HEADER VIRAL PROTEIN 18-AUG-23 8KGE TITLE DIMERIC TAIL TUBE PROTEIN GPVS OF BACTERIOPHAGE LAMBDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAIL TUBE PROTEIN; COMPND 3 CHAIN: V, v; COMPND 4 SYNONYM: TTP,GENE PRODUCT V,GPV,MAJOR TAIL PROTEIN V; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE LAMBDA; SOURCE 3 ORGANISM_TAXID: 2681611; SOURCE 4 GENE: V, LAMBDAP13; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BACTERIOPHAGE, CAUDOVIRALES, SIPHOVIRIDAE, TAIL COMPLEX, DELIVERY KEYWDS 2 DEVICE, PHAGE LAMBDA, CRYO-EM, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.W.WANG REVDAT 4 24-JAN-24 8KGE 1 JRNL REVDAT 3 15-NOV-23 8KGE 1 JRNL REVDAT 2 08-NOV-23 8KGE 1 JRNL REVDAT 1 18-OCT-23 8KGE 0 JRNL AUTH C.WANG,J.DUAN,Z.GU,X.GE,J.ZENG,J.WANG JRNL TITL ARCHITECTURE OF THE BACTERIOPHAGE LAMBDA TAIL. JRNL REF STRUCTURE V. 32 35 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 37918400 JRNL DOI 10.1016/J.STR.2023.10.006 REMARK 2 REMARK 2 RESOLUTION. 3.80 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 15620 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8KGE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 23-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300040398. 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 : BACTERIOPHAGE LAMBDA TAIL 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 : GATAN K3 (6K 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 : 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: V, v 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 V 1 REMARK 465 PRO V 2 REMARK 465 VAL V 3 REMARK 465 MET v 1 REMARK 465 PRO v 2 REMARK 465 VAL v 3 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 OG1 THR V 180 OG1 THR V 213 2.10 REMARK 500 OH TYR V 108 OD1 ASN V 145 2.18 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 PRO V 168 N - CD - CG ANGL. DEV. = -10.3 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 ASP V 35 54.76 -99.32 REMARK 500 PRO V 168 -168.90 -79.93 REMARK 500 ALA V 169 -106.10 63.34 REMARK 500 LYS V 175 65.65 65.03 REMARK 500 GLN V 177 -108.93 42.52 REMARK 500 PRO V 187 55.69 -67.56 REMARK 500 GLU V 188 5.88 54.97 REMARK 500 LYS V 202 -2.91 73.40 REMARK 500 MET V 212 -0.83 66.36 REMARK 500 PRO v 113 45.42 -77.55 REMARK 500 ALA v 161 -160.61 68.67 REMARK 500 ALA v 169 -102.67 28.66 REMARK 500 GLN v 177 -95.45 59.36 REMARK 500 LYS v 202 -4.25 66.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-35818 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-35824 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-35825 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-37218 RELATED DB: EMDB REMARK 900 DIMERIC TAIL TUBE PROTEIN GPVS OF BACTERIOPHAGE LAMBDA DBREF 8KGE V 1 246 UNP P03733 TUBE_LAMBD 1 246 DBREF 8KGE v 1 246 UNP P03733 TUBE_LAMBD 1 246 SEQRES 1 V 246 MET PRO VAL PRO ASN PRO THR MET PRO VAL LYS GLY ALA SEQRES 2 V 246 GLY THR THR LEU TRP VAL TYR LYS GLY SER GLY ASP PRO SEQRES 3 V 246 TYR ALA ASN PRO LEU SER ASP VAL ASP TRP SER ARG LEU SEQRES 4 V 246 ALA LYS VAL LYS ASP LEU THR PRO GLY GLU LEU THR ALA SEQRES 5 V 246 GLU SER TYR ASP ASP SER TYR LEU ASP ASP GLU ASP ALA SEQRES 6 V 246 ASP TRP THR ALA THR GLY GLN GLY GLN LYS SER ALA GLY SEQRES 7 V 246 ASP THR SER PHE THR LEU ALA TRP MET PRO GLY GLU GLN SEQRES 8 V 246 GLY GLN GLN ALA LEU LEU ALA TRP PHE ASN GLU GLY ASP SEQRES 9 V 246 THR ARG ALA TYR LYS ILE ARG PHE PRO ASN GLY THR VAL SEQRES 10 V 246 ASP VAL PHE ARG GLY TRP VAL SER SER ILE GLY LYS ALA SEQRES 11 V 246 VAL THR ALA LYS GLU VAL ILE THR ARG THR VAL LYS VAL SEQRES 12 V 246 THR ASN VAL GLY ARG PRO SER MET ALA GLU ASP ARG SER SEQRES 13 V 246 THR VAL THR ALA ALA THR GLY MET THR VAL THR PRO ALA SEQRES 14 V 246 SER THR SER VAL VAL LYS GLY GLN SER THR THR LEU THR SEQRES 15 V 246 VAL ALA PHE GLN PRO GLU GLY VAL THR ASP LYS SER PHE SEQRES 16 V 246 ARG ALA VAL SER ALA ASP LYS THR LYS ALA THR VAL SER SEQRES 17 V 246 VAL SER GLY MET THR ILE THR VAL ASN GLY VAL ALA ALA SEQRES 18 V 246 GLY LYS VAL ASN ILE PRO VAL VAL SER GLY ASN GLY GLU SEQRES 19 V 246 PHE ALA ALA VAL ALA GLU ILE THR VAL THR ALA SER SEQRES 1 v 246 MET PRO VAL PRO ASN PRO THR MET PRO VAL LYS GLY ALA SEQRES 2 v 246 GLY THR THR LEU TRP VAL TYR LYS GLY SER GLY ASP PRO SEQRES 3 v 246 TYR ALA ASN PRO LEU SER ASP VAL ASP TRP SER ARG LEU SEQRES 4 v 246 ALA LYS VAL LYS ASP LEU THR PRO GLY GLU LEU THR ALA SEQRES 5 v 246 GLU SER TYR ASP ASP SER TYR LEU ASP ASP GLU ASP ALA SEQRES 6 v 246 ASP TRP THR ALA THR GLY GLN GLY GLN LYS SER ALA GLY SEQRES 7 v 246 ASP THR SER PHE THR LEU ALA TRP MET PRO GLY GLU GLN SEQRES 8 v 246 GLY GLN GLN ALA LEU LEU ALA TRP PHE ASN GLU GLY ASP SEQRES 9 v 246 THR ARG ALA TYR LYS ILE ARG PHE PRO ASN GLY THR VAL SEQRES 10 v 246 ASP VAL PHE ARG GLY TRP VAL SER SER ILE GLY LYS ALA SEQRES 11 v 246 VAL THR ALA LYS GLU VAL ILE THR ARG THR VAL LYS VAL SEQRES 12 v 246 THR ASN VAL GLY ARG PRO SER MET ALA GLU ASP ARG SER SEQRES 13 v 246 THR VAL THR ALA ALA THR GLY MET THR VAL THR PRO ALA SEQRES 14 v 246 SER THR SER VAL VAL LYS GLY GLN SER THR THR LEU THR SEQRES 15 v 246 VAL ALA PHE GLN PRO GLU GLY VAL THR ASP LYS SER PHE SEQRES 16 v 246 ARG ALA VAL SER ALA ASP LYS THR LYS ALA THR VAL SER SEQRES 17 v 246 VAL SER GLY MET THR ILE THR VAL ASN GLY VAL ALA ALA SEQRES 18 v 246 GLY LYS VAL ASN ILE PRO VAL VAL SER GLY ASN GLY GLU SEQRES 19 v 246 PHE ALA ALA VAL ALA GLU ILE THR VAL THR ALA SER HELIX 1 AA1 GLY V 92 GLY V 103 1 12 HELIX 2 AA2 GLY v 92 GLY v 103 1 12 HELIX 3 AA3 MET v 151 SER v 156 5 6 SHEET 1 AA1 7 TRP V 36 ARG V 38 0 SHEET 2 AA1 7 THR V 16 TYR V 20 -1 N VAL V 19 O SER V 37 SHEET 3 AA1 7 ARG V 106 ARG V 111 -1 O LYS V 109 N TRP V 18 SHEET 4 AA1 7 VAL V 117 ALA V 130 -1 O PHE V 120 N TYR V 108 SHEET 5 AA1 7 THR V 138 ASN V 145 -1 O THR V 144 N TRP V 123 SHEET 6 AA1 7 ASP V 79 ALA V 85 -1 N PHE V 82 O VAL V 141 SHEET 7 AA1 7 VAL V 42 THR V 46 -1 N THR V 46 O SER V 81 SHEET 1 AA2 6 TRP V 36 ARG V 38 0 SHEET 2 AA2 6 THR V 16 TYR V 20 -1 N VAL V 19 O SER V 37 SHEET 3 AA2 6 ARG V 106 ARG V 111 -1 O LYS V 109 N TRP V 18 SHEET 4 AA2 6 VAL V 117 ALA V 130 -1 O PHE V 120 N TYR V 108 SHEET 5 AA2 6 LEU v 50 ASP v 56 -1 O LEU v 50 N ILE V 127 SHEET 6 AA2 6 THR v 70 SER v 76 -1 O SER v 76 N THR v 51 SHEET 1 AA3 2 THR V 51 ASP V 56 0 SHEET 2 AA3 2 THR V 70 SER V 76 -1 O GLY V 71 N TYR V 55 SHEET 1 AA4 4 MET V 164 VAL V 166 0 SHEET 2 AA4 4 THR V 179 PHE V 185 -1 O ALA V 184 N THR V 165 SHEET 3 AA4 4 THR V 213 GLY V 218 -1 O VAL V 216 N THR V 179 SHEET 4 AA4 4 ALA V 205 VAL V 207 -1 N THR V 206 O ASN V 217 SHEET 1 AA5 3 ARG V 196 ALA V 197 0 SHEET 2 AA5 3 GLY V 222 VAL V 229 -1 O VAL V 229 N ARG V 196 SHEET 3 AA5 3 ALA V 236 VAL V 243 -1 O ALA V 239 N ILE V 226 SHEET 1 AA6 7 TRP v 36 ARG v 38 0 SHEET 2 AA6 7 THR v 16 TYR v 20 -1 N VAL v 19 O SER v 37 SHEET 3 AA6 7 ARG v 106 ARG v 111 -1 O LYS v 109 N TRP v 18 SHEET 4 AA6 7 VAL v 117 ALA v 130 -1 O PHE v 120 N TYR v 108 SHEET 5 AA6 7 THR v 138 ASN v 145 -1 O THR v 140 N GLY v 128 SHEET 6 AA6 7 ASP v 79 ALA v 85 -1 N PHE v 82 O VAL v 141 SHEET 7 AA6 7 VAL v 42 THR v 46 -1 N THR v 46 O SER v 81 SHEET 1 AA7 4 THR v 165 VAL v 166 0 SHEET 2 AA7 4 THR v 179 ALA v 184 -1 O ALA v 184 N THR v 165 SHEET 3 AA7 4 THR v 213 GLY v 218 -1 O ILE v 214 N LEU v 181 SHEET 4 AA7 4 ALA v 205 VAL v 207 -1 N THR v 206 O ASN v 217 SHEET 1 AA8 3 PHE v 195 ALA v 197 0 SHEET 2 AA8 3 GLY v 222 SER v 230 -1 O VAL v 229 N ARG v 196 SHEET 3 AA8 3 ALA v 236 VAL v 243 -1 O ALA v 239 N ILE v 226 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