HEADER VIRAL PROTEIN 02-AUG-22 7YP1 TITLE CRYO-EM STRUCTURE OF EBV GHGL-GP42 IN COMPLEX WITH MAB 10E4 (LOCALIZED TITLE 2 REFINEMENT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: EBV GH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: EBV GL; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 10E4 HEAVY CHAIN; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: 10E4 LIGHT CHAIN; COMPND 15 CHAIN: G; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN GAMMAHERPESVIRUS 4; SOURCE 3 ORGANISM_TAXID: 10376; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HUMAN GAMMAHERPESVIRUS 4; SOURCE 9 ORGANISM_TAXID: 10376; SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 15 ORGANISM_TAXID: 9986; SOURCE 16 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 19 MOL_ID: 4; SOURCE 20 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 21 ORGANISM_TAXID: 9986; SOURCE 22 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 24 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS EBV, CRYO-EM, GLYCOPROTEIN, GHGL-GP42 COMPLEX, ANTIBODY, VIRAL KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR L.LIU,H.SUN,Y.JIANG,J.HONG,Q.ZHENG,S.LI,Y.CHEN,N.XIA REVDAT 1 31-JAN-24 7YP1 0 JRNL AUTH J.HONG,L.ZHONG,L.LIU,Q.WU,W.ZHANG,K.CHEN,D.WEI,H.SUN,X.ZHOU, JRNL AUTH 2 X.ZHANG,Y.F.KANG,Y.HUANG,J.CHEN,G.WANG,Y.ZHOU,Y.CHEN, JRNL AUTH 3 Q.S.FENG,H.YU,S.LI,M.S.ZENG,Y.X.ZENG,M.XU,Q.ZHENG,Y.CHEN, JRNL AUTH 4 X.ZHANG,N.XIA JRNL TITL NON-OVERLAPPING EPITOPES ON THE GHGL-GP42 COMPLEX FOR THE JRNL TITL 2 RATIONAL DESIGN OF A TRIPLE-ANTIBODY COCKTAIL AGAINST EBV JRNL TITL 3 INFECTION. JRNL REF CELL REP MED V. 4 01296 2023 JRNL REFN ESSN 2666-3791 JRNL PMID 37992686 JRNL DOI 10.1016/J.XCRM.2023.101296 REMARK 2 REMARK 2 RESOLUTION. 3.54 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) : 3.540 REMARK 3 NUMBER OF PARTICLES : 402382 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 7YP1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031335. 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 : GHGL-GP42 IN COMPLEX WITH MAB REMARK 245 10E4; GH,GL; 10E4 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 : FEI TECNAI F30 REMARK 245 DETECTOR TYPE : GATAN K3 (6K 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 : 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, G 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 LEU A 160 REMARK 465 SER A 161 REMARK 465 ILE A 162 REMARK 465 ASN A 163 REMARK 465 GLY A 164 REMARK 465 ASP A 165 REMARK 465 LYS A 166 REMARK 465 PHE A 167 REMARK 465 GLN A 168 REMARK 465 VAL A 185 REMARK 465 THR A 186 REMARK 465 GLU A 187 REMARK 465 LYS A 188 REMARK 465 GLY A 189 REMARK 465 ASP A 190 REMARK 465 GLU A 191 REMARK 465 GLY B 125 REMARK 465 ALA B 126 REMARK 465 ASN B 127 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 CYS G 23 CA - CB - SG ANGL. DEV. = 8.4 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 SER A 21 -66.60 -96.55 REMARK 500 SER A 51 84.63 -156.41 REMARK 500 LYS A 73 34.52 -98.02 REMARK 500 PRO A 143 38.09 -95.30 REMARK 500 TYR A 235 30.74 -88.57 REMARK 500 SER B 96 57.15 -96.52 REMARK 500 ALA D 89 -166.91 -161.64 REMARK 500 ALA G 51 -6.05 67.96 REMARK 500 ALA G 81 52.13 -92.76 REMARK 500 ILE G 96 -68.27 -95.85 REMARK 500 ASN G 100 37.77 -144.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33992 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF EBV GHGL-GP42 IN COMPLEX WITH MAB 10E4 REMARK 900 (LOCALIZED REFINEMENT) DBREF 7YP1 A 20 255 PDB 7YP1 7YP1 20 255 DBREF 7YP1 B 40 127 PDB 7YP1 7YP1 40 127 DBREF 7YP1 D 2 116 PDB 7YP1 7YP1 2 116 DBREF 7YP1 G 1 111 PDB 7YP1 7YP1 1 111 SEQRES 1 A 201 LEU SER GLU VAL LYS LEU HIS LEU ASP ILE GLU GLY HIS SEQRES 2 A 201 ALA SER HIS TYR THR ILE PRO TRP THR GLU LEU MET ALA SEQRES 3 A 201 LYS VAL PRO GLY LEU SER PRO GLU ALA LEU TRP ARG GLU SEQRES 4 A 201 ALA ASN VAL THR GLU ASP LEU ALA SER MET LEU ASN ARG SEQRES 5 A 201 TYR LYS LEU ILE TYR LYS THR SER GLY THR LEU GLY ILE SEQRES 6 A 201 ALA LEU ALA SER ALA PRO LEU GLU LYS GLN LEU PHE TYR SEQRES 7 A 201 TYR ILE GLY THR MET LEU PRO ASN THR ARG PRO HIS SER SEQRES 8 A 201 TYR VAL PHE TYR GLN LEU ARG CYS HIS LEU SER TYR VAL SEQRES 9 A 201 ALA LEU SER ILE ASN GLY ASP LYS PHE GLN TYR THR GLY SEQRES 10 A 201 ALA MET THR SER LYS PHE LEU MET GLY THR TYR LYS ARG SEQRES 11 A 201 VAL THR GLU LYS GLY ASP GLU HIS VAL LEU SER LEU VAL SEQRES 12 A 201 PHE GLY LYS THR LYS ASP LEU PRO ASP LEU ARG GLY PRO SEQRES 13 A 201 PHE SER TYR PRO SER LEU THR SER ALA GLN SER GLY ASP SEQRES 14 A 201 TYR SER LEU VAL ILE VAL THR THR PHE VAL HIS TYR ALA SEQRES 15 A 201 ASN PHE HIS ASN TYR PHE VAL PRO ASN LEU LYS ASP MET SEQRES 16 A 201 PHE SER ARG ALA VAL THR SEQRES 1 B 80 LEU ALA LEU GLU ASN ILE SER ASP ILE TYR LEU VAL SER SEQRES 2 B 80 ASN GLN THR CYS ASP GLY PHE SER LEU ALA SER LEU ASN SEQRES 3 B 80 SER VAL ILE SER ARG CYS ALA ASN GLY LEU ASN VAL VAL SEQRES 4 B 80 SER PHE PHE ILE SER ILE LEU LYS ARG SER SER SER ALA SEQRES 5 B 80 LEU THR GLY HIS LEU ARG GLU LEU LEU THR THR LEU GLU SEQRES 6 B 80 THR LEU TYR GLY SER PHE SER VAL GLU ASP LEU PHE GLY SEQRES 7 B 80 ALA ASN SEQRES 1 D 115 GLN GLN VAL LYS GLU SER GLY GLY ARG LEU VAL THR PRO SEQRES 2 D 115 GLY THR PRO LEU THR LEU THR CYS THR ALA SER GLY PHE SEQRES 3 D 115 SER LEU SER THR TYR TRP MET SER TRP VAL ARG GLN ALA SEQRES 4 D 115 PRO GLY LYS GLY LEU GLU TYR ILE GLY VAL ILE GLY GLY SEQRES 5 D 115 SER GLY SER THR TYR TYR ALA SER TRP ALA LYS GLY ARG SEQRES 6 D 115 PHE THR ILE SER LYS THR SER THR THR VAL ASP LEU LYS SEQRES 7 D 115 ILE THR SER PRO THR THR GLU ASP THR ALA THR TYR PHE SEQRES 8 D 115 CYS ALA ARG ASP SER GLY ALA GLY VAL ARG PHE ARG PHE SEQRES 9 D 115 TRP GLY PRO GLY THR LEU VAL THR VAL SER SER SEQRES 1 G 113 ASP LEU VAL MET THR GLN THR PRO ALA SER VAL GLU ALA SEQRES 2 G 113 GLY VAL GLY GLY THR VAL THR ILE ASN CYS GLN ALA SER SEQRES 3 G 113 GLU ASN ILE GLY SER ARG LEU ALA TRP TYR GLN GLN LYS SEQRES 4 G 113 PRO GLY GLN PRO PRO LYS LEU LEU ILE TYR ARG ALA SER SEQRES 5 G 113 THR LEU GLU SER GLY VAL PRO SER ARG PHE LYS GLY SER SEQRES 6 G 113 GLY SER GLY THR GLU PHE THR LEU THR ILE SER ASP LEU SEQRES 7 G 113 GLU CYS ALA ASP ALA ALA THR TYR TYR CYS GLN CYS THR SEQRES 8 G 113 TYR GLY VAL SER ILE THR ILE ASN TYR GLY ASN ASP PHE SEQRES 9 G 113 GLY GLY GLY THR GLU VAL VAL VAL LYS HELIX 1 AA1 GLU A 42 VAL A 47 1 6 HELIX 2 AA2 SER A 51 ASN A 60 1 10 HELIX 3 AA3 SER A 67 LYS A 73 1 7 HELIX 4 AA4 ALA A 124 PHE A 131 1 8 HELIX 5 AA5 SER A 212 SER A 215 5 4 HELIX 6 AA6 ALA B 41 ILE B 45 5 5 HELIX 7 AA7 GLY B 82 LYS B 94 1 13 HELIX 8 AA8 HIS B 103 SER B 117 1 15 HELIX 9 AA9 SER B 119 LEU B 123 5 5 HELIX 10 AB1 THR D 84 THR D 88 5 5 HELIX 11 AB2 GLU G 79 ALA G 83 5 5 SHEET 1 AA1 4 HIS A 32 SER A 34 0 SHEET 2 AA1 4 LYS A 24 ILE A 29 -1 N LEU A 27 O SER A 34 SHEET 3 AA1 4 ASP B 47 VAL B 51 1 O ILE B 48 N HIS A 26 SHEET 4 AA1 4 LEU B 64 ASN B 65 -1 O ASN B 65 N ASP B 47 SHEET 1 AA2 2 GLY A 135 LEU A 138 0 SHEET 2 AA2 2 LEU A 151 CYS A 153 -1 O CYS A 153 N GLY A 135 SHEET 1 AA3 2 SER A 156 VAL A 158 0 SHEET 2 AA3 2 GLY A 171 MET A 173 -1 O GLY A 171 N VAL A 158 SHEET 1 AA4 4 PHE A 177 TYR A 182 0 SHEET 2 AA4 4 LEU A 194 LYS A 200 -1 O PHE A 198 N LEU A 178 SHEET 3 AA4 4 TYR A 224 VAL A 229 -1 O VAL A 227 N VAL A 197 SHEET 4 AA4 4 THR A 217 SER A 221 -1 N SER A 218 O LEU A 226 SHEET 1 AA5 2 LEU B 61 ALA B 62 0 SHEET 2 AA5 2 ALA B 80 ASN B 81 -1 O ALA B 80 N ALA B 62 SHEET 1 AA6 4 VAL D 4 SER D 7 0 SHEET 2 AA6 4 LEU D 18 ALA D 24 -1 O THR D 21 N SER D 7 SHEET 3 AA6 4 THR D 75 ILE D 80 -1 O LEU D 78 N LEU D 20 SHEET 4 AA6 4 PHE D 67 LYS D 71 -1 N SER D 70 O ASP D 77 SHEET 1 AA7 5 THR D 57 TYR D 59 0 SHEET 2 AA7 5 GLU D 46 ILE D 51 -1 N VAL D 50 O TYR D 58 SHEET 3 AA7 5 MET D 34 GLN D 39 -1 N ARG D 38 O GLU D 46 SHEET 4 AA7 5 THR D 90 ARG D 95 -1 O ALA D 94 N SER D 35 SHEET 5 AA7 5 PHE D 105 TRP D 106 -1 O PHE D 105 N ARG D 95 SHEET 1 AA8 4 MET G 4 THR G 7 0 SHEET 2 AA8 4 ILE G 21 ALA G 25 -1 O ASN G 22 N THR G 7 SHEET 3 AA8 4 GLU G 70 LEU G 73 -1 O PHE G 71 N CYS G 23 SHEET 4 AA8 4 GLY G 64 SER G 65 -1 N SER G 65 O THR G 72 SHEET 1 AA9 2 SER G 10 ALA G 13 0 SHEET 2 AA9 2 GLU G 107 VAL G 110 1 O GLU G 107 N VAL G 11 SHEET 1 AB1 4 THR G 53 LEU G 54 0 SHEET 2 AB1 4 LYS G 45 TYR G 49 -1 N TYR G 49 O THR G 53 SHEET 3 AB1 4 ALA G 34 GLN G 38 -1 N TRP G 35 O LEU G 47 SHEET 4 AB1 4 THR G 85 GLN G 89 -1 O GLN G 89 N ALA G 34 SSBOND 1 CYS D 22 CYS D 93 1555 1555 2.03 SSBOND 2 CYS G 23 CYS G 88 1555 1555 2.04 CISPEP 1 PRO A 48 GLY A 49 0 -2.41 CISPEP 2 ARG A 142 PRO A 143 0 -1.38 CISPEP 3 THR G 7 PRO G 8 0 -1.04 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