HEADER VIRAL PROTEIN 09-JUL-22 7YFW TITLE CYANOPHAGE PAM3 FIBER COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAM3 FIBER PROREINS; COMPND 3 CHAIN: a, b, c SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCULTURED CYANOPHAGE; SOURCE 3 ORGANISM_TAXID: 215796 KEYWDS FIBER, VIRUS, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR F.YANG,Y.L.JIANG,C.Z.ZHOU REVDAT 2 01-FEB-23 7YFW 1 JRNL REVDAT 1 18-JAN-23 7YFW 0 JRNL AUTH F.YANG,Y.L.JIANG,J.T.ZHANG,J.ZHU,K.DU,R.C.YU,Z.L.WEI, JRNL AUTH 2 W.W.KONG,N.CUI,W.F.LI,Y.CHEN,Q.LI,C.Z.ZHOU JRNL TITL FINE STRUCTURE AND ASSEMBLY PATTERN OF A MINIMAL MYOPHAGE JRNL TITL 2 PAM3. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 27120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 36656854 JRNL DOI 10.1073/PNAS.2213727120 REMARK 2 REMARK 2 RESOLUTION. 3.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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) : 3.960 REMARK 3 NUMBER OF PARTICLES : 45155 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7YFW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030832. 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 : UNCULTURED CYANOPHAGE 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 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 5000.00 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: a, b, c 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 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 ALA c 242 NZ LYS c 266 2.17 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 SER a 11 32.28 71.44 REMARK 500 LEU a 63 -5.47 67.94 REMARK 500 LEU b 6 71.06 -110.93 REMARK 500 SER b 11 61.74 60.98 REMARK 500 LEU b 63 -4.53 67.97 REMARK 500 ALA b 69 10.14 59.15 REMARK 500 ASN b 77 -0.65 65.58 REMARK 500 ASN b 239 60.43 35.71 REMARK 500 LEU c 6 71.14 -111.44 REMARK 500 LEU c 63 0.78 59.48 REMARK 500 THR c 74 -60.14 -94.66 REMARK 500 ASN c 239 61.70 34.91 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 LEU b 6 PRO b 7 146.06 REMARK 500 LEU c 6 PRO c 7 148.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33799 RELATED DB: EMDB REMARK 900 CYANOPHAGE PAM3 FIBER DBREF 7YFW a 1 280 PDB 7YFW 7YFW 1 280 DBREF 7YFW b 1 280 PDB 7YFW 7YFW 1 280 DBREF 7YFW c 1 280 PDB 7YFW 7YFW 1 280 SEQRES 1 a 280 MET ALA SER ILE ASN LEU PRO PHE SER LEU SER GLY SER SEQRES 2 a 280 LYS ARG ILE PRO THR SER GLU GLU LEU ALA ASP GLY TYR SEQRES 3 a 280 GLN CYS GLY PRO LEU ASP VAL GLU LEU ASP ASN TRP LEU SEQRES 4 a 280 MET TRP TRP LEU THR GLY GLN VAL ASP GLY VAL ILE GLU SEQRES 5 a 280 GLY ALA GLY LEU THR THR ASP ASP THR ASP LEU ALA ARG SEQRES 6 a 280 LEU TYR LYS ALA ILE GLN SER MET THR SER GLY ASN LEU SEQRES 7 a 280 ARG THR VAL VAL LEU THR ALA ALA SER GLY ASN LEU PRO SEQRES 8 a 280 ILE PRO SER ASP VAL SER VAL LEU ASN TRP VAL ARG ALA SEQRES 9 a 280 VAL GLY GLY GLY GLY ALA GLY GLY ASN SER ASN THR GLY SEQRES 10 a 280 ASN SER LYS ALA SER GLY GLY GLY GLY GLY ALA GLY PHE SEQRES 11 a 280 ASP ARG PHE ASN VAL ALA VAL THR PRO GLY SER ASN VAL SEQRES 12 a 280 PRO TYR THR VAL GLY ALA ALA GLY ALA VAL ASN GLY LEU SEQRES 13 a 280 GLY ALA GLY TYR ASN GLY GLY ALA GLY GLY SER THR ALA SEQRES 14 a 280 ILE LEU GLY THR THR ALA GLY GLY GLY ALA GLY GLY LEU SEQRES 15 a 280 GLY VAL ASN ASN ASN ALA THR ALA VAL GLN VAL ASN GLY SEQRES 16 a 280 GLY THR THR SER GLY THR THR PRO GLU ILE SER TYR PRO SEQRES 17 a 280 GLY GLY LEU GLY THR GLU GLY ILE VAL GLY THR GLY GLY SEQRES 18 a 280 GLY SER VAL LEU SER GLN PRO THR GLN ARG ALA PHE THR SEQRES 19 a 280 ASN ALA GLY ASN ASN ASN PRO ALA ASN SER TRP GLY GLY SEQRES 20 a 280 GLY GLY PRO GLY GLY SER ASP PHE GLY GLY ALA TRP GLN SEQRES 21 a 280 PRO GLY GLY VAL GLY LYS GLN GLY ILE ILE ILE VAL GLN SEQRES 22 a 280 TYR PHE SER ARG PHE ALA PRO SEQRES 1 b 280 MET ALA SER ILE ASN LEU PRO PHE SER LEU SER GLY SER SEQRES 2 b 280 LYS ARG ILE PRO THR SER GLU GLU LEU ALA ASP GLY TYR SEQRES 3 b 280 GLN CYS GLY PRO LEU ASP VAL GLU LEU ASP ASN TRP LEU SEQRES 4 b 280 MET TRP TRP LEU THR GLY GLN VAL ASP GLY VAL ILE GLU SEQRES 5 b 280 GLY ALA GLY LEU THR THR ASP ASP THR ASP LEU ALA ARG SEQRES 6 b 280 LEU TYR LYS ALA ILE GLN SER MET THR SER GLY ASN LEU SEQRES 7 b 280 ARG THR VAL VAL LEU THR ALA ALA SER GLY ASN LEU PRO SEQRES 8 b 280 ILE PRO SER ASP VAL SER VAL LEU ASN TRP VAL ARG ALA SEQRES 9 b 280 VAL GLY GLY GLY GLY ALA GLY GLY ASN SER ASN THR GLY SEQRES 10 b 280 ASN SER LYS ALA SER GLY GLY GLY GLY GLY ALA GLY PHE SEQRES 11 b 280 ASP ARG PHE ASN VAL ALA VAL THR PRO GLY SER ASN VAL SEQRES 12 b 280 PRO TYR THR VAL GLY ALA ALA GLY ALA VAL ASN GLY LEU SEQRES 13 b 280 GLY ALA GLY TYR ASN GLY GLY ALA GLY GLY SER THR ALA SEQRES 14 b 280 ILE LEU GLY THR THR ALA GLY GLY GLY ALA GLY GLY LEU SEQRES 15 b 280 GLY VAL ASN ASN ASN ALA THR ALA VAL GLN VAL ASN GLY SEQRES 16 b 280 GLY THR THR SER GLY THR THR PRO GLU ILE SER TYR PRO SEQRES 17 b 280 GLY GLY LEU GLY THR GLU GLY ILE VAL GLY THR GLY GLY SEQRES 18 b 280 GLY SER VAL LEU SER GLN PRO THR GLN ARG ALA PHE THR SEQRES 19 b 280 ASN ALA GLY ASN ASN ASN PRO ALA ASN SER TRP GLY GLY SEQRES 20 b 280 GLY GLY PRO GLY GLY SER ASP PHE GLY GLY ALA TRP GLN SEQRES 21 b 280 PRO GLY GLY VAL GLY LYS GLN GLY ILE ILE ILE VAL GLN SEQRES 22 b 280 TYR PHE SER ARG PHE ALA PRO SEQRES 1 c 280 MET ALA SER ILE ASN LEU PRO PHE SER LEU SER GLY SER SEQRES 2 c 280 LYS ARG ILE PRO THR SER GLU GLU LEU ALA ASP GLY TYR SEQRES 3 c 280 GLN CYS GLY PRO LEU ASP VAL GLU LEU ASP ASN TRP LEU SEQRES 4 c 280 MET TRP TRP LEU THR GLY GLN VAL ASP GLY VAL ILE GLU SEQRES 5 c 280 GLY ALA GLY LEU THR THR ASP ASP THR ASP LEU ALA ARG SEQRES 6 c 280 LEU TYR LYS ALA ILE GLN SER MET THR SER GLY ASN LEU SEQRES 7 c 280 ARG THR VAL VAL LEU THR ALA ALA SER GLY ASN LEU PRO SEQRES 8 c 280 ILE PRO SER ASP VAL SER VAL LEU ASN TRP VAL ARG ALA SEQRES 9 c 280 VAL GLY GLY GLY GLY ALA GLY GLY ASN SER ASN THR GLY SEQRES 10 c 280 ASN SER LYS ALA SER GLY GLY GLY GLY GLY ALA GLY PHE SEQRES 11 c 280 ASP ARG PHE ASN VAL ALA VAL THR PRO GLY SER ASN VAL SEQRES 12 c 280 PRO TYR THR VAL GLY ALA ALA GLY ALA VAL ASN GLY LEU SEQRES 13 c 280 GLY ALA GLY TYR ASN GLY GLY ALA GLY GLY SER THR ALA SEQRES 14 c 280 ILE LEU GLY THR THR ALA GLY GLY GLY ALA GLY GLY LEU SEQRES 15 c 280 GLY VAL ASN ASN ASN ALA THR ALA VAL GLN VAL ASN GLY SEQRES 16 c 280 GLY THR THR SER GLY THR THR PRO GLU ILE SER TYR PRO SEQRES 17 c 280 GLY GLY LEU GLY THR GLU GLY ILE VAL GLY THR GLY GLY SEQRES 18 c 280 GLY SER VAL LEU SER GLN PRO THR GLN ARG ALA PHE THR SEQRES 19 c 280 ASN ALA GLY ASN ASN ASN PRO ALA ASN SER TRP GLY GLY SEQRES 20 c 280 GLY GLY PRO GLY GLY SER ASP PHE GLY GLY ALA TRP GLN SEQRES 21 c 280 PRO GLY GLY VAL GLY LYS GLN GLY ILE ILE ILE VAL GLN SEQRES 22 c 280 TYR PHE SER ARG PHE ALA PRO HELIX 1 AA1 THR a 18 ASP a 24 1 7 HELIX 2 AA2 ASP a 32 ALA a 54 1 23 HELIX 3 AA3 ALA a 64 ALA a 69 1 6 HELIX 4 AA4 ILE a 70 SER a 75 1 6 HELIX 5 AA5 SER b 19 ASP b 24 1 6 HELIX 6 AA6 ASP b 32 GLY b 53 1 22 HELIX 7 AA7 ALA b 64 ALA b 69 1 6 HELIX 8 AA8 ALA b 69 SER b 75 1 7 HELIX 9 AA9 THR c 18 ASP c 24 1 7 HELIX 10 AB1 ASP c 32 ALA c 54 1 23 HELIX 11 AB2 ALA c 64 ALA c 69 1 6 HELIX 12 AB3 ILE c 70 SER c 75 1 6 SHEET 1 AA1 4 LEU a 78 LEU a 83 0 SHEET 2 AA1 4 ILE a 270 PHE a 275 -1 O ILE a 270 N LEU a 83 SHEET 3 AA1 4 VAL a 98 VAL a 105 -1 N ARG a 103 O ILE a 271 SHEET 4 AA1 4 VAL a 135 ALA a 136 -1 O VAL a 135 N LEU a 99 SHEET 1 AA2 5 LEU a 78 LEU a 83 0 SHEET 2 AA2 5 ILE a 270 PHE a 275 -1 O ILE a 270 N LEU a 83 SHEET 3 AA2 5 VAL a 98 VAL a 105 -1 N ARG a 103 O ILE a 271 SHEET 4 AA2 5 GLY a 129 ARG a 132 -1 O ARG a 132 N VAL a 102 SHEET 5 AA2 5 ILE a 205 TYR a 207 -1 O TYR a 207 N GLY a 129 SHEET 1 AA3 2 PRO a 91 ILE a 92 0 SHEET 2 AA3 2 GLY a 140 SER a 141 -1 O GLY a 140 N ILE a 92 SHEET 1 AA4 3 THR a 168 ILE a 170 0 SHEET 2 AA4 3 THR a 173 ALA a 175 -1 O ALA a 175 N THR a 168 SHEET 3 AA4 3 THR a 198 GLY a 200 -1 O SER a 199 N THR a 174 SHEET 1 AA5 4 VAL b 81 LEU b 83 0 SHEET 2 AA5 4 ILE b 270 GLN b 273 -1 O ILE b 270 N LEU b 83 SHEET 3 AA5 4 VAL b 98 VAL b 105 -1 N ARG b 103 O ILE b 271 SHEET 4 AA5 4 VAL b 135 ALA b 136 -1 O VAL b 135 N LEU b 99 SHEET 1 AA6 5 VAL b 81 LEU b 83 0 SHEET 2 AA6 5 ILE b 270 GLN b 273 -1 O ILE b 270 N LEU b 83 SHEET 3 AA6 5 VAL b 98 VAL b 105 -1 N ARG b 103 O ILE b 271 SHEET 4 AA6 5 GLY b 129 ARG b 132 -1 O ARG b 132 N VAL b 102 SHEET 5 AA6 5 ILE b 205 TYR b 207 -1 O TYR b 207 N GLY b 129 SHEET 1 AA7 2 SER b 87 GLY b 88 0 SHEET 2 AA7 2 TYR b 145 THR b 146 -1 O TYR b 145 N GLY b 88 SHEET 1 AA8 2 PRO b 91 ILE b 92 0 SHEET 2 AA8 2 GLY b 140 SER b 141 -1 O GLY b 140 N ILE b 92 SHEET 1 AA9 3 THR b 168 ILE b 170 0 SHEET 2 AA9 3 THR b 173 ALA b 175 -1 O ALA b 175 N THR b 168 SHEET 3 AA9 3 THR b 198 GLY b 200 -1 O SER b 199 N THR b 174 SHEET 1 AB1 2 ASP b 254 PHE b 255 0 SHEET 2 AB1 2 ALA b 258 TRP b 259 -1 O ALA b 258 N PHE b 255 SHEET 1 AB2 4 LEU c 78 LEU c 83 0 SHEET 2 AB2 4 ILE c 270 PHE c 275 -1 O ILE c 270 N LEU c 83 SHEET 3 AB2 4 VAL c 98 VAL c 105 -1 N ARG c 103 O ILE c 271 SHEET 4 AB2 4 VAL c 135 ALA c 136 -1 O VAL c 135 N LEU c 99 SHEET 1 AB3 5 LEU c 78 LEU c 83 0 SHEET 2 AB3 5 ILE c 270 PHE c 275 -1 O ILE c 270 N LEU c 83 SHEET 3 AB3 5 VAL c 98 VAL c 105 -1 N ARG c 103 O ILE c 271 SHEET 4 AB3 5 GLY c 129 ARG c 132 -1 O ARG c 132 N VAL c 102 SHEET 5 AB3 5 ILE c 205 TYR c 207 -1 O TYR c 207 N GLY c 129 SHEET 1 AB4 2 PRO c 91 ILE c 92 0 SHEET 2 AB4 2 GLY c 140 SER c 141 -1 O GLY c 140 N ILE c 92 SHEET 1 AB5 3 THR c 168 ILE c 170 0 SHEET 2 AB5 3 THR c 173 ALA c 175 -1 O ALA c 175 N THR c 168 SHEET 3 AB5 3 THR c 198 GLY c 200 -1 O SER c 199 N THR c 174 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