HEADER VIRAL PROTEIN 02-AUG-22 7YP2 TITLE CRYO-EM STRUCTURE OF EBV GHGL-GP42 IN COMPLEX WITH MAB 6H2 (LOCALIZED TITLE 2 REFINEMENT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN H; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GH; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 6H2 HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 6H2 LIGHT CHAIN; COMPND 12 CHAIN: L; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN GAMMAHERPESVIRUS 4; SOURCE 3 ORGANISM_COMMON: EPSTEIN-BARR VIRUS; SOURCE 4 ORGANISM_TAXID: 10376; SOURCE 5 STRAIN: GD1; SOURCE 6 GENE: GH; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 18 ORGANISM_TAXID: 10090; SOURCE 19 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 21 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 7YP2 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. 3.52 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) : 3.520 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 7YP2 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_1300031336. 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 : EBV GHGL-GP42 IN COMPLEX WITH REMARK 245 MAB 6H2; GH; 6H2 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L 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 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 GLU A 363 56.09 -95.86 REMARK 500 LEU A 517 51.85 -91.66 REMARK 500 TRP A 527 -5.70 75.35 REMARK 500 ASN A 549 -1.81 67.87 REMARK 500 TYR A 572 -159.39 -90.98 REMARK 500 CYS A 612 77.54 -100.84 REMARK 500 PHE A 614 -7.16 67.64 REMARK 500 SER H 119 -169.50 -165.70 REMARK 500 ASN L 37 70.02 58.75 REMARK 500 LEU L 53 -62.56 -94.26 REMARK 500 ALA L 57 -10.66 69.90 REMARK 500 GLU L 87 35.99 -99.48 REMARK 500 ASP L 88 14.49 -141.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33994 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF EBV GHGL-GP42 IN COMPLEX WITH MAB 6H2 REMARK 900 (LOCALIZED REFINEMENT) DBREF1 7YP2 A 361 674 UNP A0A385J8N2_EBVG DBREF2 7YP2 A A0A385J8N2 361 674 DBREF 7YP2 H 1 120 PDB 7YP2 7YP2 1 120 DBREF 7YP2 L 1 112 PDB 7YP2 7YP2 1 112 SEQRES 1 A 314 MET GLU GLU LEU GLY HIS LEU THR THR GLU LYS GLN GLU SEQRES 2 A 314 TYR ALA LEU ARG LEU ALA THR VAL GLY TYR PRO LYS ALA SEQRES 3 A 314 GLY VAL TYR SER GLY LEU ILE GLY GLY ALA THR SER VAL SEQRES 4 A 314 LEU LEU SER ALA TYR ASN ARG HIS PRO LEU PHE GLN PRO SEQRES 5 A 314 LEU HIS THR VAL MET ARG GLU THR LEU PHE ILE GLY SER SEQRES 6 A 314 HIS VAL VAL LEU ARG GLU LEU ARG LEU ASN VAL THR THR SEQRES 7 A 314 GLN GLY PRO ASN LEU ALA LEU TYR GLN LEU LEU SER THR SEQRES 8 A 314 ALA LEU CYS SER ALA LEU GLU ILE GLY GLU VAL LEU ARG SEQRES 9 A 314 GLY LEU ALA LEU GLY THR GLU SER GLY LEU PHE SER PRO SEQRES 10 A 314 CYS TYR LEU SER LEU ARG PHE ASP LEU THR ARG ASP LYS SEQRES 11 A 314 LEU LEU SER MET ALA PRO GLN GLU ALA THR LEU ASP GLN SEQRES 12 A 314 ALA ALA VAL SER ASN ALA VAL ASP GLY PHE LEU GLY ARG SEQRES 13 A 314 LEU SER LEU GLU ARG GLU ASP ARG ASP ALA TRP HIS LEU SEQRES 14 A 314 PRO ALA TYR LYS CYS VAL ASP ARG LEU ASP LYS VAL LEU SEQRES 15 A 314 MET ILE ILE PRO LEU ILE ASN VAL THR PHE ILE ILE SER SEQRES 16 A 314 SER ASP ARG GLU VAL ARG GLY SER ALA LEU TYR GLU ALA SEQRES 17 A 314 SER THR THR TYR LEU SER SER SER LEU PHE LEU SER PRO SEQRES 18 A 314 VAL ILE MET ASN LYS CYS SER GLN GLY ALA VAL ALA GLY SEQRES 19 A 314 GLU PRO ARG GLN ILE PRO LYS ILE GLN ASN PHE THR ARG SEQRES 20 A 314 THR GLN LYS SER CYS ILE PHE CYS GLY PHE ALA LEU LEU SEQRES 21 A 314 SER TYR ASP GLU LYS GLU GLY LEU GLU THR THR THR TYR SEQRES 22 A 314 ILE THR SER GLN GLU VAL GLN ASN SER ILE LEU SER SER SEQRES 23 A 314 ASN TYR PHE ASP PHE ASP ASN LEU HIS VAL HIS TYR LEU SEQRES 24 A 314 LEU LEU THR THR ASN GLY THR VAL MET GLU ILE ALA GLY SEQRES 25 A 314 LEU TYR SEQRES 1 H 120 GLU VAL LYS LEU LEU GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 120 PRO GLY GLY SER LEU LYS LEU SER CYS ALA ALA SER GLY SEQRES 3 H 120 PHE ASP PHE SER ARG TYR TRP MET THR TRP VAL ARG GLN SEQRES 4 H 120 ALA PRO GLY GLN GLY LEU GLU TRP ILE GLY GLU ILE ASN SEQRES 5 H 120 PRO ASP SER SER THR ILE ASN TYR THR PRO SER LEU LYS SEQRES 6 H 120 ASP LYS PHE ILE ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 H 120 LEU TYR LEU GLN VAL SER LYS LEU ARG SER GLU ASP THR SEQRES 8 H 120 ALA LEU TYR TYR CYS ALA ARG SER PRO TYR TYR TYR GLY SEQRES 9 H 120 SER SER TYR ASP VAL TRP GLY ALA GLY THR ALA VAL THR SEQRES 10 H 120 VAL SER SER SEQRES 1 L 112 ASP ILE VAL MET SER GLN SER PRO SER SER LEU ALA VAL SEQRES 2 L 112 SER ALA GLY GLU LYS VAL THR MET ASN CYS LYS SER SER SEQRES 3 L 112 GLN SER LEU LEU ASN SER ARG THR ARG LYS ASN TYR LEU SEQRES 4 L 112 ALA TRP TYR GLN GLN LYS PRO GLY GLN SER PRO LYS LEU SEQRES 5 L 112 LEU ILE TYR TRP ALA SER THR ARG GLU SER GLY VAL PRO SEQRES 6 L 112 ASP ARG PHE THR GLY SER GLY SER GLY THR ASP PHE THR SEQRES 7 L 112 LEU THR ILE SER SER VAL GLN ALA GLU ASP LEU ALA PHE SEQRES 8 L 112 TYR TYR CYS LYS GLN SER TYR ASN LEU PRO THR PHE GLY SEQRES 9 L 112 GLY GLY THR LYS LEU GLU ILE LYS HELIX 1 AA1 THR A 369 TYR A 383 1 15 HELIX 2 AA2 TYR A 389 GLY A 391 5 3 HELIX 3 AA3 LEU A 392 ASN A 405 1 14 HELIX 4 AA4 VAL A 416 GLY A 424 1 9 HELIX 5 AA5 SER A 425 ARG A 430 1 6 HELIX 6 AA6 GLY A 440 LEU A 453 1 14 HELIX 7 AA7 SER A 455 GLY A 469 1 15 HELIX 8 AA8 SER A 476 LEU A 480 5 5 HELIX 9 AA9 THR A 487 LEU A 492 1 6 HELIX 10 AB1 ASP A 502 LEU A 517 1 16 HELIX 11 AB2 GLU A 520 ARG A 524 5 5 HELIX 12 AB3 LEU A 529 CYS A 534 5 6 HELIX 13 AB4 ARG A 537 ASP A 539 5 3 HELIX 14 AB5 SER A 636 SER A 645 1 10 HELIX 15 AB6 GLN L 85 LEU L 89 5 5 SHEET 1 AA1 3 VAL A 541 PRO A 546 0 SHEET 2 AA1 3 VAL A 550 SER A 555 -1 O PHE A 552 N ILE A 545 SHEET 3 AA1 3 PHE A 578 ILE A 583 -1 O PHE A 578 N SER A 555 SHEET 1 AA2 2 TYR A 566 GLU A 567 0 SHEET 2 AA2 2 ARG A 597 GLN A 598 1 O ARG A 597 N GLU A 567 SHEET 1 AA3 5 LYS A 601 ILE A 602 0 SHEET 2 AA3 5 VAL A 667 ILE A 670 1 O GLU A 669 N ILE A 602 SHEET 3 AA3 5 VAL A 656 LEU A 661 -1 N LEU A 660 O MET A 668 SHEET 4 AA3 5 SER A 621 ASP A 623 -1 N TYR A 622 O HIS A 657 SHEET 5 AA3 5 GLY A 627 THR A 630 -1 O THR A 630 N SER A 621 SHEET 1 AA4 4 LEU H 5 SER H 7 0 SHEET 2 AA4 4 SER H 17 ALA H 23 -1 O ALA H 23 N LEU H 5 SHEET 3 AA4 4 THR H 78 SER H 84 -1 O LEU H 81 N LEU H 20 SHEET 4 AA4 4 PHE H 68 ASP H 73 -1 N SER H 71 O TYR H 80 SHEET 1 AA5 2 GLY H 10 VAL H 12 0 SHEET 2 AA5 2 VAL H 116 VAL H 118 1 O THR H 117 N VAL H 12 SHEET 1 AA6 4 ILE H 58 TYR H 60 0 SHEET 2 AA6 4 GLU H 46 ILE H 51 -1 N GLU H 50 O ASN H 59 SHEET 3 AA6 4 TRP H 33 ARG H 38 -1 N ARG H 38 O GLU H 46 SHEET 4 AA6 4 TYR H 94 SER H 99 -1 O TYR H 95 N VAL H 37 SHEET 1 AA7 6 SER L 10 VAL L 13 0 SHEET 2 AA7 6 THR L 107 ILE L 111 1 O GLU L 110 N VAL L 13 SHEET 3 AA7 6 PHE L 91 LYS L 95 -1 N TYR L 92 O THR L 107 SHEET 4 AA7 6 ALA L 40 GLN L 44 -1 N TYR L 42 O TYR L 93 SHEET 5 AA7 6 LYS L 51 TYR L 55 -1 O LEU L 53 N TRP L 41 SHEET 6 AA7 6 THR L 59 ARG L 60 -1 O THR L 59 N TYR L 55 SHEET 1 AA8 3 VAL L 19 LYS L 24 0 SHEET 2 AA8 3 ASP L 76 ILE L 81 -1 O PHE L 77 N CYS L 23 SHEET 3 AA8 3 PHE L 68 GLY L 72 -1 N SER L 71 O THR L 78 SSBOND 1 CYS A 454 CYS A 478 1555 1555 2.03 SSBOND 2 CYS A 534 CYS A 587 1555 1555 2.03 SSBOND 3 CYS A 612 CYS A 615 1555 1555 2.04 SSBOND 4 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 5 CYS L 23 CYS L 94 1555 1555 2.03 CISPEP 1 SER L 7 PRO L 8 0 -4.21 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