HEADER VIRUS LIKE PARTICLE 16-APR-19 6RGL TITLE CRYO-EM STRUCTURE OF THE ANTI-FEEDING PROPHAGE (AFP) BASEPLATE IN TITLE 2 CONTRACTED STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AFP2; COMPND 3 CHAIN: B, A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: AFP3; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: AFP4; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SERRATIA ENTOMOPHILA; SOURCE 3 ORGANISM_TAXID: 42906; SOURCE 4 GENE: AFP2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: SERRATIA ENTOMOPHILA; SOURCE 9 ORGANISM_TAXID: 42906; SOURCE 10 GENE: AFP3; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: SERRATIA ENTOMOPHILA; SOURCE 15 ORGANISM_TAXID: 42906; SOURCE 16 GENE: AFP4; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTI-FEEDING PROPHAGE, SECRETION SYSTEM, AFP, CONTRACTILE, VIRUS LIKE KEYWDS 2 PARTICLE, BASEPLATE, CONTRACTED EXPDTA ELECTRON MICROSCOPY AUTHOR A.DESFOSSES REVDAT 3 06-NOV-19 6RGL 1 JRNL REVDAT 2 14-AUG-19 6RGL 1 JRNL REMARK REVDAT 1 24-APR-19 6RGL 0 JRNL AUTH A.DESFOSSES,H.VENUGOPAL,T.JOSHI,J.FELIX,M.JESSOP,H.JEONG, JRNL AUTH 2 J.HYUN,J.B.HEYMANN,M.R.H.HURST,I.GUTSCHE,A.K.MITRA JRNL TITL ATOMIC STRUCTURES OF AN ENTIRE CONTRACTILE INJECTION SYSTEM JRNL TITL 2 IN BOTH THE EXTENDED AND CONTRACTED STATES. JRNL REF NAT MICROBIOL V. 4 1885 2019 JRNL REFN ESSN 2058-5276 JRNL PMID 31384001 JRNL DOI 10.1038/S41564-019-0530-6 REMARK 2 REMARK 2 RESOLUTION. 5.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EMAN2, CTFFIND, 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) : 5.400 REMARK 3 NUMBER OF PARTICLES : 3816 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: VERY LARGE ANISOTROPY IN RESOLUTION REMARK 4 REMARK 4 6RGL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101882. 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 : CRYO-EM STRUCTURE OF THE ANTI REMARK 245 -FEEDING PROPHAGE (AFP) REMARK 245 BASEPLATE IN CONTRACTED STATE 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 : 7.00 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 : FEI FALCON II (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) : 27.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 24-MERIC REMARK 350 SOFTWARE USED: UCSF CHIMERA 1.11.2_B41362. REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, C, D 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 0.500000 -0.866025 0.000000 -0.00010 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -0.00004 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00010 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 -0.00003 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00017 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00011 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 -0.00025 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00003 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 0.866025 0.000000 0.00008 REMARK 350 BIOMT2 5 -0.866025 -0.500000 0.000000 -0.00008 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -0.00010 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 -0.00021 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 0.00008 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00012 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 B 1 REMARK 465 THR B 2 REMARK 465 VAL B 3 REMARK 465 ILE B 352 REMARK 465 ALA B 353 REMARK 465 GLN B 354 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 VAL A 3 REMARK 465 ILE A 352 REMARK 465 ALA A 353 REMARK 465 GLN A 354 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 THR C 3 REMARK 465 SER C 66 REMARK 465 SER C 67 REMARK 465 ALA C 68 REMARK 465 ARG C 69 REMARK 465 VAL C 70 REMARK 465 THR C 71 REMARK 465 VAL C 72 REMARK 465 SER C 73 REMARK 465 SER C 74 REMARK 465 THR C 75 REMARK 465 ALA C 76 REMARK 465 VAL C 77 REMARK 465 GLU C 78 REMARK 465 PRO C 79 REMARK 465 SER C 80 REMARK 465 PRO C 81 REMARK 465 GLU C 82 REMARK 465 PHE C 83 REMARK 465 ASP C 84 REMARK 465 ALA C 85 REMARK 465 LEU C 86 REMARK 465 GLU C 87 REMARK 465 THR C 88 REMARK 465 ALA C 89 REMARK 465 SER C 90 REMARK 465 SER C 91 REMARK 465 LYS C 92 REMARK 465 ALA C 93 REMARK 465 THR C 94 REMARK 465 THR C 95 REMARK 465 THR C 96 REMARK 465 TYR C 97 REMARK 465 THR C 98 REMARK 465 TYR C 99 REMARK 465 GLN C 100 REMARK 465 ILE C 101 REMARK 465 ASP C 102 REMARK 465 ASP C 103 REMARK 465 THR C 104 REMARK 465 GLU C 105 REMARK 465 VAL C 106 REMARK 465 VAL C 107 REMARK 465 ASP C 108 REMARK 465 ARG C 217 REMARK 465 LYS C 218 REMARK 465 LEU C 219 REMARK 465 ASP C 220 REMARK 465 ASP C 221 REMARK 465 ALA C 222 REMARK 465 GLU C 223 REMARK 465 VAL C 224 REMARK 465 ALA C 225 REMARK 465 ILE C 226 REMARK 465 ASP C 227 REMARK 465 GLY C 228 REMARK 465 TYR C 229 REMARK 465 LEU C 230 REMARK 465 ASP C 231 REMARK 465 ASP C 232 REMARK 465 GLU C 233 REMARK 465 GLY C 234 REMARK 465 LYS C 235 REMARK 465 ALA C 236 REMARK 465 VAL C 237 REMARK 465 THR C 238 REMARK 465 THR C 239 REMARK 465 LEU C 240 REMARK 465 ALA C 241 REMARK 465 ALA C 242 REMARK 465 LEU C 243 REMARK 465 ARG C 244 REMARK 465 VAL C 245 REMARK 465 VAL C 246 REMARK 465 ASN C 247 REMARK 465 THR C 248 REMARK 465 GLU C 249 REMARK 465 PHE C 250 REMARK 465 ALA C 251 REMARK 465 GLY C 252 REMARK 465 GLU C 253 REMARK 465 ILE C 254 REMARK 465 ALA C 255 REMARK 465 GLN C 256 REMARK 465 SER C 257 REMARK 465 LEU C 258 REMARK 465 SER C 259 REMARK 465 GLY C 260 REMARK 465 ASP C 261 REMARK 465 LEU C 262 REMARK 465 SER C 263 REMARK 465 MET C 449 REMARK 465 SER C 450 REMARK 465 GLN C 451 REMARK 465 MET D 1 REMARK 465 ASP D 36 REMARK 465 THR D 37 REMARK 465 ALA D 38 REMARK 465 ILE D 39 REMARK 465 SER D 133 REMARK 465 SER D 134 REMARK 465 THR D 135 REMARK 465 SER D 136 REMARK 465 LEU D 137 REMARK 465 SER D 138 REMARK 465 ALA D 139 REMARK 465 GLU D 140 REMARK 465 GLY D 141 REMARK 465 VAL D 142 REMARK 465 ASP D 143 REMARK 465 ALA D 144 REMARK 465 ALA D 145 REMARK 465 GLU D 146 REMARK 465 VAL D 147 REMARK 465 GLY D 407 REMARK 465 THR D 408 REMARK 465 ALA D 409 REMARK 465 SER D 410 REMARK 465 ALA D 411 REMARK 465 GLN D 412 REMARK 465 THR D 413 REMARK 465 GLY D 414 REMARK 465 GLY D 415 REMARK 465 GLN D 416 REMARK 465 SER D 417 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 O SER C 326 NE2 GLN D 268 2.05 REMARK 500 OG SER C 23 NE2 HIS D 378 2.16 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 PHE B 272 C GLU B 273 N -0.183 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 THR B 61 C - N - CA ANGL. DEV. = 19.7 DEGREES REMARK 500 LEU D 96 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 ASP D 116 CB - CG - OD1 ANGL. DEV. = 5.6 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 ALA B 16 -62.91 -98.22 REMARK 500 SER B 24 -73.24 -63.91 REMARK 500 THR B 27 -14.79 72.37 REMARK 500 HIS B 77 33.58 -93.88 REMARK 500 GLN B 96 -60.47 -93.07 REMARK 500 ALA B 106 51.67 -94.25 REMARK 500 LYS B 136 70.67 56.06 REMARK 500 ALA B 141 -152.88 -158.94 REMARK 500 GLU B 145 6.13 -69.06 REMARK 500 PHE B 159 72.80 58.13 REMARK 500 PRO B 161 -4.43 -55.95 REMARK 500 LEU B 165 72.17 57.63 REMARK 500 PRO B 194 74.84 -69.81 REMARK 500 VAL B 208 -72.02 -80.85 REMARK 500 SER B 209 -176.97 176.95 REMARK 500 LYS B 220 -158.58 -139.88 REMARK 500 ALA B 221 53.49 -115.29 REMARK 500 THR B 233 41.61 38.69 REMARK 500 TRP B 236 117.28 -161.23 REMARK 500 ARG B 239 138.14 -171.87 REMARK 500 ARG B 248 -167.54 -123.84 REMARK 500 TYR B 249 71.90 60.05 REMARK 500 THR B 304 67.91 36.79 REMARK 500 MET B 319 70.88 46.01 REMARK 500 THR B 320 -166.15 -72.06 REMARK 500 SER A 24 -74.77 -64.86 REMARK 500 THR A 27 -16.53 73.79 REMARK 500 ASP A 99 14.62 -140.55 REMARK 500 LYS A 136 71.91 60.23 REMARK 500 LYS A 142 75.26 52.34 REMARK 500 PHE A 159 75.20 59.44 REMARK 500 PRO A 161 0.81 -60.34 REMARK 500 TRP A 162 70.28 59.58 REMARK 500 LEU A 165 74.50 58.44 REMARK 500 PRO A 194 78.01 -68.91 REMARK 500 VAL A 208 -75.54 -83.59 REMARK 500 SER A 209 -172.55 174.59 REMARK 500 THR A 233 37.15 39.78 REMARK 500 ARG A 248 -167.51 -125.87 REMARK 500 TYR A 249 77.36 60.26 REMARK 500 SER A 276 -166.65 -126.48 REMARK 500 THR A 304 79.60 42.07 REMARK 500 PRO A 305 1.76 -62.14 REMARK 500 MET A 319 74.28 48.44 REMARK 500 ALA C 28 -158.28 -162.27 REMARK 500 VAL C 29 79.24 47.68 REMARK 500 ASN C 191 -159.85 -151.41 REMARK 500 ALA C 292 -50.37 -127.45 REMARK 500 LYS C 317 56.96 39.31 REMARK 500 ASN C 372 37.51 -96.40 REMARK 500 REMARK 500 THIS ENTRY HAS 78 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN B 23 SER B 24 -149.64 REMARK 500 TYR B 160 PRO B 161 -144.00 REMARK 500 TRP B 247 ARG B 248 142.11 REMARK 500 THR B 304 PRO B 305 -145.85 REMARK 500 TRP B 309 PHE B 310 145.91 REMARK 500 TYR A 160 PRO A 161 -143.45 REMARK 500 LYS A 220 ALA A 221 -149.32 REMARK 500 LYS C 317 GLY C 318 -147.06 REMARK 500 GLN D 17 ALA D 18 -145.25 REMARK 500 ASN D 20 ASP D 21 -148.93 REMARK 500 GLY D 88 LYS D 89 -148.80 REMARK 500 ASN D 293 GLU D 294 -149.58 REMARK 500 TRP D 299 ARG D 300 147.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-4783 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-4782 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-4800 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-4784 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-4801 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-4802 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-4803 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-4859 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-4871 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-4876 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE ANTI-FEEDING PROPHAGE (AFP) BASEPLATE IN REMARK 900 CONTRACTED STATE DBREF 6RGL B 1 354 UNP Q6HAD7 Q6HAD7_9GAMM 1 354 DBREF 6RGL A 1 354 UNP Q6HAD7 Q6HAD7_9GAMM 1 354 DBREF 6RGL C 1 451 UNP Q6HAD6 Q6HAD6_9GAMM 1 451 DBREF 6RGL D 1 417 UNP Q6HAD5 Q6HAD5_9GAMM 1 417 SEQRES 1 B 354 MET THR VAL THR THR THR TYR PRO GLY VAL TYR LEU SER SEQRES 2 B 354 GLU ASP ALA VAL SER SER PHE SER VAL ASN SER ALA ALA SEQRES 3 B 354 THR ALA VAL PRO LEU PHE ALA TYR ASP SER GLU ASN THR SEQRES 4 B 354 ASN THR ILE ASN LYS PRO ILE GLN VAL PHE ARG ASN TRP SEQRES 5 B 354 ALA GLU PHE THR VAL GLU TYR PRO THR PRO LEU GLU ASP SEQRES 6 B 354 ALA PHE TYR THR SER LEU SER LEU TRP PHE MET HIS GLY SEQRES 7 B 354 GLY GLY LYS CYS TYR LEU VAL ASN GLU ALA ASN ILE ALA SEQRES 8 B 354 ASP ALA VAL ALA GLN TYR ASP ASP ILE THR LEU ILE VAL SEQRES 9 B 354 ALA ALA GLY THR ASP THR THR THR TYR THR ALA PHE THR SEQRES 10 B 354 THR VAL VAL GLY GLN GLY TYR ARG ILE PHE GLY LEU PHE SEQRES 11 B 354 ASP GLY PRO LYS GLU LYS ILE ALA GLY THR ALA LYS PRO SEQRES 12 B 354 ASP GLU VAL MET GLU GLU TYR PRO THR SER PRO PHE GLY SEQRES 13 B 354 ALA VAL PHE TYR PRO TRP GLY THR LEU ALA SER GLY ALA SEQRES 14 B 354 ALA VAL PRO PRO SER ALA ILE ALA ALA ALA SER ILE THR SEQRES 15 B 354 GLN THR ASP ARG THR ARG GLY VAL TRP LYS ALA PRO ALA SEQRES 16 B 354 ASN GLN ALA VAL ASN GLY VAL THR PRO ALA PHE ALA VAL SEQRES 17 B 354 SER ASP ASP PHE GLN GLY LYS TYR ASN GLN GLY LYS ALA SEQRES 18 B 354 LEU ASN MET ILE ARG THR PHE SER GLY GLN GLY THR VAL SEQRES 19 B 354 VAL TRP GLY ALA ARG THR LEU GLU ASP SER ASP ASN TRP SEQRES 20 B 354 ARG TYR ILE PRO VAL ARG ARG LEU PHE ASN ALA VAL GLU SEQRES 21 B 354 ARG ASP ILE GLN LYS SER LEU ASN LYS LEU VAL PHE GLU SEQRES 22 B 354 PRO ASN SER GLN PRO THR TRP GLN ARG VAL LYS ALA ALA SEQRES 23 B 354 VAL ASP SER TYR LEU HIS SER LEU TRP GLN GLN GLY ALA SEQRES 24 B 354 LEU ALA GLY ASN THR PRO ALA ASP ALA TRP PHE VAL GLN SEQRES 25 B 354 VAL GLY LYS ASP LEU THR MET THR GLN GLU GLU ILE ASN SEQRES 26 B 354 GLN GLY LYS MET ILE ILE LYS ILE GLY LEU ALA ALA VAL SEQRES 27 B 354 ARG PRO ALA GLU PHE ILE ILE LEU GLN PHE SER GLN ASP SEQRES 28 B 354 ILE ALA GLN SEQRES 1 A 354 MET THR VAL THR THR THR TYR PRO GLY VAL TYR LEU SER SEQRES 2 A 354 GLU ASP ALA VAL SER SER PHE SER VAL ASN SER ALA ALA SEQRES 3 A 354 THR ALA VAL PRO LEU PHE ALA TYR ASP SER GLU ASN THR SEQRES 4 A 354 ASN THR ILE ASN LYS PRO ILE GLN VAL PHE ARG ASN TRP SEQRES 5 A 354 ALA GLU PHE THR VAL GLU TYR PRO THR PRO LEU GLU ASP SEQRES 6 A 354 ALA PHE TYR THR SER LEU SER LEU TRP PHE MET HIS GLY SEQRES 7 A 354 GLY GLY LYS CYS TYR LEU VAL ASN GLU ALA ASN ILE ALA SEQRES 8 A 354 ASP ALA VAL ALA GLN TYR ASP ASP ILE THR LEU ILE VAL SEQRES 9 A 354 ALA ALA GLY THR ASP THR THR THR TYR THR ALA PHE THR SEQRES 10 A 354 THR VAL VAL GLY GLN GLY TYR ARG ILE PHE GLY LEU PHE SEQRES 11 A 354 ASP GLY PRO LYS GLU LYS ILE ALA GLY THR ALA LYS PRO SEQRES 12 A 354 ASP GLU VAL MET GLU GLU TYR PRO THR SER PRO PHE GLY SEQRES 13 A 354 ALA VAL PHE TYR PRO TRP GLY THR LEU ALA SER GLY ALA SEQRES 14 A 354 ALA VAL PRO PRO SER ALA ILE ALA ALA ALA SER ILE THR SEQRES 15 A 354 GLN THR ASP ARG THR ARG GLY VAL TRP LYS ALA PRO ALA SEQRES 16 A 354 ASN GLN ALA VAL ASN GLY VAL THR PRO ALA PHE ALA VAL SEQRES 17 A 354 SER ASP ASP PHE GLN GLY LYS TYR ASN GLN GLY LYS ALA SEQRES 18 A 354 LEU ASN MET ILE ARG THR PHE SER GLY GLN GLY THR VAL SEQRES 19 A 354 VAL TRP GLY ALA ARG THR LEU GLU ASP SER ASP ASN TRP SEQRES 20 A 354 ARG TYR ILE PRO VAL ARG ARG LEU PHE ASN ALA VAL GLU SEQRES 21 A 354 ARG ASP ILE GLN LYS SER LEU ASN LYS LEU VAL PHE GLU SEQRES 22 A 354 PRO ASN SER GLN PRO THR TRP GLN ARG VAL LYS ALA ALA SEQRES 23 A 354 VAL ASP SER TYR LEU HIS SER LEU TRP GLN GLN GLY ALA SEQRES 24 A 354 LEU ALA GLY ASN THR PRO ALA ASP ALA TRP PHE VAL GLN SEQRES 25 A 354 VAL GLY LYS ASP LEU THR MET THR GLN GLU GLU ILE ASN SEQRES 26 A 354 GLN GLY LYS MET ILE ILE LYS ILE GLY LEU ALA ALA VAL SEQRES 27 A 354 ARG PRO ALA GLU PHE ILE ILE LEU GLN PHE SER GLN ASP SEQRES 28 A 354 ILE ALA GLN SEQRES 1 C 451 MET ALA THR VAL THR SER VAL PRO GLY VAL TYR ILE GLU SEQRES 2 C 451 GLU ASP ALA SER PRO ALA MET SER VAL SER ALA SER ALA SEQRES 3 C 451 THR ALA VAL PRO LEU PHE VAL ALA ARG PHE THR PRO LEU SEQRES 4 C 451 LYS PRO GLU LEU ALA GLY VAL ILE THR ARG ILE GLY SER SEQRES 5 C 451 TRP LEU ASP TYR THR ILE LEU PHE ASP SER ASN VAL PRO SEQRES 6 C 451 SER SER ALA ARG VAL THR VAL SER SER THR ALA VAL GLU SEQRES 7 C 451 PRO SER PRO GLU PHE ASP ALA LEU GLU THR ALA SER SER SEQRES 8 C 451 LYS ALA THR THR THR TYR THR TYR GLN ILE ASP ASP THR SEQRES 9 C 451 GLU VAL VAL ASP PRO THR ALA SER VAL ALA LEU ARG LEU SEQRES 10 C 451 TYR PHE GLN ASN GLY GLY GLY PRO CYS TYR LEU TYR PRO SEQRES 11 C 451 LEU GLU LYS ALA ASP ASP ASN GLY PRO LEU ALA ALA LEU SEQRES 12 C 451 PRO ASP LEU ILE ASP GLU VAL GLY GLU ILE THR LEU LEU SEQRES 13 C 451 ALA SER PRO ASP PRO ASP GLU THR TYR ARG THR ALA VAL SEQRES 14 C 451 TYR GLY ALA LEU ALA ALA SER LEU ASP GLN HIS LYS GLY SEQRES 15 C 451 TYR PHE LEU LEU ALA ASP SER VAL ASN GLY ASP ALA PRO SEQRES 16 C 451 SER ALA VAL GLY GLY SER ALA GLN VAL ALA VAL TYR TYR SEQRES 17 C 451 PRO ASN VAL GLU VAL PRO HIS THR ARG LYS LEU ASP ASP SEQRES 18 C 451 ALA GLU VAL ALA ILE ASP GLY TYR LEU ASP ASP GLU GLY SEQRES 19 C 451 LYS ALA VAL THR THR LEU ALA ALA LEU ARG VAL VAL ASN SEQRES 20 C 451 THR GLU PHE ALA GLY GLU ILE ALA GLN SER LEU SER GLY SEQRES 21 C 451 ASP LEU SER ALA PRO LEU SER LEU PRO PRO SER ALA LEU SEQRES 22 C 451 ILE ALA GLY VAL TYR GLY LYS THR ASP GLY GLU ARG GLY SEQRES 23 C 451 VAL TRP LYS ALA PRO ALA ASN VAL VAL LEU ASN GLY VAL SEQRES 24 C 451 SER ASP VAL SER VAL ARG VAL THR ASN GLU GLN GLN ALA SEQRES 25 C 451 GLU LEU ASN PRO LYS GLY ILE ASN VAL ILE ARG HIS PHE SEQRES 26 C 451 SER ASP ARG GLY LEU VAL VAL TRP GLY SER ARG THR GLN SEQRES 27 C 451 LYS ASP ASP ASP ASP TRP ARG TYR ILE PRO VAL ARG ARG SEQRES 28 C 451 LEU PHE ASP ALA ALA GLU ARG ASP ILE LYS LYS ALA LEU SEQRES 29 C 451 GLN PRO MET VAL PHE GLU PRO ASN SER GLN LEU THR TRP SEQRES 30 C 451 LYS ARG VAL GLN THR ALA ILE ASP ASN TYR LEU TYR ARG SEQRES 31 C 451 LEU TRP GLN GLN GLY ALA LEU ALA GLY ASN LYS ALA GLU SEQRES 32 C 451 GLU ALA TYR PHE VAL ARG VAL GLY LYS GLY ILE THR MET SEQRES 33 C 451 THR GLN ASP GLU ILE ASN GLN GLY LYS MET ILE ILE GLN SEQRES 34 C 451 VAL GLY MET ALA ALA VAL ARG PRO ALA GLU PHE ILE ILE SEQRES 35 C 451 LEU LYS PHE THR GLN ASP MET SER GLN SEQRES 1 D 417 MET THR MET VAL LEU PRO GLY VAL SER TYR ASN GLU THR SEQRES 2 D 417 LEU LEU THR GLN ALA SER ASN ASP ASP PRO VAL THR MET SEQRES 3 D 417 PRO LEU PHE ILE GLY TYR THR PRO PRO ASP THR ALA ILE SEQRES 4 D 417 PRO VAL THR VAL MET GLN PRO VAL SER VAL GLY SER LEU SEQRES 5 D 417 THR GLN ALA ASN SER LEU PHE GLY GLN ARG GLY THR LEU SEQRES 6 D 417 ALA TYR SER LEU ARG HIS PHE PHE GLU ASN GLY GLY LEU SEQRES 7 D 417 GLN CYS TYR VAL LEU PRO LEU GLY PRO GLY LYS GLY GLU SEQRES 8 D 417 PRO ALA ALA ARG LEU GLN GLU LEU ILE ALA ALA LEU GLN SEQRES 9 D 417 THR PRO GLN MET LEU GLU THR LEU LEU ALA ASP ASP LYS SEQRES 10 D 417 THR GLY LEU VAL LEU VAL PRO GLU LEU SER GLU LEU ASN SEQRES 11 D 417 GLU VAL SER SER THR SER LEU SER ALA GLU GLY VAL ASP SEQRES 12 D 417 ALA ALA GLU VAL ASP ALA ASP ALA LEU TRP TYR GLN GLY SEQRES 13 D 417 TRP GLN VAL LEU LEU THR LEU CYS ARG GLN ALA PRO GLN SEQRES 14 D 417 ARG PHE ALA LEU LEU GLU LEU PRO GLU ASP PRO ALA SER SEQRES 15 D 417 ALA VAL THR LEU THR GLN GLN SER PHE SER ALA ASP GLN SEQRES 16 D 417 CYS GLN ARG GLY ALA ALA TRP TRP PRO ARG LEU GLU THR SEQRES 17 D 417 SER TYR GLN ASP GLU SER SER ALA PRO VAL VAL LEU SER SEQRES 18 D 417 PRO LEU PRO ALA VAL ALA ALA ALA ILE GLN ARG SER ALA SEQRES 19 D 417 HIS ASP ASN GLY VAL TRP LYS ALA PRO ALA ASN ILE ALA SEQRES 20 D 417 LEU ALA LYS THR ARG ARG PRO THR GLN SER ILE LEU THR SEQRES 21 D 417 SER GLN ALA LEU LEU ASP ASN GLN GLY VAL SER CYS ASN SEQRES 22 D 417 LEU ILE ARG SER PHE VAL GLY LYS GLY VAL ARG LEU TRP SEQRES 23 D 417 GLY CYS ARG THR LEU LEU ASN GLU GLU ASN THR ALA TRP SEQRES 24 D 417 ARG TYR ILE GLN ILE ARG LEU LEU VAL SER SER VAL GLU SEQRES 25 D 417 HIS TYR LEU SER LYS LEU ALA ARG ALA TYR LEU PHE GLU SEQRES 26 D 417 PRO ASN THR ALA PRO THR TRP MET LYS LEU LYS GLY GLN SEQRES 27 D 417 VAL TRP THR TRP LEU ARG GLN GLN TRP LEU ALA GLY ALA SEQRES 28 D 417 PHE PHE GLY THR VAL GLU ASP GLU ALA PHE SER LEU SER SEQRES 29 D 417 ILE GLY LEU ASP GLU THR MET THR GLU ASP ASP ILE ARG SEQRES 30 D 417 HIS GLY LYS MET ILE LEU GLN VAL ARG LEU ALA LEU LEU SEQRES 31 D 417 ALA PRO ALA GLU PHE ILE ALA ILE SER LEU THR LEU ASP SEQRES 32 D 417 LEU ARG ASP GLY THR ALA SER ALA GLN THR GLY GLY GLN SEQRES 33 D 417 SER HELIX 1 AA1 ASN B 51 TYR B 59 1 9 HELIX 2 AA2 ASP B 65 HIS B 77 1 13 HELIX 3 AA3 ASN B 89 ASP B 98 1 10 HELIX 4 AA4 ASP B 109 GLY B 121 1 13 HELIX 5 AA5 PRO B 172 GLY B 189 1 18 HELIX 6 AA6 ASP B 210 LYS B 215 1 6 HELIX 7 AA7 TYR B 249 VAL B 259 1 11 HELIX 8 AA8 GLU B 260 LEU B 267 1 8 HELIX 9 AA9 ASN B 268 VAL B 271 5 4 HELIX 10 AB1 SER B 276 GLN B 297 1 22 HELIX 11 AB2 THR B 320 GLN B 326 1 7 HELIX 12 AB3 ASN A 51 TYR A 59 1 9 HELIX 13 AB4 PHE A 67 HIS A 77 1 11 HELIX 14 AB5 ASN A 89 ASP A 98 1 10 HELIX 15 AB6 THR A 111 GLN A 122 1 12 HELIX 16 AB7 PRO A 172 GLY A 189 1 18 HELIX 17 AB8 TYR A 249 VAL A 259 1 11 HELIX 18 AB9 ASP A 262 LEU A 267 1 6 HELIX 19 AC1 ASN A 268 LEU A 270 5 3 HELIX 20 AC2 SER A 276 GLN A 296 1 21 HELIX 21 AC3 THR A 320 GLN A 326 1 7 HELIX 22 AC4 LYS C 40 ALA C 44 5 5 HELIX 23 AC5 TRP C 53 PHE C 60 1 8 HELIX 24 AC6 THR C 110 GLY C 122 1 13 HELIX 25 AC7 ASP C 136 ALA C 142 1 7 HELIX 26 AC8 LEU C 143 ASP C 148 1 6 HELIX 27 AC9 ASP C 162 GLY C 171 1 10 HELIX 28 AD1 LEU C 173 ASP C 178 5 6 HELIX 29 AD2 VAL C 277 ARG C 285 1 9 HELIX 30 AD3 THR C 307 ASN C 315 1 9 HELIX 31 AD4 TYR C 346 LEU C 364 1 19 HELIX 32 AD5 SER C 373 GLN C 393 1 21 HELIX 33 AD6 THR C 417 ILE C 421 5 5 HELIX 34 AD7 SER D 51 ASN D 56 1 6 HELIX 35 AD8 THR D 64 GLU D 74 1 11 HELIX 36 AD9 GLU D 91 GLN D 104 1 14 HELIX 37 AE1 MET D 108 LEU D 113 1 6 HELIX 38 AE2 LEU D 126 VAL D 132 1 7 HELIX 39 AE3 ALA D 149 ALA D 167 1 19 HELIX 40 AE4 ALA D 183 GLN D 188 1 6 HELIX 41 AE5 SER D 192 ARG D 198 1 7 HELIX 42 AE6 PRO D 222 ASN D 237 1 16 HELIX 43 AE7 SER D 257 SER D 261 5 5 HELIX 44 AE8 ILE D 302 ARG D 320 1 19 HELIX 45 AE9 THR D 328 ALA D 349 1 22 HELIX 46 AF1 THR D 372 HIS D 378 1 7 SHEET 1 AA1 5 GLN B 47 VAL B 48 0 SHEET 2 AA1 5 TYR B 83 VAL B 85 -1 O LEU B 84 N GLN B 47 SHEET 3 AA1 5 PRO B 30 ALA B 33 1 N PRO B 30 O TYR B 83 SHEET 4 AA1 5 LEU B 102 ILE B 103 1 O LEU B 102 N LEU B 31 SHEET 5 AA1 5 PHE B 127 GLY B 128 1 O PHE B 127 N ILE B 103 SHEET 1 AA2 2 TRP B 309 GLN B 312 0 SHEET 2 AA2 2 LYS B 332 LEU B 335 -1 O LYS B 332 N GLN B 312 SHEET 1 AA3 2 PRO B 340 ALA B 341 0 SHEET 2 AA3 2 GLU D 325 PRO D 326 -1 O GLU D 325 N ALA B 341 SHEET 1 AA4 3 GLN B 347 SER B 349 0 SHEET 2 AA4 3 GLN D 384 LEU D 387 1 O VAL D 385 N GLN B 347 SHEET 3 AA4 3 PHE D 361 LEU D 363 -1 N SER D 362 O ARG D 386 SHEET 1 AA5 5 GLN A 47 PHE A 49 0 SHEET 2 AA5 5 CYS A 82 VAL A 85 -1 O LEU A 84 N GLN A 47 SHEET 3 AA5 5 PRO A 30 ALA A 33 1 N PRO A 30 O TYR A 83 SHEET 4 AA5 5 LEU A 102 VAL A 104 1 O LEU A 102 N LEU A 31 SHEET 5 AA5 5 PHE A 127 LEU A 129 1 O LEU A 129 N ILE A 103 SHEET 1 AA6 2 ILE A 225 ARG A 226 0 SHEET 2 AA6 2 VAL A 234 VAL A 235 -1 O VAL A 234 N ARG A 226 SHEET 1 AA7 2 TRP A 309 GLN A 312 0 SHEET 2 AA7 2 LYS A 332 LEU A 335 -1 O GLY A 334 N PHE A 310 SHEET 1 AA8 2 PHE A 343 GLN A 350 0 SHEET 2 AA8 2 LYS C 425 MET C 432 1 O VAL C 430 N GLN A 347 SHEET 1 AA9 5 THR C 48 ILE C 50 0 SHEET 2 AA9 5 CYS C 126 LEU C 128 -1 O CYS C 126 N ILE C 50 SHEET 3 AA9 5 LEU C 31 PHE C 32 1 N PHE C 32 O TYR C 127 SHEET 4 AA9 5 LEU C 155 ALA C 157 1 O ALA C 157 N LEU C 31 SHEET 5 AA9 5 PHE C 184 LEU C 185 1 O PHE C 184 N LEU C 156 SHEET 1 AB1 2 ALA C 187 ASP C 188 0 SHEET 2 AB1 2 VAL C 206 TYR C 207 1 O TYR C 207 N ALA C 187 SHEET 1 AB2 2 VAL C 211 VAL C 213 0 SHEET 2 AB2 2 LEU C 266 LEU C 268 -1 O LEU C 268 N VAL C 211 SHEET 1 AB3 2 VAL C 321 PHE C 325 0 SHEET 2 AB3 2 GLY C 329 TRP C 333 -1 O VAL C 331 N ARG C 323 SHEET 1 AB4 5 VAL D 47 SER D 48 0 SHEET 2 AB4 5 TYR D 81 VAL D 82 -1 O VAL D 82 N VAL D 47 SHEET 3 AB4 5 PRO D 27 PHE D 29 1 N PHE D 29 O TYR D 81 SHEET 4 AB4 5 LEU D 120 LEU D 122 1 O LEU D 120 N LEU D 28 SHEET 5 AB4 5 PHE D 171 LEU D 173 1 O PHE D 171 N VAL D 121 SHEET 1 AB5 3 PRO D 217 LEU D 220 0 SHEET 2 AB5 3 LEU D 206 GLN D 211 -1 N TYR D 210 O VAL D 218 SHEET 3 AB5 3 THR D 251 PRO D 254 -1 O ARG D 253 N GLU D 207 SHEET 1 AB6 2 LEU D 274 SER D 277 0 SHEET 2 AB6 2 VAL D 283 TRP D 286 -1 O ARG D 284 N ARG D 276 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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