HEADER VIRAL PROTEIN 29-JAN-24 8Y3T TITLE THE SELF-ASSEMBLED NANOTUBE OF CPC46A/Q70H COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: COAT PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EMESVIRUS ZINDERI; SOURCE 3 ORGANISM_TAXID: 329852; SOURCE 4 GENE: CP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CAPSID PROTEIN, SELF-ASSEMBLY, NANOTUBE, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.YANG,G.RAO,L.LI,L.QI,C.MA,H.ZHANG,J.GONG,B.WEI,X.E.ZHANG,G.CHEN, AUTHOR 2 S.CAO,F.LI REVDAT 1 06-NOV-24 8Y3T 0 JRNL AUTH M.YANG,G.RAO,L.LI,L.QI,C.MA,H.ZHANG,J.GONG,B.WEI,X.E.ZHANG, JRNL AUTH 2 G.CHEN,S.CAO,F.LI JRNL TITL TRANSFORMATION OF A VIRAL CAPSID FROM NANOCAGES TO NANOTUBES JRNL TITL 2 AND THEN TO HYDROGELS: REDIRECTED SELF-ASSEMBLY AND EFFECTS JRNL TITL 3 ON IMMUNOGENICITY. JRNL REF ACS NANO V. 18 13755 2024 JRNL REFN ESSN 1936-086X JRNL PMID 38752610 JRNL DOI 10.1021/ACSNANO.4C01969 REMARK 2 REMARK 2 RESOLUTION. 2.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 2.610 REMARK 3 NUMBER OF PARTICLES : 456045 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 8Y3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300044629. 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 : HELICAL ARRAY REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : CPC46A/Q70H 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 : 7.40 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 : JEOL CRYO ARM 300 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 THR A 69 REMARK 465 HIS A 70 REMARK 465 THR A 71 REMARK 465 VAL A 72 REMARK 465 GLY A 73 REMARK 465 GLY A 74 REMARK 465 VAL A 75 REMARK 465 GLU A 76 REMARK 465 LEU A 77 REMARK 465 PRO A 78 REMARK 465 THR B 69 REMARK 465 HIS B 70 REMARK 465 THR B 71 REMARK 465 VAL B 72 REMARK 465 GLY B 73 REMARK 465 GLY B 74 REMARK 465 VAL B 75 REMARK 465 GLU B 76 REMARK 465 LEU B 77 REMARK 465 PRO B 78 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 126 -169.11 -79.93 REMARK 500 SER B 126 -169.15 -79.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8Y3N RELATED DB: PDB REMARK 900 DIFFERENT ASSEMBLY OF THE SAME PROTEIN REMARK 900 RELATED ID: EMD-38898 RELATED DB: EMDB REMARK 900 THE SELF-ASSEMBLED NANOTUBE OF CPC46A/Q70H DBREF 8Y3T A 1 129 UNP C8XPD7 C8XPD7_9VIRU 2 130 DBREF 8Y3T B 1 129 UNP C8XPD7 C8XPD7_9VIRU 2 130 SEQADV 8Y3T ALA A 46 UNP C8XPD7 CYS 47 ENGINEERED MUTATION SEQADV 8Y3T HIS A 70 UNP C8XPD7 GLN 71 ENGINEERED MUTATION SEQADV 8Y3T ALA B 46 UNP C8XPD7 CYS 47 ENGINEERED MUTATION SEQADV 8Y3T HIS B 70 UNP C8XPD7 GLN 71 ENGINEERED MUTATION SEQRES 1 A 129 ALA SER ASN PHE THR GLN PHE VAL LEU VAL ASP ASN GLY SEQRES 2 A 129 GLY THR GLY ASP VAL THR VAL ALA PRO SER ASN PHE ALA SEQRES 3 A 129 ASN GLY VAL ALA GLU TRP ILE SER SER ASN SER ARG SER SEQRES 4 A 129 GLN ALA TYR LYS VAL THR ALA SER VAL ARG GLN SER SER SEQRES 5 A 129 ALA GLN ASN ARG LYS TYR THR ILE LYS VAL GLU VAL PRO SEQRES 6 A 129 LYS VAL ALA THR HIS THR VAL GLY GLY VAL GLU LEU PRO SEQRES 7 A 129 VAL ALA ALA TRP ARG SER TYR LEU ASN MET GLU LEU THR SEQRES 8 A 129 ILE PRO ILE PHE ALA THR ASN SER ASP CYS GLU LEU ILE SEQRES 9 A 129 VAL LYS ALA MET GLN GLY LEU LEU LYS ASP GLY ASN PRO SEQRES 10 A 129 ILE PRO SER ALA ILE ALA ALA ASN SER GLY ILE TYR SEQRES 1 B 129 ALA SER ASN PHE THR GLN PHE VAL LEU VAL ASP ASN GLY SEQRES 2 B 129 GLY THR GLY ASP VAL THR VAL ALA PRO SER ASN PHE ALA SEQRES 3 B 129 ASN GLY VAL ALA GLU TRP ILE SER SER ASN SER ARG SER SEQRES 4 B 129 GLN ALA TYR LYS VAL THR ALA SER VAL ARG GLN SER SER SEQRES 5 B 129 ALA GLN ASN ARG LYS TYR THR ILE LYS VAL GLU VAL PRO SEQRES 6 B 129 LYS VAL ALA THR HIS THR VAL GLY GLY VAL GLU LEU PRO SEQRES 7 B 129 VAL ALA ALA TRP ARG SER TYR LEU ASN MET GLU LEU THR SEQRES 8 B 129 ILE PRO ILE PHE ALA THR ASN SER ASP CYS GLU LEU ILE SEQRES 9 B 129 VAL LYS ALA MET GLN GLY LEU LEU LYS ASP GLY ASN PRO SEQRES 10 B 129 ILE PRO SER ALA ILE ALA ALA ASN SER GLY ILE TYR HELIX 1 AA1 THR A 97 LEU A 112 1 16 HELIX 2 AA2 ASN A 116 ALA A 124 1 9 HELIX 3 AA3 THR B 97 LEU B 112 1 16 HELIX 4 AA4 ASN B 116 ALA B 124 1 9 SHEET 1 AA112 PHE A 7 VAL A 10 0 SHEET 2 AA112 VAL A 18 ALA A 26 -1 O VAL A 18 N VAL A 10 SHEET 3 AA112 VAL A 29 SER A 34 -1 O ILE A 33 N ALA A 21 SHEET 4 AA112 LYS A 43 ARG A 49 -1 O ALA A 46 N ALA A 30 SHEET 5 AA112 ASN A 55 PRO A 65 -1 O LYS A 61 N THR A 45 SHEET 6 AA112 ARG A 83 PRO A 93 -1 O SER A 84 N VAL A 64 SHEET 7 AA112 ARG B 83 PRO B 93 -1 O THR B 91 N TYR A 85 SHEET 8 AA112 ASN B 55 PRO B 65 -1 N VAL B 64 O SER B 84 SHEET 9 AA112 LYS B 43 ARG B 49 -1 N THR B 45 O LYS B 61 SHEET 10 AA112 VAL B 29 SER B 34 -1 N ALA B 30 O ALA B 46 SHEET 11 AA112 VAL B 18 ALA B 26 -1 N ALA B 21 O ILE B 33 SHEET 12 AA112 PHE B 7 VAL B 10 -1 N VAL B 10 O VAL B 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