HEADER VIRUS 21-DEC-19 6TSV TITLE TAIL OF EMPTY GTA PARTICLE COMPUTED WITH HELICAL REFINEMENT, C6 TITLE 2 SYMMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAIL TUBE PROTEIN RCC01691; COMPND 3 CHAIN: B, A, C, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER CAPSULATUS DE442; SOURCE 3 ORGANISM_TAXID: 1415160 KEYWDS "HELICAL REFINEMENT", "GENE TRANSFER AGENT", "BACTERIOPHAGE", "TAIL", KEYWDS 2 VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR P.BARDY,T.FUZIK,D.HREBIK,R.PANTUCEK,J.T.BEATTY,P.PLEVKA REVDAT 1 22-JUL-20 6TSV 0 JRNL AUTH P.BARDY,T.FUZIK,D.HREBIK,R.PANTUCEK,J.THOMAS BEATTY,P.PLEVKA JRNL TITL STRUCTURE AND MECHANISM OF DNA DELIVERY OF A GENE TRANSFER JRNL TITL 2 AGENT. JRNL REF NAT COMMUN V. 11 3034 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32541663 JRNL DOI 10.1038/S41467-020-16669-9 REMARK 2 REMARK 2 RESOLUTION. 3.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, RELION, COOT, RELION, REMARK 3 RELION, RELION, RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION 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 : 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) : 3.780 REMARK 3 NUMBER OF PARTICLES : 49821 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 6TSV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1292105054. 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 : PARTICLE REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : RHODOBACTER CAPSULATUS DE442 REMARK 245 GENE TRANSFER AGENT TAIL TUBE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 20.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.80 REMARK 245 SAMPLE DETAILS : TUBULAR STRUCTURE REMARK 245 INTERCONNECTING HEAD TO BASEPLATE (HOST RECOGNITION DEVICE), REMARK 245 PARTIAL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 3114 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 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) : 42.75 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 75000 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: 24-MERIC 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 185.86688 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -49.80288 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 321.93088 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 86.26112 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 272.12800 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 272.12800 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 0.866025 0.000000 86.26112 REMARK 350 BIOMT2 5 -0.866025 -0.500000 0.000000 321.93088 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 -49.80288 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 185.86688 REMARK 350 BIOMT3 6 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 B 1 REMARK 465 ALA B 2 REMARK 465 ILE B 137 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ILE A 137 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 ILE C 137 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 ILE D 137 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 25 -164.12 -164.12 REMARK 500 SER B 46 28.49 -144.20 REMARK 500 GLN B 102 72.62 61.26 REMARK 500 ALA A 25 -164.09 -164.10 REMARK 500 SER A 46 28.49 -144.23 REMARK 500 GLN A 102 72.64 61.21 REMARK 500 ALA C 25 -164.14 -164.05 REMARK 500 SER C 46 28.52 -144.21 REMARK 500 GLN C 102 72.58 61.24 REMARK 500 ALA D 25 -164.10 -164.04 REMARK 500 SER D 46 28.44 -144.21 REMARK 500 GLN D 102 72.55 61.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-10542 RELATED DB: EMDB REMARK 900 NECK OF EMPTY GTA PARTICLE COMPUTED WITH C6 SYMMETRY REMARK 900 RELATED ID: EMD-10478 RELATED DB: EMDB REMARK 900 TAIL TUBE OF NATIVE GTA PARTICLE, HELICAL C6 SYMMETRY REMARK 900 RELATED ID: 6TOA RELATED DB: PDB REMARK 900 NECK OF EMPTY GTA PARTICLE COMPUTED WITH C6 SYMMETRY REMARK 900 RELATED ID: 6TEA RELATED DB: PDB REMARK 900 TAIL TUBE OF NATIVE GTA PARTICLE REMARK 900 RELATED ID: EMD-10592 RELATED DB: EMDB REMARK 900 WHOLE VIRION OF EMPTY GTA PARTICLE REMARK 900 RELATED ID: 6TUI RELATED DB: PDB REMARK 900 MODEL OF WHOLE VIRION OF GTA PARTICLE REMARK 900 RELATED ID: EMD-10565 RELATED DB: EMDB REMARK 900 TAIL TUBE OF NATIVE GTA PARTICLE, C3 SYMMETRY REMARK 900 RELATED ID: EMD-10566 RELATED DB: EMDB REMARK 900 TAIL OF EMPTY GTA PARTICLE COMPUTED WITH HELICAL REFINEMENT, C6 REMARK 900 SYMMETRY DBREF 6TSV B 1 137 UNP D5ATZ7 D5ATZ7_RHOCB 1 137 DBREF 6TSV A 1 137 UNP D5ATZ7 D5ATZ7_RHOCB 1 137 DBREF 6TSV C 1 137 UNP D5ATZ7 D5ATZ7_RHOCB 1 137 DBREF 6TSV D 1 137 UNP D5ATZ7 D5ATZ7_RHOCB 1 137 SEQRES 1 B 137 MET ALA ALA GLN ASN GLY LYS ASP LEU LEU ILE LYS LEU SEQRES 2 B 137 ASP LEU THR GLY SER GLY GLN PHE GLU THR ILE ALA GLY SEQRES 3 B 137 LEU ARG ALA THR ARG ILE SER PHE ASN ALA GLU THR VAL SEQRES 4 B 137 ASP VAL THR SER LEU GLU SER GLN GLY GLY TRP ARG GLU SEQRES 5 B 137 LEU LEU GLY GLY ALA GLY VAL ARG SER ALA SER ILE SER SEQRES 6 B 137 GLY ALA GLY VAL PHE LYS ASP ALA ASP THR ASP GLU ARG SEQRES 7 B 137 ALA ARG GLN ILE PHE PHE ASP GLY GLU VAL PRO GLU PHE SEQRES 8 B 137 GLN VAL ILE ILE PRO ASP PHE GLY ILE VAL GLN GLY PRO SEQRES 9 B 137 PHE MET ILE THR SER ILE ASP TYR ALA GLY SER HIS ASN SEQRES 10 B 137 GLY GLU ALA SER TYR GLU LEU ALA MET ALA SER ALA GLY SEQRES 11 B 137 ALA LEU SER PHE THR ALA ILE SEQRES 1 A 137 MET ALA ALA GLN ASN GLY LYS ASP LEU LEU ILE LYS LEU SEQRES 2 A 137 ASP LEU THR GLY SER GLY GLN PHE GLU THR ILE ALA GLY SEQRES 3 A 137 LEU ARG ALA THR ARG ILE SER PHE ASN ALA GLU THR VAL SEQRES 4 A 137 ASP VAL THR SER LEU GLU SER GLN GLY GLY TRP ARG GLU SEQRES 5 A 137 LEU LEU GLY GLY ALA GLY VAL ARG SER ALA SER ILE SER SEQRES 6 A 137 GLY ALA GLY VAL PHE LYS ASP ALA ASP THR ASP GLU ARG SEQRES 7 A 137 ALA ARG GLN ILE PHE PHE ASP GLY GLU VAL PRO GLU PHE SEQRES 8 A 137 GLN VAL ILE ILE PRO ASP PHE GLY ILE VAL GLN GLY PRO SEQRES 9 A 137 PHE MET ILE THR SER ILE ASP TYR ALA GLY SER HIS ASN SEQRES 10 A 137 GLY GLU ALA SER TYR GLU LEU ALA MET ALA SER ALA GLY SEQRES 11 A 137 ALA LEU SER PHE THR ALA ILE SEQRES 1 C 137 MET ALA ALA GLN ASN GLY LYS ASP LEU LEU ILE LYS LEU SEQRES 2 C 137 ASP LEU THR GLY SER GLY GLN PHE GLU THR ILE ALA GLY SEQRES 3 C 137 LEU ARG ALA THR ARG ILE SER PHE ASN ALA GLU THR VAL SEQRES 4 C 137 ASP VAL THR SER LEU GLU SER GLN GLY GLY TRP ARG GLU SEQRES 5 C 137 LEU LEU GLY GLY ALA GLY VAL ARG SER ALA SER ILE SER SEQRES 6 C 137 GLY ALA GLY VAL PHE LYS ASP ALA ASP THR ASP GLU ARG SEQRES 7 C 137 ALA ARG GLN ILE PHE PHE ASP GLY GLU VAL PRO GLU PHE SEQRES 8 C 137 GLN VAL ILE ILE PRO ASP PHE GLY ILE VAL GLN GLY PRO SEQRES 9 C 137 PHE MET ILE THR SER ILE ASP TYR ALA GLY SER HIS ASN SEQRES 10 C 137 GLY GLU ALA SER TYR GLU LEU ALA MET ALA SER ALA GLY SEQRES 11 C 137 ALA LEU SER PHE THR ALA ILE SEQRES 1 D 137 MET ALA ALA GLN ASN GLY LYS ASP LEU LEU ILE LYS LEU SEQRES 2 D 137 ASP LEU THR GLY SER GLY GLN PHE GLU THR ILE ALA GLY SEQRES 3 D 137 LEU ARG ALA THR ARG ILE SER PHE ASN ALA GLU THR VAL SEQRES 4 D 137 ASP VAL THR SER LEU GLU SER GLN GLY GLY TRP ARG GLU SEQRES 5 D 137 LEU LEU GLY GLY ALA GLY VAL ARG SER ALA SER ILE SER SEQRES 6 D 137 GLY ALA GLY VAL PHE LYS ASP ALA ASP THR ASP GLU ARG SEQRES 7 D 137 ALA ARG GLN ILE PHE PHE ASP GLY GLU VAL PRO GLU PHE SEQRES 8 D 137 GLN VAL ILE ILE PRO ASP PHE GLY ILE VAL GLN GLY PRO SEQRES 9 D 137 PHE MET ILE THR SER ILE ASP TYR ALA GLY SER HIS ASN SEQRES 10 D 137 GLY GLU ALA SER TYR GLU LEU ALA MET ALA SER ALA GLY SEQRES 11 D 137 ALA LEU SER PHE THR ALA ILE HELIX 1 AA1 ASN B 5 LEU B 9 5 5 HELIX 2 AA2 ALA B 73 ASP B 85 1 13 HELIX 3 AA3 ASN A 5 LEU A 9 5 5 HELIX 4 AA4 ALA A 73 ASP A 85 1 13 HELIX 5 AA5 ASN C 5 LEU C 9 5 5 HELIX 6 AA6 ALA C 73 ASP C 85 1 13 HELIX 7 AA7 ASN D 5 LEU D 9 5 5 HELIX 8 AA8 ALA D 73 ASP D 85 1 13 SHEET 1 AA1 7 PHE B 21 THR B 23 0 SHEET 2 AA1 7 LEU B 10 ASP B 14 -1 N LEU B 13 O GLU B 22 SHEET 3 AA1 7 GLU B 90 ILE B 95 -1 O GLN B 92 N LYS B 12 SHEET 4 AA1 7 GLY B 103 ALA B 113 -1 O GLY B 103 N PHE B 91 SHEET 5 AA1 7 SER B 121 SER B 128 -1 O SER B 121 N ALA B 113 SHEET 6 AA1 7 SER B 61 VAL B 69 -1 N GLY B 66 O LEU B 124 SHEET 7 AA1 7 LEU B 27 ASN B 35 -1 N SER B 33 O SER B 63 SHEET 1 AA2 4 PHE B 21 THR B 23 0 SHEET 2 AA2 4 LEU B 10 ASP B 14 -1 N LEU B 13 O GLU B 22 SHEET 3 AA2 4 GLU B 90 ILE B 95 -1 O GLN B 92 N LYS B 12 SHEET 4 AA2 4 GLY B 99 ILE B 100 -1 O GLY B 99 N ILE B 95 SHEET 1 AA3 7 PHE A 21 THR A 23 0 SHEET 2 AA3 7 LEU A 10 ASP A 14 -1 N LEU A 13 O GLU A 22 SHEET 3 AA3 7 GLU A 90 ILE A 95 -1 O GLN A 92 N LYS A 12 SHEET 4 AA3 7 GLY A 103 ALA A 113 -1 O GLY A 103 N PHE A 91 SHEET 5 AA3 7 SER A 121 SER A 128 -1 O SER A 121 N ALA A 113 SHEET 6 AA3 7 SER A 61 VAL A 69 -1 N GLY A 66 O LEU A 124 SHEET 7 AA3 7 LEU A 27 ASN A 35 -1 N SER A 33 O SER A 63 SHEET 1 AA4 4 PHE A 21 THR A 23 0 SHEET 2 AA4 4 LEU A 10 ASP A 14 -1 N LEU A 13 O GLU A 22 SHEET 3 AA4 4 GLU A 90 ILE A 95 -1 O GLN A 92 N LYS A 12 SHEET 4 AA4 4 GLY A 99 ILE A 100 -1 O GLY A 99 N ILE A 95 SHEET 1 AA5 7 PHE C 21 THR C 23 0 SHEET 2 AA5 7 LEU C 10 ASP C 14 -1 N LEU C 13 O GLU C 22 SHEET 3 AA5 7 GLU C 90 ILE C 95 -1 O GLN C 92 N LYS C 12 SHEET 4 AA5 7 GLY C 103 ALA C 113 -1 O GLY C 103 N PHE C 91 SHEET 5 AA5 7 SER C 121 SER C 128 -1 O SER C 121 N ALA C 113 SHEET 6 AA5 7 SER C 61 VAL C 69 -1 N GLY C 66 O LEU C 124 SHEET 7 AA5 7 LEU C 27 ASN C 35 -1 N SER C 33 O SER C 63 SHEET 1 AA6 4 PHE C 21 THR C 23 0 SHEET 2 AA6 4 LEU C 10 ASP C 14 -1 N LEU C 13 O GLU C 22 SHEET 3 AA6 4 GLU C 90 ILE C 95 -1 O GLN C 92 N LYS C 12 SHEET 4 AA6 4 GLY C 99 ILE C 100 -1 O GLY C 99 N ILE C 95 SHEET 1 AA7 7 PHE D 21 THR D 23 0 SHEET 2 AA7 7 LEU D 10 ASP D 14 -1 N LEU D 13 O GLU D 22 SHEET 3 AA7 7 GLU D 90 ILE D 95 -1 O GLN D 92 N LYS D 12 SHEET 4 AA7 7 GLY D 103 ALA D 113 -1 O GLY D 103 N PHE D 91 SHEET 5 AA7 7 SER D 121 SER D 128 -1 O SER D 121 N ALA D 113 SHEET 6 AA7 7 SER D 61 VAL D 69 -1 N GLY D 66 O LEU D 124 SHEET 7 AA7 7 LEU D 27 ASN D 35 -1 N SER D 33 O SER D 63 SHEET 1 AA8 4 PHE D 21 THR D 23 0 SHEET 2 AA8 4 LEU D 10 ASP D 14 -1 N LEU D 13 O GLU D 22 SHEET 3 AA8 4 GLU D 90 ILE D 95 -1 O GLN D 92 N LYS D 12 SHEET 4 AA8 4 GLY D 99 ILE D 100 -1 O GLY D 99 N ILE D 95 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