HEADER VIRAL PROTEIN/IMMUNE SYSTEM 05-JUN-24 8ZRR TITLE DIMER-AB AND FAB-HL COMPLEX OF HBCAG COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEACY CHAIN OF D4 FAB; COMPND 3 CHAIN: h; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LIGHT CHAIN OF D4 FAB; COMPND 7 CHAIN: l; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: CAPSID PROTEIN; COMPND 11 CHAIN: A, B; COMPND 12 SYNONYM: CORE ANTIGEN,CORE PROTEIN,HBCAG,P21.5; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HEPATITIS B VIRUS GENOTYPE C; SOURCE 13 ORGANISM_TAXID: 2764122; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA PHAGE ECSZW-2; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 2419741 KEYWDS DIMER-AB, FAB-HL, D4 ANTIBODY, VIRUS LIKE PARTICLE, VIRAL PROTEIN- KEYWDS 2 IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Z.ZHANG,B.JU,C.LIU,H.YAN REVDAT 5 19-FEB-25 8ZRR 1 JRNL REVDAT 4 12-FEB-25 8ZRR 1 JRNL REVDAT 3 11-DEC-24 8ZRR 1 JRNL REVDAT 2 27-NOV-24 8ZRR 1 REMARK REVDAT 1 13-NOV-24 8ZRR 0 JRNL AUTH H.YAN,C.LIU,Y.LI,S.TANG,H.GUO,B.ZHOU,Q.FAN,H.WANG,X.GE, JRNL AUTH 2 X.WANG,X.LIAO,J.LI,Z.ZHANG,B.JU JRNL TITL THE CHARACTERIZATION AND STRUCTURAL BASIS OF A HUMAN BROADLY JRNL TITL 2 BINDING ANTIBODY TO HBV CORE PROTEIN. JRNL REF J.VIROL. V. 99 69424 2025 JRNL REFN ESSN 1098-5514 JRNL PMID 39601613 JRNL DOI 10.1128/JVI.01694-24 REMARK 2 REMARK 2 RESOLUTION. 3.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CTFFIND, UCSF CHIMERA, REMARK 3 PHENIX, CRYOSPARC, CRYOSPARC, RELION, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 3J2V 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 : 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) : 3.610 REMARK 3 NUMBER OF PARTICLES : 199391 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 8ZRR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1300048433. 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 : DIMER-AB AND FAB-HL FROM HBCAG REMARK 245 -D4 FAB COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 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 : 4137 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 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) : 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: h, l, 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 MET B 1 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 OH TYR h 53 OE1 GLU B 83 1.34 REMARK 500 OD1 ASN l 33 CD1 LEU A 84 1.71 REMARK 500 OH TYR h 53 CD GLU B 83 2.04 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 h 104 -63.03 -126.90 REMARK 500 LYS A 7 -63.03 -2.18 REMARK 500 CYS A 48 -158.59 -157.75 REMARK 500 SER A 49 83.76 17.35 REMARK 500 ASN A 75 -136.35 -96.50 REMARK 500 LEU A 76 78.08 59.19 REMARK 500 ALA A 80 -71.38 -69.70 REMARK 500 SER A 81 -41.25 -27.76 REMARK 500 VAL A 91 -62.32 -94.97 REMARK 500 THR A 109 -71.29 -70.47 REMARK 500 PHE A 110 -128.26 -96.33 REMARK 500 SER A 141 -174.27 57.89 REMARK 500 TYR B 38 25.66 -140.25 REMARK 500 CYS B 48 -127.23 50.78 REMARK 500 ASN B 75 -125.47 -86.90 REMARK 500 SER B 81 -38.62 -39.51 REMARK 500 SER B 141 -167.20 61.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-60395 RELATED DB: EMDB REMARK 900 RELATED ID: 8ZRE RELATED DB: PDB REMARK 900 RELATED ID: EMD-60396 RELATED DB: EMDB REMARK 900 RELATED ID: 8ZRH RELATED DB: PDB REMARK 900 RELATED ID: EMD-60403 RELATED DB: EMDB REMARK 900 DIMER-AB AND FAB-HL COMPLEX OF HBCAG DBREF 8ZRR h 1 121 PDB 8ZRR 8ZRR 1 121 DBREF 8ZRR l 1 114 PDB 8ZRR 8ZRR 1 114 DBREF1 8ZRR A 1 142 UNP A0A679FG23_HBV DBREF2 8ZRR A A0A679FG23 1 142 DBREF1 8ZRR B 1 142 UNP A0A679FG23_HBV DBREF2 8ZRR B A0A679FG23 1 142 SEQRES 1 h 121 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 h 121 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 h 121 PHE ASN PHE ASN LYS PHE GLY MET HIS TRP VAL ARG GLN SEQRES 4 h 121 VAL PRO GLY LYS GLY LEU GLU TRP LEU THR TYR ILE TRP SEQRES 5 h 121 TYR ASP GLY SER ASN ALA ASP TYR VAL ASP SER VAL LYS SEQRES 6 h 121 GLY ARG PHE THR ILE SER ARG ASP ASN SER ILE ASN THR SEQRES 7 h 121 LEU TYR LEU GLN MET ASN SER LEU ARG ALA ASP ASP THR SEQRES 8 h 121 ALA VAL TYR PHE CYS ALA ARG GLY PHE TYR ASP SER SER SEQRES 9 h 121 SER LEU GLU SER TRP GLY GLN GLY ALA LEU VAL ILE VAL SEQRES 10 h 121 SER SER ALA SER SEQRES 1 l 114 ASP ILE VAL MET THR GLN SER PRO LEU SER LEU ALA VAL SEQRES 2 l 114 THR PRO GLY GLU PRO ALA SER ILE SER CYS ARG SER SER SEQRES 3 l 114 GLN THR LEU LEU HIS ASN ASN GLY TYR ASN TYR PHE SER SEQRES 4 l 114 TRP TYR LEU GLN LYS PRO GLY GLN ALA PRO GLN LEU LEU SEQRES 5 l 114 ILE TYR LEU GLY SER ASN ARG ALA PRO GLY VAL SER ASP SEQRES 6 l 114 ARG PHE SER GLY SER GLY SER GLY THR SER PHE THR LEU SEQRES 7 l 114 GLU ILE SER ARG VAL GLU ALA GLU ASP VAL GLY VAL TYR SEQRES 8 l 114 TYR CYS MET GLN GLY ARG HIS THR PRO TRP THR PHE GLY SEQRES 9 l 114 GLN GLY THR LYS VAL GLU ILE LYS ARG THR SEQRES 1 A 142 MET ASP ILE ASP PRO TYR LYS GLU PHE GLY ALA SER VAL SEQRES 2 A 142 GLU LEU LEU SER PHE LEU PRO SER ASP PHE PHE PRO SER SEQRES 3 A 142 ILE ARG ASP LEU LEU ASP THR ALA SER ALA LEU TYR ARG SEQRES 4 A 142 GLU ALA LEU GLU SER PRO GLU HIS CYS SER PRO HIS HIS SEQRES 5 A 142 THR ALA LEU ARG GLN ALA ILE LEU CYS TRP GLY GLU LEU SEQRES 6 A 142 MET ASN LEU ALA THR TRP VAL GLY SER ASN LEU GLU ASP SEQRES 7 A 142 PRO ALA SER ARG GLU LEU VAL VAL SER TYR VAL ASN VAL SEQRES 8 A 142 ASN MET GLY LEU LYS ILE ARG GLN LEU LEU TRP PHE HIS SEQRES 9 A 142 ILE SER CYS LEU THR PHE GLY ARG GLU THR VAL LEU GLU SEQRES 10 A 142 TYR LEU VAL SER PHE GLY VAL TRP ILE ARG THR PRO PRO SEQRES 11 A 142 ALA TYR ARG PRO PRO ASN ALA PRO ILE LEU SER THR SEQRES 1 B 142 MET ASP ILE ASP PRO TYR LYS GLU PHE GLY ALA SER VAL SEQRES 2 B 142 GLU LEU LEU SER PHE LEU PRO SER ASP PHE PHE PRO SER SEQRES 3 B 142 ILE ARG ASP LEU LEU ASP THR ALA SER ALA LEU TYR ARG SEQRES 4 B 142 GLU ALA LEU GLU SER PRO GLU HIS CYS SER PRO HIS HIS SEQRES 5 B 142 THR ALA LEU ARG GLN ALA ILE LEU CYS TRP GLY GLU LEU SEQRES 6 B 142 MET ASN LEU ALA THR TRP VAL GLY SER ASN LEU GLU ASP SEQRES 7 B 142 PRO ALA SER ARG GLU LEU VAL VAL SER TYR VAL ASN VAL SEQRES 8 B 142 ASN MET GLY LEU LYS ILE ARG GLN LEU LEU TRP PHE HIS SEQRES 9 B 142 ILE SER CYS LEU THR PHE GLY ARG GLU THR VAL LEU GLU SEQRES 10 B 142 TYR LEU VAL SER PHE GLY VAL TRP ILE ARG THR PRO PRO SEQRES 11 B 142 ALA TYR ARG PRO PRO ASN ALA PRO ILE LEU SER THR HELIX 1 AA1 ASN h 28 PHE h 32 5 5 HELIX 2 AA2 ARG h 87 THR h 91 5 5 HELIX 3 AA3 GLU l 84 VAL l 88 5 5 HELIX 4 AA4 TYR A 6 GLY A 10 5 5 HELIX 5 AA5 SER A 12 PHE A 18 1 7 HELIX 6 AA6 SER A 26 GLU A 43 1 18 HELIX 7 AA7 PRO A 50 ASN A 75 1 26 HELIX 8 AA8 ASP A 78 ASN A 92 1 15 HELIX 9 AA9 GLY A 94 PHE A 110 1 17 HELIX 10 AB1 GLY A 111 THR A 128 1 18 HELIX 11 AB2 ASP B 4 GLY B 10 5 7 HELIX 12 AB3 SER B 12 PHE B 18 1 7 HELIX 13 AB4 SER B 26 SER B 44 1 19 HELIX 14 AB5 SER B 49 ASN B 75 1 27 HELIX 15 AB6 ALA B 80 VAL B 91 1 12 HELIX 16 AB7 MET B 93 GLY B 111 1 19 HELIX 17 AB8 GLY B 111 THR B 128 1 18 HELIX 18 AB9 PRO B 129 ARG B 133 5 5 SHEET 1 AA1 4 GLN h 3 SER h 7 0 SHEET 2 AA1 4 LEU h 18 SER h 25 -1 O SER h 21 N SER h 7 SHEET 3 AA1 4 THR h 78 MET h 83 -1 O LEU h 79 N CYS h 22 SHEET 4 AA1 4 PHE h 68 ARG h 72 -1 N THR h 69 O GLN h 82 SHEET 1 AA2 6 GLY h 10 VAL h 12 0 SHEET 2 AA2 6 ALA h 113 VAL h 117 1 O ILE h 116 N VAL h 12 SHEET 3 AA2 6 ALA h 92 ARG h 98 -1 N TYR h 94 O ALA h 113 SHEET 4 AA2 6 MET h 34 GLN h 39 -1 N VAL h 37 O PHE h 95 SHEET 5 AA2 6 GLU h 46 ILE h 51 -1 O GLU h 46 N ARG h 38 SHEET 6 AA2 6 ALA h 58 TYR h 60 -1 O ASP h 59 N TYR h 50 SHEET 1 AA3 4 GLY h 10 VAL h 12 0 SHEET 2 AA3 4 ALA h 113 VAL h 117 1 O ILE h 116 N VAL h 12 SHEET 3 AA3 4 ALA h 92 ARG h 98 -1 N TYR h 94 O ALA h 113 SHEET 4 AA3 4 SER h 108 TRP h 109 -1 O SER h 108 N ARG h 98 SHEET 1 AA4 4 MET l 4 SER l 7 0 SHEET 2 AA4 4 ALA l 19 SER l 25 -1 O SER l 22 N SER l 7 SHEET 3 AA4 4 SER l 75 ILE l 80 -1 O LEU l 78 N ILE l 21 SHEET 4 AA4 4 PHE l 67 SER l 72 -1 N SER l 68 O GLU l 79 SHEET 1 AA5 6 SER l 10 ALA l 12 0 SHEET 2 AA5 6 THR l 107 GLU l 110 1 O LYS l 108 N LEU l 11 SHEET 3 AA5 6 VAL l 90 GLN l 95 -1 N TYR l 91 O THR l 107 SHEET 4 AA5 6 PHE l 38 GLN l 43 -1 N TYR l 41 O TYR l 92 SHEET 5 AA5 6 GLN l 50 TYR l 54 -1 O GLN l 50 N LEU l 42 SHEET 6 AA5 6 ASN l 58 ARG l 59 -1 O ASN l 58 N TYR l 54 SHEET 1 AA6 4 SER l 10 ALA l 12 0 SHEET 2 AA6 4 THR l 107 GLU l 110 1 O LYS l 108 N LEU l 11 SHEET 3 AA6 4 VAL l 90 GLN l 95 -1 N TYR l 91 O THR l 107 SHEET 4 AA6 4 THR l 102 PHE l 103 -1 O THR l 102 N GLN l 95 SSBOND 1 CYS h 22 CYS h 96 1555 1555 2.04 SSBOND 2 CYS l 23 CYS l 93 1555 1555 2.04 CISPEP 1 SER l 7 PRO l 8 0 -3.64 CISPEP 2 THR l 99 PRO l 100 0 -0.44 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 TER 942 SER h 121 TER 1823 THR l 114 TER 2942 THR A 142 TER 4069 THR B 142 CONECT 157 759 CONECT 759 157 CONECT 1101 1649 CONECT 1649 1101 MASTER 162 0 0 18 28 0 0 6 4065 4 4 41 END