAT 1 04-DEC-24 8R68 0 JRNL AUTH H.HU,P.F.POPP,T.C.D.HUGHES,A.ROA-EGUIARA,N.R.RUTBEEK, JRNL AUTH 2 F.J.O.MARTIN,I.A.HENDRIKS,L.J.PAYNE,Y.YAN,D.HUMOLLI, JRNL AUTH 3 V.KLEIN-SOUSA,I.SONGAILIENE,Y.WANG,M.L.NIELSEN,R.M.BERRY, JRNL AUTH 4 A.HARMS,M.ERHARDT,S.A.JACKSON,N.M.I.TAYLOR JRNL TITL STRUCTURE AND MECHANISM OF THE ZORYA ANTI-PHAGE DEFENCE JRNL TITL 2 SYSTEM. JRNL REF NATURE V. 639 1093 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 39662505 JRNL DOI 10.1038/S41586-024-08493-8 REMARK 2 REMARK 2 RESOLUTION. 3.60 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) : 3.600 REMARK 3 NUMBER OF PARTICLES : 168569 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 8R68 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1292134780. 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 : ZORYA ANTI-BACTERIOPHAGE REMARK 245 DEFENSE SYSTEM ZORC 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 : 7.50 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 II (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 3950.00 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 ILE A 2 REMARK 465 PRO A 3 REMARK 465 ALA A 4 REMARK 465 LEU A 5 REMARK 465 ASN A 6 REMARK 465 SER A 7 REMARK 465 LEU A 8 REMARK 465 SER A 9 REMARK 465 GLN A 10 REMARK 465 ARG A 11 REMARK 465 ILE A 12 REMARK 465 ALA A 13 REMARK 465 ALA A 14 REMARK 465 ARG A 15 REMARK 465 LEU A 16 REMARK 465 SER A 17 REMARK 465 SER A 18 REMARK 465 SER A 19 REMARK 465 GLN A 20 REMARK 465 ARG A 21 REMARK 465 ASP A 22 REMARK 465 ASP A 23 REMARK 465 HIS A 24 REMARK 465 TYR A 25 REMARK 465 LEU A 26 REMARK 465 HIS A 27 REMARK 465 ASN A 28 REMARK 465 ASP A 29 REMARK 465 PHE A 30 REMARK 465 HIS A 31 REMARK 465 ALA A 32 REMARK 465 LEU A 33 REMARK 465 THR A 34 REMARK 465 ALA A 35 REMARK 465 ALA A 36 REMARK 465 THR A 37 REMARK 465 LEU A 38 REMARK 465 ASP A 39 REMARK 465 MET A 40 REMARK 465 GLU A 41 REMARK 465 LYS A 42 REMARK 465 ARG A 43 REMARK 465 PHE A 44 REMARK 465 ASP A 45 REMARK 465 ARG A 46 REMARK 465 ALA A 47 REMARK 465 GLU A 48 REMARK 465 ARG A 49 REMARK 465 ILE A 50 REMARK 465 PRO A 51 REMARK 465 SER A 52 REMARK 465 PRO A 53 REMARK 465 PRO A 54 REMARK 465 GLN A 55 REMARK 465 GLU A 56 REMARK 465 MET A 57 REMARK 465 GLN A 69 REMARK 465 GLU A 70 REMARK 465 LEU A 71 REMARK 465 THR A 72 REMARK 465 GLU A 73 REMARK 465 ARG A 74 REMARK 465 GLU A 140 REMARK 465 THR A 141 REMARK 465 ASN A 142 REMARK 465 PRO A 143 REMARK 465 HIS A 144 REMARK 465 ALA A 161 REMARK 465 ALA A 162 REMARK 465 ILE A 163 REMARK 465 ARG A 164 REMARK 465 ARG A 165 REMARK 465 GLU A 166 REMARK 465 LYS A 167 REMARK 465 SER A 168 REMARK 465 GLY A 195 REMARK 465 GLU A 196 REMARK 465 ASN A 197 REMARK 465 ASN A 198 REMARK 465 LEU A 290 REMARK 465 LYS A 291 REMARK 465 SER A 292 REMARK 465 GLN A 293 REMARK 465 GLN A 294 REMARK 465 ASN A 295 REMARK 465 TYR A 300 REMARK 465 VAL A 479 REMARK 465 ARG A 480 REMARK 465 PHE A 481 REMARK 465 VAL A 482 REMARK 465 ASP A 483 REMARK 465 LYS A 484 REMARK 465 LYS A 485 REMARK 465 VAL A 486 REMARK 465 PRO A 487 REMARK 465 PRO A 488 REMARK 465 PRO A 489 REMARK 465 VAL A 490 REMARK 465 ALA A 491 REMARK 465 MET A 492 REMARK 465 SER A 493 REMARK 465 ASP A 494 REMARK 465 ILE A 495 REMARK 465 LYS A 496 REMARK 465 ILE A 497 REMARK 465 ILE A 498 REMARK 465 ASN A 499 REMARK 465 PRO A 500 REMARK 465 LEU A 501 REMARK 465 ARG A 502 REMARK 465 ASP A 503 REMARK 465 THR A 504 REMARK 465 ALA A 505 REMARK 465 ILE A 506 REMARK 465 GLN A 507 REMARK 465 HIS A 508 REMARK 465 LEU A 509 REMARK 465 VAL A 510 REMARK 465 LYS A 511 REMARK 465 CYS A 512 REMARK 465 SER A 513 REMARK 465 SER A 514 REMARK 465 CYS A 515 REMARK 465 ILE A 516 REMARK 465 VAL A 517 REMARK 465 SER A 518 REMARK 465 ASP A 519 REMARK 465 ASN A 520 REMARK 465 ARG A 521 REMARK 465 HIS A 522 REMARK 465 LYS A 523 REMARK 465 GLY A 524 REMARK 465 GLY A 525 REMARK 465 ILE A 526 REMARK 465 LEU A 527 REMARK 465 SER A 528 REMARK 465 VAL A 529 REMARK 465 GLN A 530 REMARK 465 LEU A 531 REMARK 465 ILE A 532 REMARK 465 THR A 533 REMARK 465 PRO A 534 REMARK 465 ASP A 535 REMARK 465 ASP A 536 REMARK 465 THR A 537 REMARK 465 VAL A 538 REMARK 465 GLU A 539 REMARK 465 LYS A 540 REMARK 465 GLU A 541 REMARK 465 LEU A 542 REMARK 465 LEU A 543 REMARK 465 ARG A 544 REMARK 465 LEU A 545 REMARK 465 GLY A 546 REMARK 465 PHE A 547 REMARK 465 ALA A 548 REMARK 465 PRO A 549 REMARK 465 VAL A 550 REMARK 465 ALA A 551 REMARK 465 LYS A 552 REMARK 465 GLU A 553 REMARK 465 PRO A 554 REMARK 465 HIS A 555 REMARK 465 ARG A 556 REMARK 465 TYR A 557 REMARK 465 TRP A 558 REMARK 465 ILE A 559 REMARK 465 LYS A 560 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 HIS A 177 35.81 -99.43 REMARK 500 THR A 229 -168.91 -123.73 REMARK 500 LEU A 230 140.11 72.62 REMARK 500 TYR A 269 39.05 -99.34 REMARK 500 LEU A 325 36.20 -99.04 REMARK 500 PHE A 342 46.23 -92.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-18948 RELATED DB: EMDB REMARK 900 ZORYA ANTI-BACTERIOPHAGE DEFENSE SYSTEM ZORC WT DBREF1 8R68 A 1 560 UNP A0A4C2FPK5_ECOLX DBREF2 8R68 A A0A4C2FPK5 1 560 SEQADV 8R68 LYS A 540 UNP A0A4C2FPK ARG 540 CONFLICT SEQRES 1 A 560 MET ILE PRO ALA LEU ASN SER LEU SER GLN ARG ILE ALA SEQRES 2 A 560 ALA ARG LEU SER SER SER GLN ARG ASP ASP HIS TYR LEU SEQRES 3 A 560 HIS ASN ASP PHE HIS ALA LEU THR ALA ALA THR LEU ASP SEQRES 4 A 560 MET GLU LYS ARG PHE ASP ARG ALA GLU ARG ILE PRO SER SEQRES 5 A 560 PRO PRO GLN GLU MET ARG LEU GLU ALA LEU ARG ARG PHE SEQRES 6 A 560 ARG LEU ALA GLN GLU LEU THR GLU ARG GLU TRP ARG MET SEQRES 7 A 560 VAL PHE TYR GLY LEU ALA ASP ASN ASP PRO LEU TYR PRO SEQRES 8 A 560 ASP GLN PRO ILE LEU LEU GLU ASP ASP THR PHE PHE PRO SEQRES 9 A 560 ARG VAL ASN SER ALA ILE LYS LYS ARG ILE GLU THR LYS SEQRES 10 A 560 THR LEU LYS ARG ARG ASP TRP ALA ALA LEU CYS SER SER SEQRES 11 A 560 TYR PHE ALA TYR GLN HIS GLN SER PRO GLU THR ASN PRO SEQRES 12 A 560 HIS TRP CYS VAL LEU ARG GLY HIS ILE ALA GLN GLY TYR SEQRES 13 A 560 LEU VAL VAL LYS ALA ALA ILE ARG ARG GLU LYS SER TRP SEQRES 14 A 560 MET LYS THR ILE GLU PHE TYR HIS ASP ILE PHE THR PRO SEQRES 15 A 560 GLN ALA GLY GLY VAL ILE SER ARG GLN LEU LEU ALA GLY SEQRES 16 A 560 GLU ASN ASN SER LEU SER SER LEU GLU LYS ILE ALA GLN SEQRES 17 A 560 ILE PRO ASP SER SER TRP LEU TRP LYS ARG ILE PHE THR SEQRES 18 A 560 VAL LEU LEU ALA GLN LEU ASP THR LEU ASP ASP PRO GLN SEQRES 19 A 560 PHE LEU SER LYS ILE SER TRP LEU LEU GLY LEU ALA ALA SEQRES 20 A 560 GLN TRP VAL ARG PHE ARG ASP ASP ILE MET THR ALA THR SEQRES 21 A 560 LEU THR ARG TYR TYR HIS SER GLY TYR ARG ASP GLN SER SEQRES 22 A 560 HIS PRO ALA LEU LYS GLN ALA ALA LEU GLU TYR TRP ASP SEQRES 23 A 560 ASN PRO GLN LEU LYS SER GLN GLN ASN LYS TRP HIS GLN SEQRES 24 A 560 TYR VAL SER GLU SER VAL ALA ALA MET VAL ARG GLY TRP SEQRES 25 A 560 LEU ALA LYS GLN ASP LEU THR HIS PHE PHE GLU LEU LEU SEQRES 26 A 560 ARG GLY ASN GLY ASP VAL ASP GLN ALA ARG LEU HIS TYR SEQRES 27 A 560 TRP LEU ARG PHE ALA ASN GLN MET GLY PHE THR ARG ILE SEQRES 28 A 560 ILE MET GLY SER ASP ALA TRP GLN ASP ARG GLY SER ASP SEQRES 29 A 560 PHE VAL LYS PHE ARG GLU GLU ASN LYS GLY ARG LEU SER SEQRES 30 A 560 TYR LEU ARG GLY GLY ARG ASN PHE ASP ASN ALA MET VAL SEQRES 31 A 560 MET GLN ILE ASN ASP TYR LEU PHE VAL GLU PHE SER GLY SEQRES 32 A 560 THR GLY ASN ALA MET TYR ALA TYR GLN ILE GLY HIS ALA SEQRES 33 A 560 PRO PHE ASN PRO GLU SER ARG THR LEU ASP ILE ASN ILE SEQRES 34 A 560 HIS LEU LYS ASP GLN GLY ARG CYS ALA LEU ARG LEU PRO SEQRES 35 A 560 HIS ALA PRO ARG ALA GLU GLY TYR ASN LYS VAL ARG ILE SEQRES 36 A 560 THR GLY TRP MET LEU LYS TYR ASP ASP GLU LEU ARG LYS SEQRES 37 A 560 LEU GLY ILE ARG TRP MET ALA GLU GLU PRO VAL ARG PHE SEQRES 38 A 560 VAL ASP LYS LYS VAL PRO PRO PRO VAL ALA MET SER ASP SEQRES 39 A 560 ILE LYS ILE ILE ASN PRO LEU ARG ASP THR ALA ILE GLN SEQRES 40 A 560 HIS LEU VAL LYS CYS SER SER CYS ILE VAL SER ASP ASN SEQRES 41 A 560 ARG HIS LYS GLY GLY ILE LEU SER VAL GLN LEU ILE THR SEQRES 42 A 560 PRO ASP ASP THR VAL GLU LYS GLU LEU LEU ARG LEU GLY SEQRES 43 A 560 PHE ALA PRO VAL ALA LYS GLU PRO HIS ARG TYR TRP ILE SEQRES 44 A 560 LYS HELIX 1 AA1 GLU A 60 PHE A 65 1 6 HELIX 2 AA2 ARG A 66 ALA A 68 5 3 HELIX 3 AA3 VAL A 79 LEU A 83 5 5 HELIX 4 AA4 ILE A 95 ASP A 99 5 5 HELIX 5 AA5 PHE A 102 ARG A 113 1 12 HELIX 6 AA6 ARG A 122 ALA A 133 1 12 HELIX 7 AA7 CYS A 146 VAL A 159 1 14 HELIX 8 AA8 GLY A 186 ALA A 194 1 9 HELIX 9 AA9 SER A 201 ILE A 206 5 6 HELIX 10 AB1 LEU A 215 LEU A 224 1 10 HELIX 11 AB2 GLN A 234 TRP A 249 1 16 HELIX 12 AB3 TRP A 249 GLY A 268 1 20 HELIX 13 AB4 HIS A 274 TRP A 285 1 12 HELIX 14 AB5 SER A 302 ALA A 314 1 13 HELIX 15 AB6 ALA A 314 LEU A 324 1 11 HELIX 16 AB7 ASP A 332 PHE A 342 1 11 HELIX 17 AB8 GLY A 354 GLN A 359 1 6 HELIX 18 AB9 GLY A 362 ASN A 372 1 11 HELIX 19 AC1 THR A 456 LYS A 468 1 13 SHEET 1 AA1 7 THR A 424 ASP A 426 0 SHEET 2 AA1 7 LEU A 376 ARG A 380 1 N ARG A 380 O LEU A 425 SHEET 3 AA1 7 THR A 349 ILE A 352 1 N ILE A 351 O SER A 377 SHEET 4 AA1 7 ALA A 388 GLN A 392 -1 O ALA A 388 N ILE A 352 SHEET 5 AA1 7 TYR A 396 PHE A 401 -1 O PHE A 398 N MET A 391 SHEET 6 AA1 7 MET A 408 GLN A 412 -1 O TYR A 411 N LEU A 397 SHEET 7 AA1 7 LEU A 439 LEU A 441 -1 O LEU A 439 N ALA A 410 CISPEP 1 ASN A 86 ASP A 87 0 -5.66 CISPEP 2 ALA A 444 PRO A 445 0 -4.79 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