HEADER VIRUS 14-FEB-23 8CK0 TITLE CARIN1 BACTERIOPHAGE PORTAL ASSEMBLY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORTAL PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTERIOPHAGE SP.; SOURCE 3 ORGANISM_TAXID: 3801 KEYWDS BACTERIOPHAGES; VIRUS STRUCTURE, CRYO-EM, MARINE PODOVIRUS, PORTAL KEYWDS 2 PROTEIN, TAIL, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR A.D'ACAPITO,E.NEUMANN,G.SCHOEHN REVDAT 3 10-MAY-23 8CK0 1 JRNL REVDAT 2 05-APR-23 8CK0 1 JRNL REVDAT 1 15-MAR-23 8CK0 0 JRNL AUTH A.D'ACAPITO,T.RORET,E.ZARKADAS,P.Y.MOCAER,F.LELCHAT, JRNL AUTH 2 A.C.BAUDOUX,G.SCHOEHN,E.NEUMANN JRNL TITL STRUCTURAL STUDY OF THE COBETIA MARINA BACTERIOPHAGE 1 JRNL TITL 2 (CARIN-1) BY CRYO-EM. JRNL REF J.VIROL. V. 97 24823 2023 JRNL REFN ESSN 1098-5514 JRNL PMID 36943070 JRNL DOI 10.1128/JVI.00248-23 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, RELION, RELION, RELION 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 11395 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 8CK0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292127614. 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 : BACTERIOPHAGE SP. COBETIA REMARK 245 MARINA VIRUS CARIN1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : 25MA REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : COBETIA MARINA VIRUS CARIN1 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 : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4000.00 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) : 3000.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : 36000 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 LYS A 2 REMARK 465 VAL A 3 REMARK 465 ASP A 219 REMARK 465 GLU A 220 REMARK 465 ARG A 221 REMARK 465 ASN A 222 REMARK 465 GLU A 223 REMARK 465 GLY A 224 REMARK 465 LYS A 225 REMARK 465 LEU A 226 REMARK 465 ASP A 227 REMARK 465 SER A 228 REMARK 465 LYS A 229 REMARK 465 ASN A 230 REMARK 465 PHE A 369 REMARK 465 MET A 370 REMARK 465 MET A 371 REMARK 465 ILE A 372 REMARK 465 ALA A 373 REMARK 465 ASN A 374 REMARK 465 ASP A 375 REMARK 465 GLN A 376 REMARK 465 ARG A 377 REMARK 465 SER A 378 REMARK 465 ASN A 379 REMARK 465 ILE A 380 REMARK 465 THR A 381 REMARK 465 ALA A 382 REMARK 465 ARG A 383 REMARK 465 GLU A 384 REMARK 465 ILE A 385 REMARK 465 GLN A 386 REMARK 465 GLU A 387 REMARK 465 ARG A 388 REMARK 465 HIS A 389 REMARK 465 GLU A 390 REMARK 465 GLU A 391 REMARK 465 LYS A 392 REMARK 465 LEU A 393 REMARK 465 LEU A 394 REMARK 465 ALA A 395 REMARK 465 LEU A 396 REMARK 465 GLY A 397 REMARK 465 PRO A 398 REMARK 465 ALA A 524 REMARK 465 GLN A 525 REMARK 465 GLN A 526 REMARK 465 ALA A 527 REMARK 465 ALA A 528 REMARK 465 GLN A 529 REMARK 465 GLY A 530 REMARK 465 ALA A 531 REMARK 465 LYS A 532 REMARK 465 LEU A 533 REMARK 465 LEU A 534 REMARK 465 SER A 535 REMARK 465 GLU A 536 REMARK 465 THR A 537 REMARK 465 ASP A 538 REMARK 465 ALA A 539 REMARK 465 GLY A 540 REMARK 465 THR A 541 REMARK 465 GLY A 542 REMARK 465 GLN A 543 REMARK 465 ASN A 544 REMARK 465 GLY A 545 REMARK 465 LEU A 546 REMARK 465 SER A 547 REMARK 465 ALA A 548 REMARK 465 MET A 549 REMARK 465 MET A 550 REMARK 465 GLN A 551 REMARK 465 GLN A 552 REMARK 465 MET A 553 REMARK 465 GLY A 554 REMARK 465 LEU A 555 REMARK 465 ALA A 556 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 PRO A 80 C - N - CD ANGL. DEV. = -12.8 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 ILE A 35 -55.81 -127.69 REMARK 500 ARG A 39 -79.14 -98.88 REMARK 500 ASN A 48 -4.70 72.24 REMARK 500 ARG A 52 47.50 35.59 REMARK 500 PRO A 80 0.60 -67.84 REMARK 500 ASP A 90 49.39 -82.85 REMARK 500 ASN A 91 110.40 -160.06 REMARK 500 PHE A 316 56.04 -98.37 REMARK 500 SER A 443 -70.66 -59.91 REMARK 500 MET A 445 134.98 -175.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-16688 RELATED DB: EMDB REMARK 900 CARIN1 BACTERIOPHAGE PORTAL ASSEMBLY DBREF 8CK0 A 1 556 PDB 8CK0 8CK0 1 556 SEQRES 1 A 556 MET LYS VAL GLU THR LYS ARG GLN ARG TYR ASN LYS ARG SEQRES 2 A 556 LEU HIS ALA LEU LYS THR GLU ARG SER SER TRP GLU GLY SEQRES 3 A 556 SER TRP ARG ASP ILE SER ASP HIS ILE GLN PRO TRP ARG SEQRES 4 A 556 SER ARG PHE CYS MET SER ASP SER ASN LYS GLY ASN ARG SEQRES 5 A 556 HIS ASN LYS ALA LEU VAL ASP ASP THR PRO PHE LYS ALA SEQRES 6 A 556 SER ARG THR LEU ALA SER GLY MET MET SER GLY LEU THR SEQRES 7 A 556 SER PRO ALA ARG PRO TRP PHE LYS LEU ALA ILE ASP ASN SEQRES 8 A 556 PRO GLU LEU MET GLU SER ALA ALA VAL LYS GLN TRP LEU SEQRES 9 A 556 TYR LEU VAL THR GLN ARG MET GLN SER VAL MET SER LYS SEQRES 10 A 556 SER ASN LEU TYR ASN GLN LEU HIS GLN LEU TYR GLY GLU SEQRES 11 A 556 LEU GLY THR PHE GLY THR SER CYS ILE LEU ILE VAL GLU SEQRES 12 A 556 ASP LYS GLU ASP VAL ILE ARG ALA ILE PRO MET THR VAL SEQRES 13 A 556 GLY THR TYR TYR LEU ALA THR SER SER ARG GLY MET VAL SEQRES 14 A 556 ASP THR ILE TYR ARG GLU MET ARG LYS THR VAL ARG GLN SEQRES 15 A 556 LEU VAL GLN GLU PHE GLY LEU LYS ASN CYS SER ASN SER SEQRES 16 A 556 VAL GLN THR MET TYR ASP ASN ASP ASN LEU GLU ALA TRP SEQRES 17 A 556 VAL GLU VAL VAL HIS LEU ILE GLU PRO ASN ASP GLU ARG SEQRES 18 A 556 ASN GLU GLY LYS LEU ASP SER LYS ASN LYS PRO TYR ARG SEQRES 19 A 556 SER VAL TYR TYR GLU SER GLY CYS THR GLU ASP LYS LEU SEQRES 20 A 556 LEU ARG GLU SER GLY PHE ASP GLU PHE PRO GLY VAL ALA SEQRES 21 A 556 PRO ARG TRP GLU VAL LEU GLY ASP ASP VAL TYR GLY TYR SEQRES 22 A 556 GLY PRO GLY HIS ALA ALA LEU GLY PRO SER ARG SER LEU SEQRES 23 A 556 GLN VAL MET GLN LYS LYS LYS ALA GLN ALA VAL GLU LYS SEQRES 24 A 556 GLN ILE ASN PRO PRO MET ASN VAL PRO SER SER SER LYS SEQRES 25 A 556 SER LYS PRO PHE SER LEU LEU PRO GLY SER LEU ASN TYR SEQRES 26 A 556 TYR ASP ALA ALA MET GLY GLY GLN GLN MET ALA GLN PRO SEQRES 27 A 556 SER GLN SER VAL ASN LEU ASN LEU ASN SER ILE MET GLU SEQRES 28 A 556 ASP ILE VAL ALA HIS GLN THR SER ILE LYS GLU THR PHE SEQRES 29 A 556 TYR ALA ASP LEU PHE MET MET ILE ALA ASN ASP GLN ARG SEQRES 30 A 556 SER ASN ILE THR ALA ARG GLU ILE GLN GLU ARG HIS GLU SEQRES 31 A 556 GLU LYS LEU LEU ALA LEU GLY PRO VAL VAL GLU ARG LEU SEQRES 32 A 556 ASP THR GLU ALA LEU ASP PRO MET ILE ASP ARG VAL PHE SEQRES 33 A 556 GLY ILE MET MET ARG GLY GLY HIS LEU PRO PRO PRO PRO SEQRES 34 A 556 GLU GLU ILE GLN GLY VAL ASP LEU ASN VAL GLN TYR ILE SEQRES 35 A 556 SER VAL MET ALA GLN ALA GLN LYS LEU VAL GLY ILE GLY SEQRES 36 A 556 ALA ILE GLU ARG ILE THR SER PHE VAL GLY ASN LEU ALA SEQRES 37 A 556 GLY ALA ASP PRO SER ALA LEU ASP LYS LEU ASN ILE ASP SEQRES 38 A 556 GLN ALA ILE ASP GLN TYR SER ASN SER VAL SER ALA PRO SEQRES 39 A 556 PRO ASP ILE ILE ARG THR ASP ASP GLU VAL ALA GLU ILE SEQRES 40 A 556 ARG GLN ALA ARG ALA GLN GLN GLN GLN GLN ALA GLN ALA SEQRES 41 A 556 MET GLU MET ALA GLN GLN ALA ALA GLN GLY ALA LYS LEU SEQRES 42 A 556 LEU SER GLU THR ASP ALA GLY THR GLY GLN ASN GLY LEU SEQRES 43 A 556 SER ALA MET MET GLN GLN MET GLY LEU ALA HELIX 1 AA1 THR A 5 SER A 22 1 18 HELIX 2 AA2 TRP A 24 ILE A 35 1 12 HELIX 3 AA3 ASP A 60 THR A 78 1 19 HELIX 4 AA4 ASN A 91 SER A 97 1 7 HELIX 5 AA5 SER A 97 SER A 118 1 22 HELIX 6 AA6 ASN A 119 GLY A 135 1 17 HELIX 7 AA7 VAL A 180 PHE A 187 1 8 HELIX 8 AA8 GLY A 188 CYS A 192 5 5 HELIX 9 AA9 SER A 193 ASN A 202 1 10 HELIX 10 AB1 GLY A 274 ASN A 302 1 29 HELIX 11 AB2 LYS A 314 LEU A 318 5 5 HELIX 12 AB3 ASN A 345 PHE A 364 1 20 HELIX 13 AB4 GLU A 401 GLU A 406 1 6 HELIX 14 AB5 LEU A 408 GLY A 422 1 15 HELIX 15 AB6 GLN A 447 LEU A 467 1 21 HELIX 16 AB7 ALA A 468 ALA A 470 5 3 HELIX 17 AB8 ASP A 471 LYS A 477 5 7 HELIX 18 AB9 ASN A 479 SER A 492 1 14 HELIX 19 AC1 PRO A 494 ILE A 498 5 5 HELIX 20 AC2 THR A 500 MET A 523 1 24 SHEET 1 AA1 2 LYS A 86 ALA A 88 0 SHEET 2 AA1 2 ASN A 438 GLN A 440 -1 O GLN A 440 N LYS A 86 SHEET 1 AA2 3 ILE A 149 MET A 154 0 SHEET 2 AA2 3 CYS A 138 GLU A 143 -1 N LEU A 140 O ILE A 152 SHEET 3 AA2 3 GLY A 258 VAL A 259 -1 O VAL A 259 N ILE A 139 SHEET 1 AA3 5 TYR A 159 THR A 163 0 SHEET 2 AA3 5 VAL A 169 THR A 179 -1 O TYR A 173 N TYR A 160 SHEET 3 AA3 5 TRP A 208 PRO A 217 -1 O ILE A 215 N ILE A 172 SHEET 4 AA3 5 TYR A 233 TYR A 238 -1 O TYR A 238 N VAL A 212 SHEET 5 AA3 5 ARG A 249 PHE A 253 -1 O PHE A 253 N TYR A 233 SHEET 1 AA4 2 MET A 305 ASN A 306 0 SHEET 2 AA4 2 GLN A 337 PRO A 338 -1 O GLN A 337 N ASN A 306 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