HEADER VIRAL PROTEIN 11-MAR-20 6M5T TITLE THE COORDINATE OF THE NUCLEASE DOMAIN OF THE APO TERMINASE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIPARTITE TERMINASE SUBUNIT 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TERMINASE LARGE SUBUNIT; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN ALPHAHERPESVIRUS 1 STRAIN 17; SOURCE 3 ORGANISM_COMMON: HHV-1; SOURCE 4 ORGANISM_TAXID: 10299; SOURCE 5 STRAIN: 17; SOURCE 6 GENE: TRM3, UL15; SOURCE 7 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS HSV-1, NUCLEASE DOMAIN, APO TERMINASE COMPLEX, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.X.YANG,P.YANG,N.WANG,Z.H.CHEN,Z.H.ZHOU,Z.H.RAO,X.X.WANG REVDAT 2 29-NOV-23 6M5T 1 REMARK REVDAT 1 28-OCT-20 6M5T 0 JRNL AUTH Y.YANG,P.YANG,N.WANG,Z.CHEN,D.SU,Z.H.ZHOU,Z.RAO,X.WANG JRNL TITL ARCHITECTURE OF THE HERPESVIRUS GENOME-PACKAGING COMPLEX AND JRNL TITL 2 IMPLICATIONS FOR DNA TRANSLOCATION. JRNL REF PROTEIN CELL V. 11 339 2020 JRNL REFN ESSN 1674-8018 JRNL PMID 32328903 JRNL DOI 10.1007/S13238-020-00710-0 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 : 42053 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 6M5T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300011062. 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 : HSV-1 NUCLEASE DOMAIN OF REMARK 245 TERMINASE COMPLEX 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 : GATAN K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 200.00 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: 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 450 REMARK 465 GLY A 451 REMARK 465 SER A 452 REMARK 465 SER A 453 REMARK 465 HIS A 454 REMARK 465 HIS A 455 REMARK 465 HIS A 456 REMARK 465 HIS A 457 REMARK 465 HIS A 458 REMARK 465 HIS A 459 REMARK 465 SER A 460 REMARK 465 SER A 461 REMARK 465 GLY A 462 REMARK 465 LEU A 463 REMARK 465 VAL A 464 REMARK 465 PRO A 465 REMARK 465 ARG A 466 REMARK 465 GLY A 467 REMARK 465 SER A 468 REMARK 465 HIS A 469 REMARK 465 MET A 470 REMARK 465 THR A 471 REMARK 465 GLY A 472 REMARK 465 ASP A 473 REMARK 465 ASP A 474 REMARK 465 ARG A 475 REMARK 465 VAL A 694 REMARK 465 ARG A 695 REMARK 465 THR A 696 REMARK 465 TYR A 697 REMARK 465 SER A 698 REMARK 465 GLY A 699 REMARK 465 LYS A 700 REMARK 465 ARG A 701 REMARK 465 ASN A 702 REMARK 465 ALA A 729 REMARK 465 PRO A 730 REMARK 465 ILE A 731 REMARK 465 THR A 732 REMARK 465 ARG A 733 REMARK 465 VAL A 734 REMARK 465 SER A 735 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 C ASP A 693 CA GLY A 703 1.54 REMARK 500 CA ASP A 693 N GLY A 703 1.68 REMARK 500 N ASP A 693 N GLY A 703 1.82 REMARK 500 O ASP A 693 N GLY A 703 2.01 REMARK 500 O ASP A 693 CA GLY A 703 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP A 693 C GLY A 703 N -0.214 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 693 CA - C - N ANGL. DEV. = -39.1 DEGREES REMARK 500 GLY A 703 C - N - CA ANGL. DEV. = -50.3 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 ARG A 490 75.11 -117.28 REMARK 500 LEU A 499 33.39 -92.27 REMARK 500 LEU A 546 64.80 60.69 REMARK 500 GLU A 607 -156.93 -150.08 REMARK 500 GLU A 661 41.41 -97.47 REMARK 500 GLU A 686 -161.64 -73.01 REMARK 500 THR A 692 72.85 64.29 REMARK 500 ASP A 693 2.20 -68.51 REMARK 500 ALA A 722 -165.18 -165.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 693 -29.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30092 RELATED DB: EMDB REMARK 900 THE COORDINATE OF THE NUCLEASE DOMAIN OF THE APO TERMINASE COMPLEX DBREF 6M5T A 471 735 UNP P04295 TRM3_HHV11 471 735 SEQADV 6M5T MET A 450 UNP P04295 INITIATING METHIONINE SEQADV 6M5T GLY A 451 UNP P04295 EXPRESSION TAG SEQADV 6M5T SER A 452 UNP P04295 EXPRESSION TAG SEQADV 6M5T SER A 453 UNP P04295 EXPRESSION TAG SEQADV 6M5T HIS A 454 UNP P04295 EXPRESSION TAG SEQADV 6M5T HIS A 455 UNP P04295 EXPRESSION TAG SEQADV 6M5T HIS A 456 UNP P04295 EXPRESSION TAG SEQADV 6M5T HIS A 457 UNP P04295 EXPRESSION TAG SEQADV 6M5T HIS A 458 UNP P04295 EXPRESSION TAG SEQADV 6M5T HIS A 459 UNP P04295 EXPRESSION TAG SEQADV 6M5T SER A 460 UNP P04295 EXPRESSION TAG SEQADV 6M5T SER A 461 UNP P04295 EXPRESSION TAG SEQADV 6M5T GLY A 462 UNP P04295 EXPRESSION TAG SEQADV 6M5T LEU A 463 UNP P04295 EXPRESSION TAG SEQADV 6M5T VAL A 464 UNP P04295 EXPRESSION TAG SEQADV 6M5T PRO A 465 UNP P04295 EXPRESSION TAG SEQADV 6M5T ARG A 466 UNP P04295 EXPRESSION TAG SEQADV 6M5T GLY A 467 UNP P04295 EXPRESSION TAG SEQADV 6M5T SER A 468 UNP P04295 EXPRESSION TAG SEQADV 6M5T HIS A 469 UNP P04295 EXPRESSION TAG SEQADV 6M5T MET A 470 UNP P04295 EXPRESSION TAG SEQRES 1 A 286 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 286 LEU VAL PRO ARG GLY SER HIS MET THR GLY ASP ASP ARG SEQRES 3 A 286 PRO VAL LEU THR LYS SER ALA GLY GLU ARG PHE LEU LEU SEQRES 4 A 286 TYR ARG PRO SER THR THR THR ASN SER GLY LEU MET ALA SEQRES 5 A 286 PRO ASP LEU TYR VAL TYR VAL ASP PRO ALA PHE THR ALA SEQRES 6 A 286 ASN THR ARG ALA SER GLY THR GLY VAL ALA VAL VAL GLY SEQRES 7 A 286 ARG TYR ARG ASP ASP TYR ILE ILE PHE ALA LEU GLU HIS SEQRES 8 A 286 PHE PHE LEU ARG ALA LEU THR GLY SER ALA PRO ALA ASP SEQRES 9 A 286 ILE ALA ARG CYS VAL VAL HIS SER LEU THR GLN VAL LEU SEQRES 10 A 286 ALA LEU HIS PRO GLY ALA PHE ARG GLY VAL ARG VAL ALA SEQRES 11 A 286 VAL GLU GLY ASN SER SER GLN ASP SER ALA VAL ALA ILE SEQRES 12 A 286 ALA THR HIS VAL HIS THR GLU MET HIS ARG LEU LEU ALA SEQRES 13 A 286 SER GLU GLY ALA ASP ALA GLY SER GLY PRO GLU LEU LEU SEQRES 14 A 286 PHE TYR HIS CYS GLU PRO PRO GLY SER ALA VAL LEU TYR SEQRES 15 A 286 PRO PHE PHE LEU LEU ASN LYS GLN LYS THR PRO ALA PHE SEQRES 16 A 286 GLU HIS PHE ILE LYS LYS PHE ASN SER GLY GLY VAL MET SEQRES 17 A 286 ALA SER GLN GLU ILE VAL SER ALA THR VAL ARG LEU GLN SEQRES 18 A 286 THR ASP PRO VAL GLU TYR LEU LEU GLU GLN LEU ASN ASN SEQRES 19 A 286 LEU THR GLU THR VAL SER PRO ASN THR ASP VAL ARG THR SEQRES 20 A 286 TYR SER GLY LYS ARG ASN GLY ALA SER ASP ASP LEU MET SEQRES 21 A 286 VAL ALA VAL ILE MET ALA ILE TYR LEU ALA ALA GLN ALA SEQRES 22 A 286 GLY PRO PRO HIS THR PHE ALA PRO ILE THR ARG VAL SER HELIX 1 AA1 THR A 479 TYR A 489 1 11 HELIX 2 AA2 THR A 495 MET A 500 5 6 HELIX 3 AA3 SER A 549 HIS A 569 1 21 HELIX 4 AA4 SER A 585 GLU A 607 1 23 HELIX 5 AA5 GLN A 639 ASN A 652 1 14 HELIX 6 AA6 ASP A 672 ASN A 682 1 11 HELIX 7 AA7 ASP A 706 ALA A 720 1 15 SHEET 1 AA1 6 LEU A 618 PHE A 619 0 SHEET 2 AA1 6 GLY A 575 VAL A 580 1 N VAL A 576 O LEU A 618 SHEET 3 AA1 6 ASP A 503 ASP A 509 1 N LEU A 504 O ARG A 577 SHEET 4 AA1 6 GLY A 522 ARG A 528 -1 O ALA A 524 N TYR A 507 SHEET 5 AA1 6 TYR A 533 LEU A 538 -1 O PHE A 536 N VAL A 525 SHEET 6 AA1 6 MET A 657 VAL A 663 1 O VAL A 663 N PHE A 536 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