HEADER VIRUS LIKE PARTICLE 29-NOV-23 8V4N TITLE MYXOCOCCUS XANTHUS ENCA 3XHIS PORE MUTANT WITH T=1 ICOSAHEDRAL TITLE 2 SYMMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE 1 ENCAPSULIN SHELL PROTEIN ENCA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYXOCOCCUS XANTHUS; SOURCE 3 ORGANISM_TAXID: 246197; SOURCE 4 STRAIN: DK1622; SOURCE 5 GENE: ENCA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ENCAPSULIN, VIRUS LIKE PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR T.N.SZYSZKA,M.P.ANDREAS,F.LIE,L.M.MILLER,L.S.R.ADAMSON,F.FATEHI, AUTHOR 2 R.TWAROCK,B.E.DRAPER,M.F.JARROLD,T.W.GIESSEN,Y.H.LAU REVDAT 1 22-MAY-24 8V4N 0 JRNL AUTH T.N.SZYSZKA,M.P.ANDREAS,F.LIE,L.M.MILLER,L.S.R.ADAMSON, JRNL AUTH 2 F.FATEHI,R.TWAROCK,B.E.DRAPER,M.F.JARROLD,T.W.GIESSEN, JRNL AUTH 3 Y.H.LAU JRNL TITL POINT MUTATION IN A VIRUS-LIKE CAPSID DRIVES SYMMETRY JRNL TITL 2 REDUCTION TO FORM TETRAHEDRAL CAGES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 121 60121 2024 JRNL REFN ESSN 1091-6490 JRNL PMID 38722807 JRNL DOI 10.1073/PNAS.2321260121 REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, CRYOSPARC, UCSF REMARK 3 CHIMERAX, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, COOT, PHENIX 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 : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : 98.500 REMARK 3 REMARK 3 FITTING PROCEDURE : THE STARTING MODEL WAS GENERATED USING ESMFOLD REMARK 3 THEN FIT INTO THE MAP USING CHIMERAX. THE PLACED COORDINATES REMARK 3 WERE THEN MANUALLY REFINED USING COOT, FOLLOWED BY REAL SPACE REMARK 3 REFINEMENT IN PHENIX. 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) : 2.430 REMARK 3 NUMBER OF PARTICLES : 77769 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 8V4N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279519. 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 : MYXOCOCCUS XANTHUS ENCA 3XHIS REMARK 245 PORE MUTANT WITH T=1 REMARK 245 ICOSAHEDRAL SYMMETRY REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 REMARK 245 SAMPLE SUPPORT DETAILS : 5 MA FOR 60 SECONDS UNDER REMARK 245 VACUUM REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FORCE: 5 BLOT TIME: 2 REMARK 245 SECONDS REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 1475 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) : 2500.00 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) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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 PRO A 2 REMARK 465 ASP A 3 REMARK 465 PHE A 4 REMARK 465 LEU A 5 REMARK 465 VAL A 59 REMARK 465 SER A 60 REMARK 465 PRO A 61 REMARK 465 GLY A 62 REMARK 465 ALA A 63 REMARK 465 VAL A 64 REMARK 465 ASP A 65 REMARK 465 ILE A 66 REMARK 465 VAL A 67 REMARK 465 GLY A 68 REMARK 465 GLU A 69 REMARK 465 GLY A 280 REMARK 465 ALA A 281 REMARK 465 GLY A 282 REMARK 465 ALA A 283 REMARK 465 THR A 284 REMARK 465 GLU A 285 REMARK 465 ARG A 286 REMARK 465 ARG A 287 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 A 8 -173.77 59.50 REMARK 500 HIS A 199 47.18 38.57 REMARK 500 ARG A 254 -116.29 57.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-42974 RELATED DB: EMDB REMARK 900 MYXOCOCCUS XANTHUS ENCA 3XHIS PORE MUTANT WITH T=1 ICOSAHEDRAL REMARK 900 SYMMETRY DBREF 8V4N A 1 287 UNP Q1D6H4 ENCAP_MYXXD 1 287 SEQADV 8V4N HIS A 199 UNP Q1D6H4 LYS 199 ENGINEERED MUTATION SEQADV 8V4N HIS A 200 UNP Q1D6H4 THR 200 ENGINEERED MUTATION SEQADV 8V4N HIS A 201 UNP Q1D6H4 GLY 201 ENGINEERED MUTATION SEQRES 1 A 287 MET PRO ASP PHE LEU GLY HIS ALA GLU ASN PRO LEU ARG SEQRES 2 A 287 GLU GLU GLU TRP ALA ARG LEU ASN GLU THR VAL ILE GLN SEQRES 3 A 287 VAL ALA ARG ARG SER LEU VAL GLY ARG ARG ILE LEU ASP SEQRES 4 A 287 ILE TYR GLY PRO LEU GLY ALA GLY VAL GLN THR VAL PRO SEQRES 5 A 287 TYR ASP GLU PHE GLN GLY VAL SER PRO GLY ALA VAL ASP SEQRES 6 A 287 ILE VAL GLY GLU GLN GLU THR ALA MET VAL PHE THR ASP SEQRES 7 A 287 ALA ARG LYS PHE LYS THR ILE PRO ILE ILE TYR LYS ASP SEQRES 8 A 287 PHE LEU LEU HIS TRP ARG ASP ILE GLU ALA ALA ARG THR SEQRES 9 A 287 HIS ASN MET PRO LEU ASP VAL SER ALA ALA ALA GLY ALA SEQRES 10 A 287 ALA ALA LEU CYS ALA GLN GLN GLU ASP GLU LEU ILE PHE SEQRES 11 A 287 TYR GLY ASP ALA ARG LEU GLY TYR GLU GLY LEU MET THR SEQRES 12 A 287 ALA ASN GLY ARG LEU THR VAL PRO LEU GLY ASP TRP THR SEQRES 13 A 287 SER PRO GLY GLY GLY PHE GLN ALA ILE VAL GLU ALA THR SEQRES 14 A 287 ARG LYS LEU ASN GLU GLN GLY HIS PHE GLY PRO TYR ALA SEQRES 15 A 287 VAL VAL LEU SER PRO ARG LEU TYR SER GLN LEU HIS ARG SEQRES 16 A 287 ILE TYR GLU HIS HIS HIS VAL LEU GLU ILE GLU THR ILE SEQRES 17 A 287 ARG GLN LEU ALA SER ASP GLY VAL TYR GLN SER ASN ARG SEQRES 18 A 287 LEU ARG GLY GLU SER GLY VAL VAL VAL SER THR GLY ARG SEQRES 19 A 287 GLU ASN MET ASP LEU ALA VAL SER MET ASP MET VAL ALA SEQRES 20 A 287 ALA TYR LEU GLY ALA SER ARG MET ASN HIS PRO PHE ARG SEQRES 21 A 287 VAL LEU GLU ALA LEU LEU LEU ARG ILE LYS HIS PRO ASP SEQRES 22 A 287 ALA ILE CYS THR LEU GLU GLY ALA GLY ALA THR GLU ARG SEQRES 23 A 287 ARG HELIX 1 AA1 ARG A 13 LEU A 32 1 20 HELIX 2 AA2 VAL A 33 ILE A 37 5 5 HELIX 3 AA3 HIS A 95 ASN A 106 1 12 HELIX 4 AA4 VAL A 111 GLY A 132 1 22 HELIX 5 AA5 GLY A 159 GLU A 174 1 16 HELIX 6 AA6 SER A 186 LEU A 193 1 8 HELIX 7 AA7 LEU A 203 ALA A 212 1 10 HELIX 8 AA8 HIS A 271 ASP A 273 5 3 SHEET 1 AA1 4 ILE A 40 TYR A 41 0 SHEET 2 AA1 4 MET A 237 TYR A 249 1 O LEU A 239 N TYR A 41 SHEET 3 AA1 4 HIS A 257 ILE A 269 -1 O LEU A 262 N VAL A 246 SHEET 4 AA1 4 ILE A 88 LEU A 94 -1 N LYS A 90 O VAL A 261 SHEET 1 AA2 2 THR A 50 PRO A 52 0 SHEET 2 AA2 2 PHE A 82 THR A 84 -1 O LYS A 83 N VAL A 51 SHEET 1 AA3 5 LEU A 148 THR A 149 0 SHEET 2 AA3 5 ILE A 275 THR A 277 1 O ILE A 275 N LEU A 148 SHEET 3 AA3 5 GLY A 227 SER A 231 -1 N VAL A 229 O CYS A 276 SHEET 4 AA3 5 TYR A 181 LEU A 185 -1 N VAL A 184 O VAL A 228 SHEET 5 AA3 5 GLY A 215 GLN A 218 1 O GLY A 215 N VAL A 183 CISPEP 1 GLY A 42 PRO A 43 0 0.57 CISPEP 2 GLY A 179 PRO A 180 0 1.18 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