HEADER VIRAL PROTEIN 17-DEC-23 8XH6 TITLE STRUCTURE OF EBV LMP1 DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: LATENT MEMBRANE PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PROTEIN P63; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN GAMMAHERPESVIRUS 4; SOURCE 3 ORGANISM_COMMON: HHV-4, HUMAN HERPESVIRUS 4; SOURCE 4 ORGANISM_TAXID: 10376; SOURCE 5 GENE: LMP1, LMP-1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EBV LATENT MEMBRANE PROTEIN 1, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR P.GAO,J.F.HUANG REVDAT 2 31-JUL-24 8XH6 1 JRNL REVDAT 1 26-JUN-24 8XH6 0 JRNL AUTH J.HUANG,X.ZHANG,X.NIE,X.ZHANG,Y.WANG,L.HUANG,X.GENG,D.LI, JRNL AUTH 2 L.ZHANG,G.GAO,P.GAO JRNL TITL ASSEMBLY AND ACTIVATION OF EBV LATENT MEMBRANE PROTEIN 1. JRNL REF CELL 2024 JRNL REFN ISSN 1097-4172 JRNL PMID 38996527 JRNL DOI 10.1016/J.CELL.2024.06.021 REMARK 2 REMARK 2 RESOLUTION. 3.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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 : 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) : 3.520 REMARK 3 NUMBER OF PARTICLES : 505597 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 8XH6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300043504. 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 : LMP1 DIMER 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 : 7.50 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 K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 6000.00 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 TYR A 185 REMARK 465 TYR B 185 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 HIS B 101 16.36 -140.25 REMARK 500 GLN B 161 0.63 -66.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38342 RELATED DB: EMDB REMARK 900 STRUCTURE OF EBV LMP1 DIMER DBREF 8XH6 A 24 185 UNP Q7T6U2 Q7T6U2_EBVG 24 185 DBREF 8XH6 B 24 185 UNP Q7T6U2 Q7T6U2_EBVG 24 185 SEQRES 1 A 162 SER ILE GLY LEU ALA LEU LEU LEU LEU LEU LEU ALA LEU SEQRES 2 A 162 LEU PHE TRP LEU TYR ILE VAL MET SER ASN TRP THR GLY SEQRES 3 A 162 GLY ALA LEU LEU VAL LEU TYR SER PHE ALA LEU MET LEU SEQRES 4 A 162 ILE ILE ILE ILE LEU ILE ILE PHE ILE PHE ARG ARG ASP SEQRES 5 A 162 LEU LEU CYS PRO LEU GLY GLY LEU GLY LEU LEU LEU LEU SEQRES 6 A 162 MET ILE THR LEU LEU LEU ILE ALA LEU TRP ASN LEU HIS SEQRES 7 A 162 GLY GLN ALA LEU TYR LEU GLY ILE VAL LEU PHE ILE PHE SEQRES 8 A 162 GLY CYS LEU LEU VAL LEU GLY LEU TRP ILE TYR PHE LEU SEQRES 9 A 162 GLU ILE LEU TRP ARG LEU GLY ALA THR ILE TRP GLN LEU SEQRES 10 A 162 LEU ALA PHE ILE LEU ALA PHE PHE LEU ALA ILE ILE LEU SEQRES 11 A 162 LEU ILE ILE ALA LEU TYR LEU GLN GLN ASN TRP TRP THR SEQRES 12 A 162 LEU LEU VAL ASP LEU LEU TRP LEU LEU LEU PHE MET ALA SEQRES 13 A 162 ILE LEU ILE TRP MET TYR SEQRES 1 B 162 SER ILE GLY LEU ALA LEU LEU LEU LEU LEU LEU ALA LEU SEQRES 2 B 162 LEU PHE TRP LEU TYR ILE VAL MET SER ASN TRP THR GLY SEQRES 3 B 162 GLY ALA LEU LEU VAL LEU TYR SER PHE ALA LEU MET LEU SEQRES 4 B 162 ILE ILE ILE ILE LEU ILE ILE PHE ILE PHE ARG ARG ASP SEQRES 5 B 162 LEU LEU CYS PRO LEU GLY GLY LEU GLY LEU LEU LEU LEU SEQRES 6 B 162 MET ILE THR LEU LEU LEU ILE ALA LEU TRP ASN LEU HIS SEQRES 7 B 162 GLY GLN ALA LEU TYR LEU GLY ILE VAL LEU PHE ILE PHE SEQRES 8 B 162 GLY CYS LEU LEU VAL LEU GLY LEU TRP ILE TYR PHE LEU SEQRES 9 B 162 GLU ILE LEU TRP ARG LEU GLY ALA THR ILE TRP GLN LEU SEQRES 10 B 162 LEU ALA PHE ILE LEU ALA PHE PHE LEU ALA ILE ILE LEU SEQRES 11 B 162 LEU ILE ILE ALA LEU TYR LEU GLN GLN ASN TRP TRP THR SEQRES 12 B 162 LEU LEU VAL ASP LEU LEU TRP LEU LEU LEU PHE MET ALA SEQRES 13 B 162 ILE LEU ILE TRP MET TYR HELIX 1 AA1 SER A 24 SER A 45 1 22 HELIX 2 AA2 GLY A 50 PHE A 72 1 23 HELIX 3 AA3 ARG A 73 LEU A 77 5 5 HELIX 4 AA4 LEU A 80 ASN A 99 1 20 HELIX 5 AA5 GLN A 103 ARG A 132 1 30 HELIX 6 AA6 THR A 136 LEU A 160 1 25 HELIX 7 AA7 GLN A 162 TRP A 183 1 22 HELIX 8 AA8 ILE B 25 MET B 44 1 20 HELIX 9 AA9 LEU B 52 PHE B 72 1 21 HELIX 10 AB1 ARG B 73 LEU B 77 5 5 HELIX 11 AB2 LEU B 80 LEU B 100 1 21 HELIX 12 AB3 GLN B 103 LEU B 133 1 31 HELIX 13 AB4 THR B 136 LEU B 160 1 25 HELIX 14 AB5 TRP B 164 TRP B 183 1 20 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