HEADER VIRAL PROTEIN 08-DEC-14 3J9A OBSLTE 14-MAR-18 3J9A 6B43 TITLE BACKBONE MODEL OF THE SMALLEST CAPSID PROTEIN (SCP) OF KAPOSI'S TITLE 2 SARCOMA-ASSOCIATED HERPESVIRUS (KSHV) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN VP26 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SMALLEST CAPSID PROTEIN, SCP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 8; SOURCE 3 ORGANISM_COMMON: KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS; SOURCE 4 ORGANISM_TAXID: 37296; SOURCE 5 STRAIN: BAC16 KEYWDS CEMENTING PROTEIN, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.DAI,D.GONG,Y.XIAO,T.-T.WU,R.SUN,H.ZHOU REVDAT 5 11-APR-18 3J9A 1 OBSLTE REVDAT 4 14-MAR-18 3J9A 1 OBSLTE REVDAT 3 04-MAR-15 3J9A 1 JRNL REVDAT 2 18-FEB-15 3J9A 1 JRNL REVDAT 1 04-FEB-15 3J9A 0 JRNL AUTH X.DAI,D.GONG,Y.XIAO,T.T.WU,R.SUN,Z.H.ZHOU JRNL TITL CRYOEM AND MUTAGENESIS REVEAL THAT THE SMALLEST CAPSID JRNL TITL 2 PROTEIN CEMENTS AND STABILIZES KAPOSI'S SARCOMA-ASSOCIATED JRNL TITL 3 HERPESVIRUS CAPSID. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 E649 2015 JRNL REFN ISSN 0027-8424 JRNL PMID 25646489 JRNL DOI 10.1073/PNAS.1420317112 REMARK 2 REMARK 2 RESOLUTION. 6.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, ELITE3D, EMAN, IMIRS 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 : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : REFINEMENT PROTOCOL--RIGID BODY REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 2.060 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 6.000 REMARK 3 NUMBER OF PARTICLES : 20395 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 3J9A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000160412. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : KSHV VIRION HUMAN HERPESVIRUS 8 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL R2/1 CU-200 EM GRIDS REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOTTED MANUALLY AND PLUNGED REMARK 245 INTO LIQUID ETHANE. REMARK 245 SAMPLE BUFFER : PBS REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 01-NOV-13 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) : 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 25.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 14000 REMARK 245 CALIBRATED MAGNIFICATION : 48500 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 ARG A 83 REMARK 465 GLU A 84 REMARK 465 ARG A 85 REMARK 465 ALA A 86 REMARK 465 ASP A 87 REMARK 465 ARG A 88 REMARK 465 VAL A 89 REMARK 465 SER A 90 REMARK 465 ALA A 91 REMARK 465 ALA A 92 REMARK 465 SER A 93 REMARK 465 ALA A 94 REMARK 465 TYR A 95 REMARK 465 ASP A 96 REMARK 465 ALA A 97 REMARK 465 GLY A 98 REMARK 465 THR A 99 REMARK 465 PHE A 100 REMARK 465 THR A 101 REMARK 465 VAL A 102 REMARK 465 PRO A 103 REMARK 465 SER A 104 REMARK 465 ARG A 105 REMARK 465 PRO A 106 REMARK 465 GLY A 107 REMARK 465 PRO A 108 REMARK 465 ALA A 109 REMARK 465 SER A 110 REMARK 465 GLY A 111 REMARK 465 THR A 112 REMARK 465 THR A 113 REMARK 465 PRO A 114 REMARK 465 GLY A 115 REMARK 465 GLY A 116 REMARK 465 GLN A 117 REMARK 465 ASP A 118 REMARK 465 SER A 119 REMARK 465 LEU A 120 REMARK 465 GLY A 121 REMARK 465 VAL A 122 REMARK 465 SER A 123 REMARK 465 GLY A 124 REMARK 465 SER A 125 REMARK 465 SER A 126 REMARK 465 ILE A 127 REMARK 465 THR A 128 REMARK 465 THR A 129 REMARK 465 LEU A 130 REMARK 465 SER A 131 REMARK 465 SER A 132 REMARK 465 GLY A 133 REMARK 465 PRO A 134 REMARK 465 HIS A 135 REMARK 465 SER A 136 REMARK 465 LEU A 137 REMARK 465 SER A 138 REMARK 465 PRO A 139 REMARK 465 ALA A 140 REMARK 465 SER A 141 REMARK 465 ASP A 142 REMARK 465 ILE A 143 REMARK 465 LEU A 144 REMARK 465 THR A 145 REMARK 465 THR A 146 REMARK 465 LEU A 147 REMARK 465 SER A 148 REMARK 465 SER A 149 REMARK 465 THR A 150 REMARK 465 THR A 151 REMARK 465 GLU A 152 REMARK 465 THR A 153 REMARK 465 ALA A 154 REMARK 465 ALA A 155 REMARK 465 PRO A 156 REMARK 465 ALA A 157 REMARK 465 VAL A 158 REMARK 465 ALA A 159 REMARK 465 ASP A 160 REMARK 465 ALA A 161 REMARK 465 ARG A 162 REMARK 465 LYS A 163 REMARK 465 PRO A 164 REMARK 465 PRO A 165 REMARK 465 SER A 166 REMARK 465 GLY A 167 REMARK 465 LYS A 168 REMARK 465 LYS A 169 REMARK 465 LYS A 170 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 2 CB OG REMARK 470 ASN A 3 CB CG OD1 ND2 REMARK 470 PHE A 4 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 5 CB CG CD CE NZ REMARK 470 VAL A 6 CB CG1 CG2 REMARK 470 ARG A 7 CB CG CD NE CZ NH1 NH2 REMARK 470 ASP A 8 CB CG OD1 OD2 REMARK 470 PRO A 9 CB CG CD REMARK 470 VAL A 10 CB CG1 CG2 REMARK 470 ILE A 11 CB CG1 CG2 CD1 REMARK 470 GLN A 12 CB CG CD OE1 NE2 REMARK 470 GLU A 13 CB CG CD OE1 OE2 REMARK 470 ARG A 14 CB CG CD NE CZ NH1 NH2 REMARK 470 LEU A 15 CB CG CD1 CD2 REMARK 470 ASP A 16 CB CG OD1 OD2 REMARK 470 HIS A 17 CB CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 18 CB CG OD1 OD2 REMARK 470 TYR A 19 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 19 OH REMARK 470 ALA A 20 CB REMARK 470 HIS A 21 CB CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 22 CB CG ND1 CD2 CE1 NE2 REMARK 470 PRO A 23 CB CG CD REMARK 470 LEU A 24 CB CG CD1 CD2 REMARK 470 VAL A 25 CB CG1 CG2 REMARK 470 ALA A 26 CB REMARK 470 ARG A 27 CB CG CD NE CZ NH1 NH2 REMARK 470 MET A 28 CB CG SD CE REMARK 470 ASN A 29 CB CG OD1 ND2 REMARK 470 THR A 30 CB OG1 CG2 REMARK 470 LEU A 31 CB CG CD1 CD2 REMARK 470 ASP A 32 CB CG OD1 OD2 REMARK 470 GLN A 33 CB CG CD OE1 NE2 REMARK 470 ASN A 35 CB CG OD1 ND2 REMARK 470 MET A 36 CB CG SD CE REMARK 470 SER A 37 CB OG REMARK 470 GLN A 38 CB CG CD OE1 NE2 REMARK 470 ALA A 39 CB REMARK 470 GLU A 40 CB CG CD OE1 OE2 REMARK 470 TYR A 41 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 41 OH REMARK 470 LEU A 42 CB CG CD1 CD2 REMARK 470 VAL A 43 CB CG1 CG2 REMARK 470 GLN A 44 CB CG CD OE1 NE2 REMARK 470 LYS A 45 CB CG CD CE NZ REMARK 470 ARG A 46 CB CG CD NE CZ NH1 NH2 REMARK 470 HIS A 47 CB CG ND1 CD2 CE1 NE2 REMARK 470 TYR A 48 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 48 OH REMARK 470 LEU A 49 CB CG CD1 CD2 REMARK 470 VAL A 50 CB CG1 CG2 REMARK 470 PHE A 51 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 52 CB CG CD1 CD2 REMARK 470 ILE A 53 CB CG1 CG2 CD1 REMARK 470 ALA A 54 CB REMARK 470 HIS A 55 CB CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 56 CB CG ND1 CD2 CE1 NE2 REMARK 470 TYR A 57 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 57 OH REMARK 470 TYR A 58 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 58 OH REMARK 470 GLU A 59 CB CG CD OE1 OE2 REMARK 470 ALA A 60 CB REMARK 470 TYR A 61 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 61 OH REMARK 470 LEU A 62 CB CG CD1 CD2 REMARK 470 ARG A 63 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG A 64 CB CG CD NE CZ NH1 NH2 REMARK 470 MET A 65 CB CG SD CE REMARK 470 ILE A 68 CB CG1 CG2 CD1 REMARK 470 GLN A 69 CB CG CD OE1 NE2 REMARK 470 ARG A 70 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG A 71 CB CG CD NE CZ NH1 NH2 REMARK 470 ASP A 72 CB CG OD1 OD2 REMARK 470 HIS A 73 CB CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 74 CB CG CD1 CD2 REMARK 470 GLN A 75 CB CG CD OE1 NE2 REMARK 470 THR A 76 CB OG1 CG2 REMARK 470 LEU A 77 CB CG CD1 CD2 REMARK 470 ARG A 78 CB CG CD NE CZ NH1 NH2 REMARK 470 ASP A 79 CB CG OD1 OD2 REMARK 470 GLN A 80 CB CG CD OE1 NE2 REMARK 470 LYS A 81 CB CG CD CE NZ REMARK 470 PRO A 82 CB CG CD 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 LEU A 31 139.15 -36.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-6038 RELATED DB: EMDB REMARK 900 THE 6-ANGSTROM RESOLUTION CRYOEM STRUCTURE OF KSHV VIRION DBREF 3J9A A 1 170 UNP Q2HR63 VP26_HHV8P 1 170 SEQRES 1 A 170 MET SER ASN PHE LYS VAL ARG ASP PRO VAL ILE GLN GLU SEQRES 2 A 170 ARG LEU ASP HIS ASP TYR ALA HIS HIS PRO LEU VAL ALA SEQRES 3 A 170 ARG MET ASN THR LEU ASP GLN GLY ASN MET SER GLN ALA SEQRES 4 A 170 GLU TYR LEU VAL GLN LYS ARG HIS TYR LEU VAL PHE LEU SEQRES 5 A 170 ILE ALA HIS HIS TYR TYR GLU ALA TYR LEU ARG ARG MET SEQRES 6 A 170 GLY GLY ILE GLN ARG ARG ASP HIS LEU GLN THR LEU ARG SEQRES 7 A 170 ASP GLN LYS PRO ARG GLU ARG ALA ASP ARG VAL SER ALA SEQRES 8 A 170 ALA SER ALA TYR ASP ALA GLY THR PHE THR VAL PRO SER SEQRES 9 A 170 ARG PRO GLY PRO ALA SER GLY THR THR PRO GLY GLY GLN SEQRES 10 A 170 ASP SER LEU GLY VAL SER GLY SER SER ILE THR THR LEU SEQRES 11 A 170 SER SER GLY PRO HIS SER LEU SER PRO ALA SER ASP ILE SEQRES 12 A 170 LEU THR THR LEU SER SER THR THR GLU THR ALA ALA PRO SEQRES 13 A 170 ALA VAL ALA ASP ALA ARG LYS PRO PRO SER GLY LYS LYS SEQRES 14 A 170 LYS HELIX 1 1 ARG A 14 TYR A 19 1 6 HELIX 2 2 HIS A 22 LEU A 31 1 10 HELIX 3 3 GLN A 38 GLY A 66 1 29 HELIX 4 4 GLN A 69 LYS A 81 1 13 CISPEP 1 SER A 37 GLN A 38 0 -13.98 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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