HEADER VIRUS 07-FEB-23 8CH5 TITLE CRYO-EM STRUCTURE OF THE FD BACTERIOPHAGE CAPSID MAJOR COAT PROTEIN TITLE 2 PVIII COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR CAPSID PROTEIN PVIII; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COAT PROTEIN B,GENE 8 PROTEIN,G8P,MAJOR COAT PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS BACTERIOPHAGE, FD, INOVIRUS, FF, HELICAL, PHAGE, FILAMENTOUS, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR J.BOEHNING,T.A.M.BHARAT REVDAT 2 10-JAN-24 8CH5 1 AUTHOR JRNL REVDAT 1 20-DEC-23 8CH5 0 JRNL AUTH J.BOHNING,M.GRAHAM,S.C.LETHAM,L.K.DAVIS,U.SCHULZE, JRNL AUTH 2 P.J.STANSFELD,R.A.COREY,P.PEARCE,A.K.TARAFDER,T.A.M.BHARAT JRNL TITL BIOPHYSICAL BASIS OF FILAMENTOUS PHAGE TACTOID-MEDIATED JRNL TITL 2 ANTIBIOTIC TOLERANCE IN P. AERUGINOSA. JRNL REF NAT COMMUN V. 14 8429 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 38114502 JRNL DOI 10.1038/S41467-023-44160-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.BOHNING,M.GRAHAM,S.LETHAM,L.DAVIS,U.SCHULZE,P.STANSFELD, REMARK 1 AUTH 2 R.COREY,P.PEARCE,A.TARAFDER,T.BHARAT REMARK 1 TITL BIOPHYSICAL BASIS OF PHAGE LIQUID CRYSTALLINE REMARK 1 TITL 2 DROPLET-MEDIATED ANTIBIOTIC TOLERANCE IN PATHOGENIC BACTERIA REMARK 1 REF BIORXIV 2023 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2022.12.13.520211 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CTFFIND, COOT, PHENIX, 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 : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 79.940 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 84458 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: RELION 3.1 REMARK 4 REMARK 4 8CH5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128495. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : ENTEROBACTERIA PHAGE FD REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : 15 MA REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : PURIFIED BY PEG PRECIPITATION REMARK 245 FROM THE SUPERNATANT OF INFECTED E. COLI CELLS. 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5390.00 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: 50-MERIC 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 350 BIOMT1 2 0.347894 -0.937534 -0.000702 260.55588 REMARK 350 BIOMT2 2 0.937533 0.347894 -0.001499 -46.51296 REMARK 350 BIOMT3 2 0.001650 -0.000137 0.999999 -66.73019 REMARK 350 BIOMT1 3 -0.281496 -0.959562 -0.000130 367.10556 REMARK 350 BIOMT2 3 0.959562 -0.281496 0.000051 52.72997 REMARK 350 BIOMT3 3 -0.000085 -0.000110 1.000000 -49.82809 REMARK 350 BIOMT1 4 -0.999079 -0.042883 -0.001679 334.45460 REMARK 350 BIOMT2 4 0.042886 -0.999079 -0.001293 320.71160 REMARK 350 BIOMT3 4 -0.001622 -0.001364 0.999998 -49.40120 REMARK 350 BIOMT1 5 -0.315790 0.948826 -0.002575 60.66295 REMARK 350 BIOMT2 5 -0.948807 -0.315762 0.007724 370.24244 REMARK 350 BIOMT3 5 0.006516 0.004882 0.999967 -51.58416 REMARK 350 BIOMT1 6 0.802272 0.596920 -0.006820 -64.67115 REMARK 350 BIOMT2 6 -0.596930 0.802293 0.000593 130.31170 REMARK 350 BIOMT3 6 0.005825 0.003596 0.999977 -51.29029 REMARK 350 BIOMT1 7 0.827161 -0.561963 -0.001441 120.63829 REMARK 350 BIOMT2 7 0.561963 0.827162 -0.000862 -63.63486 REMARK 350 BIOMT3 7 0.001676 -0.000097 0.999999 -50.12117 REMARK 350 BIOMT1 8 0.327206 -0.944953 -0.000076 264.99927 REMARK 350 BIOMT2 8 0.944953 0.327206 0.000060 -44.58509 REMARK 350 BIOMT3 8 -0.000032 -0.000092 1.000000 -33.21981 REMARK 350 BIOMT1 9 -0.789008 -0.614379 -0.002115 393.82357 REMARK 350 BIOMT2 9 0.614381 -0.789010 -0.000130 192.65692 REMARK 350 BIOMT3 9 -0.001588 -0.001402 0.999998 -32.78048 REMARK 350 BIOMT1 10 -0.807543 0.589803 0.002378 199.51353 REMARK 350 BIOMT2 10 -0.589773 -0.807532 0.007740 391.79924 REMARK 350 BIOMT3 10 0.006485 0.004847 0.999967 -34.95344 REMARK 350 BIOMT1 11 0.307318 0.951593 -0.005211 -41.74106 REMARK 350 BIOMT2 11 -0.951589 0.307341 0.004390 269.04213 REMARK 350 BIOMT3 11 0.005779 0.003610 0.999977 -34.66500 REMARK 350 BIOMT1 12 0.322400 -0.946603 -0.000847 266.33307 REMARK 350 BIOMT2 12 0.946602 0.322398 0.001869 -44.10695 REMARK 350 BIOMT3 12 -0.001496 -0.001405 0.999998 0.44470 REMARK 350 BIOMT1 13 0.999757 0.021968 -0.001673 -3.27429 REMARK 350 BIOMT2 13 -0.021968 0.999759 0.000083 3.56953 REMARK 350 BIOMT3 13 0.001675 -0.000046 0.999999 -33.50922 REMARK 350 BIOMT1 14 0.814615 -0.580002 -0.000031 125.37549 REMARK 350 BIOMT2 14 0.580002 0.814615 0.000040 -64.64224 REMARK 350 BIOMT3 14 0.000002 -0.000050 1.000000 -16.61200 REMARK 350 BIOMT1 15 -0.286394 -0.958110 -0.001802 367.91589 REMARK 350 BIOMT2 15 0.958111 -0.286397 0.001074 53.89976 REMARK 350 BIOMT3 15 -0.001545 -0.001419 0.999998 -16.16486 REMARK 350 BIOMT1 16 -0.999906 0.012097 0.006428 325.12940 REMARK 350 BIOMT2 16 -0.012066 -0.999915 0.004871 328.82641 REMARK 350 BIOMT3 16 0.006486 0.004793 0.999967 -18.32472 REMARK 350 BIOMT1 17 -0.301557 0.953447 -0.001697 57.39670 REMARK 350 BIOMT2 17 -0.953431 -0.301540 0.006546 368.75142 REMARK 350 BIOMT3 17 0.005730 0.003592 0.999977 -18.03412 REMARK 350 BIOMT1 18 0.801687 0.597742 -0.001320 -65.23623 REMARK 350 BIOMT2 18 -0.597741 0.801688 0.000987 130.18015 REMARK 350 BIOMT3 18 0.001649 -0.000002 0.999999 -16.89204 REMARK 350 BIOMT1 19 0.814624 0.579989 0.000000 -64.64029 REMARK 350 BIOMT2 19 -0.579989 0.814624 -0.000050 125.37255 REMARK 350 BIOMT3 19 -0.000029 0.000040 1.000000 16.61818 REMARK 350 BIOMT1 20 0.811654 -0.584139 0.000393 126.73967 REMARK 350 BIOMT2 20 0.584137 0.811653 0.001963 -65.02834 REMARK 350 BIOMT3 20 -0.001466 -0.001364 0.999998 17.05314 REMARK 350 BIOMT1 21 -0.338592 -0.940910 0.006672 372.53206 REMARK 350 BIOMT2 21 0.940910 -0.338625 -0.004567 65.36370 REMARK 350 BIOMT3 21 0.006557 0.004732 0.999967 14.91380 REMARK 350 BIOMT1 22 -0.999618 0.027057 0.005598 322.64978 REMARK 350 BIOMT2 22 -0.027037 -0.999628 0.003660 331.42266 REMARK 350 BIOMT3 22 0.005695 0.003508 0.999978 15.22534 REMARK 350 BIOMT1 23 -0.821552 -0.570077 0.008059 390.93459 REMARK 350 BIOMT2 23 0.570097 -0.821578 0.000194 204.67324 REMARK 350 BIOMT3 23 0.006511 0.004754 0.999968 -1.70229 REMARK 350 BIOMT1 24 -0.302501 0.953149 0.000469 57.08477 REMARK 350 BIOMT2 24 -0.953148 -0.302502 0.001483 369.23743 REMARK 350 BIOMT3 24 0.001555 0.000001 0.999999 16.36267 REMARK 350 BIOMT1 25 0.327221 0.944948 -0.000032 -44.58200 REMARK 350 BIOMT2 25 -0.944948 0.327221 -0.000094 264.99481 REMARK 350 BIOMT3 25 -0.000078 0.000061 1.000000 33.24294 REMARK 350 BIOMT1 26 0.999986 -0.005102 0.001455 0.88963 REMARK 350 BIOMT2 26 0.005100 0.999986 0.001318 -1.10906 REMARK 350 BIOMT3 26 -0.001461 -0.001310 0.999998 33.66370 REMARK 350 BIOMT1 27 0.269908 -0.962882 0.002784 276.74122 REMARK 350 BIOMT2 27 0.962864 0.269880 -0.007641 -37.44777 REMARK 350 BIOMT3 27 0.006606 0.004743 0.999967 31.52389 REMARK 350 BIOMT1 28 -0.829985 -0.557745 0.006677 390.42134 REMARK 350 BIOMT2 28 0.557756 -0.830005 -0.000317 208.21967 REMARK 350 BIOMT3 28 0.005719 0.003461 0.999978 31.84892 REMARK 350 BIOMT1 29 -0.799242 0.601008 0.001240 196.01740 REMARK 350 BIOMT2 29 -0.601007 -0.799243 0.000882 393.05305 REMARK 350 BIOMT3 29 0.001521 -0.000040 0.999999 32.99494 REMARK 350 BIOMT1 30 -0.281512 0.959558 -0.000077 52.73930 REMARK 350 BIOMT2 30 -0.959558 -0.281512 -0.000110 367.10073 REMARK 350 BIOMT3 30 -0.000128 0.000043 1.000000 49.87376 REMARK 350 BIOMT1 31 0.817574 0.575821 0.001948 -64.55824 REMARK 350 BIOMT2 31 -0.575822 0.817575 0.000181 123.94976 REMARK 350 BIOMT3 31 -0.001488 -0.001270 0.999998 50.28146 REMARK 350 BIOMT1 32 0.778324 -0.627859 -0.002165 139.08079 REMARK 350 BIOMT2 32 0.627828 0.778313 -0.007889 -65.64215 REMARK 350 BIOMT3 32 0.006638 0.004781 0.999967 48.13241 REMARK 350 BIOMT1 33 -0.352615 -0.935754 0.005252 374.17032 REMARK 350 BIOMT2 33 0.935751 -0.352637 -0.004179 68.54707 REMARK 350 BIOMT3 33 0.005763 0.003441 0.999977 48.46508 REMARK 350 BIOMT1 34 -0.798633 0.601814 0.002413 195.98853 REMARK 350 BIOMT2 34 -0.601792 -0.798628 0.006273 392.47667 REMARK 350 BIOMT3 34 0.005702 0.003558 0.999977 -1.40405 REMARK 350 BIOMT1 35 -0.999660 0.026036 0.001522 323.00810 REMARK 350 BIOMT2 35 -0.026036 -0.999661 -0.000047 331.87152 REMARK 350 BIOMT3 35 0.001520 -0.000087 0.999999 49.62283 REMARK 350 BIOMT1 36 -0.785858 0.618407 -0.000126 191.23654 REMARK 350 BIOMT2 36 -0.618407 -0.785858 -0.000092 393.83023 REMARK 350 BIOMT3 36 -0.000156 0.000006 1.000000 66.50454 REMARK 350 BIOMT1 37 0.332034 0.943266 0.001694 -45.34032 REMARK 350 BIOMT2 37 -0.943266 0.332035 -0.001035 263.78802 REMARK 350 BIOMT3 37 -0.001539 -0.001254 0.999998 66.90703 REMARK 350 BIOMT1 38 0.998176 -0.060043 -0.006340 10.58476 REMARK 350 BIOMT2 38 0.060010 0.998184 -0.005220 -8.76716 REMARK 350 BIOMT3 38 0.006642 0.004830 0.999966 64.74363 REMARK 350 BIOMT1 39 0.255487 -0.966811 0.001850 279.92343 REMARK 350 BIOMT2 39 0.966795 0.255470 -0.006502 -35.80576 REMARK 350 BIOMT3 39 0.005813 0.003450 0.999977 65.07536 REMARK 350 BIOMT1 40 -0.829450 -0.558580 0.001212 390.97211 REMARK 350 BIOMT2 40 0.558579 -0.829451 -0.000977 208.38058 REMARK 350 BIOMT3 40 0.001551 -0.000133 0.999999 66.24528 REMARK 350 BIOMT1 41 -0.998842 0.048116 -0.000156 319.54269 REMARK 350 BIOMT2 41 -0.048116 -0.998842 -0.000044 335.29683 REMARK 350 BIOMT3 41 -0.000158 -0.000037 1.000000 83.13155 REMARK 350 BIOMT1 42 -0.276603 0.960984 0.000778 51.41944 REMARK 350 BIOMT2 42 -0.960983 -0.276601 -0.001875 366.55394 REMARK 350 BIOMT3 42 -0.001587 -0.001266 0.999998 83.53696 REMARK 350 BIOMT1 43 0.847943 0.530024 -0.008195 -61.10200 REMARK 350 BIOMT2 43 -0.530046 0.847969 -0.000625 112.08799 REMARK 350 BIOMT3 43 0.006617 0.004874 0.999966 81.36058 REMARK 350 BIOMT1 44 0.768839 -0.639439 -0.002266 142.63162 REMARK 350 BIOMT2 44 0.639416 0.768834 -0.006434 -66.15069 REMARK 350 BIOMT3 44 0.005857 0.003497 0.999977 81.68064 REMARK 350 BIOMT1 45 0.306391 0.951906 -0.000505 -42.27921 REMARK 350 BIOMT2 45 -0.951904 0.306392 0.001519 269.25746 REMARK 350 BIOMT3 45 0.001601 0.000015 0.999999 -0.26709 REMARK 350 BIOMT1 46 -0.785854 -0.618412 -0.000165 393.84385 REMARK 350 BIOMT2 46 0.618412 -0.785854 0.000011 191.22979 REMARK 350 BIOMT3 46 -0.000136 -0.000093 1.000000 -66.44249 REMARK 350 BIOMT1 47 -0.838739 0.544533 -0.000648 211.81639 REMARK 350 BIOMT2 47 -0.544531 -0.838738 -0.001984 390.59634 REMARK 350 BIOMT3 47 -0.001624 -0.001311 0.999998 -66.02954 REMARK 350 BIOMT1 48 0.293050 0.956074 -0.006606 -39.94571 REMARK 350 BIOMT2 48 -0.956075 0.293083 0.004838 272.14846 REMARK 350 BIOMT3 48 0.006562 0.004898 0.999966 -68.21415 REMARK 350 BIOMT1 49 0.999763 0.020948 -0.005931 -2.88848 REMARK 350 BIOMT2 49 -0.020969 0.999774 -0.003428 4.00303 REMARK 350 BIOMT3 49 0.005858 0.003551 0.999977 -67.90841 REMARK 350 BIOMT1 50 -0.351709 -0.936109 0.000417 374.71310 REMARK 350 BIOMT2 50 0.936108 -0.351709 -0.001548 68.35850 REMARK 350 BIOMT3 50 0.001595 -0.000154 0.999999 82.86146 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 ALA A 1 REMARK 465 GLU A 2 REMARK 465 GLY A 3 REMARK 465 ASP A 4 REMARK 465 ASP A 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-16657 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE FD BACTERIOPHAGE CAPSID MAJOR COAT PROTEIN REMARK 900 PVIII DBREF 8CH5 A 1 50 UNP P69539 CAPSD_BPFD 24 73 SEQRES 1 A 50 ALA GLU GLY ASP ASP PRO ALA LYS ALA ALA PHE ASP SER SEQRES 2 A 50 LEU GLN ALA SER ALA THR GLU TYR ILE GLY TYR ALA TRP SEQRES 3 A 50 ALA MET VAL VAL VAL ILE VAL GLY ALA THR ILE GLY ILE SEQRES 4 A 50 LYS LEU PHE LYS LYS PHE THR SER LYS ALA SER HELIX 1 AA1 PRO A 6 SER A 50 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