HEADER VIRAL PROTEIN 14-JUL-25 9VUY TITLE NMR STRUCTURE OF LC3B IN COMPLEX WITH HBX BH3-LIKE MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROTUBULE-ASSOCIATED PROTEIN 1 LIGHT CHAIN 3 BETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AUTOPHAGY-RELATED PROTEIN LC3 B,AUTOPHAGY-RELATED UBIQUITIN- COMPND 5 LIKE MODIFIER LC3 B,MAP1 LIGHT CHAIN 3-LIKE PROTEIN 2,MICROTUBULE- COMPND 6 ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B,MAP1A/MAP1B LC3 B, COMPND 7 MAP1A/MAP1B LIGHT CHAIN 3 B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HBX BH3-LIKE MOTIF; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: HBX,PEPTIDE X,PX; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: PROTEIN X SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MAP1LC3B, MAP1ALC3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HEPATITIS B VIRUS; SOURCE 10 ORGANISM_TAXID: 10407; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, HBX, LC3B, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.KUSUNOKI,T.NAGATA REVDAT 1 27-MAY-26 9VUY 0 JRNL AUTH H.KUSUNOKI,T.TANAKA,T.MIZUKAMI,K.WAKAMATSU,T.NAGATA JRNL TITL STRUCTURAL INSIGHTS INTO THE INTERACTION BETWEEN THE JRNL TITL 2 BH3-LIKE DOMAIN OF HEPATITIS B VIRUS X PROTEIN AND LC3B. JRNL REF BIOCHIM BIOPHYS ACTA V.1874 41149 2026 JRNL REF 2 PROTEINS PROTEOM JRNL REFN ISSN 1878-1454 JRNL PMID 42103248 JRNL DOI 10.1016/J.BBAPAP.2026.141149 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, CYANA 3.98 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9VUY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300061405. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-13C; U-15N] LC3B, 0.5 REMARK 210 MM [U-13C; U-15N] HBX BH3-LIKE REMARK 210 MOTIF, 95% H2O/5% D2O; 0.4 MM [U- REMARK 210 15N] LC3B, 0.5 MM [U-15N] HBX REMARK 210 BH3-LIKE MOTIF, 95% H2O/5% D2O; REMARK 210 0.8 MM 1H LC3B, 0.4 MM [U-13, U- REMARK 210 15N] HBX BH3-LIKE MOTIF, 95% H2O/ REMARK 210 5% D2O; 0.5 MM [U-13, U-15N] REMARK 210 LC3B, 0.625 MM 1H HBX BH3-LIKE REMARK 210 MOTIF, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D CBCA(CO)NH; 3D HNCACB; REMARK 210 3D HBHA(CO)NH; 3D CC(CO)NH; 3D REMARK 210 1H-15N NOESY-HSQC; 2D 1H-13C REMARK 210 HSQC ALIPHATIC; 3D HCCH-TOCSY REMARK 210 ALIPHATIC; 3D CCH-TOCSY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY-HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HCCH-COSY AROMATIC; REMARK 210 3D 1H-13C NOESY-HSQC AROMATIC; REMARK 210 2D 13C,15N-[F1,F2]-FILTERED REMARK 210 NOESY; 2D 13C,15N-[F2]-FILTERED REMARK 210 NOESY; 2D 13C,15N-[F2]-FILTERED REMARK 210 TOCSY; 3D [F1] 13C-FILTERED [F3] REMARK 210 13C-EDITED NOESY-HSQC; 3D BEST- REMARK 210 HNCO; 3D BEST-HNCACO; 3D BEST- REMARK 210 HNCOCA; 3D BEST-HNCOCACB; 3D REMARK 210 BEST-HNCACB; 3D HNHA; 3D HCCH- REMARK 210 TOCSY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW, MDDNMR, MAGRO-NMRVIEW REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 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 1 SER A 3 -45.06 -140.93 REMARK 500 1 HIS A 27 74.45 -119.57 REMARK 500 1 THR A 29 33.13 -94.43 REMARK 500 1 LYS A 42 73.40 -106.15 REMARK 500 1 GLN A 43 -56.76 -178.15 REMARK 500 1 PRO A 55 155.40 -48.57 REMARK 500 1 PHE A 79 114.72 -170.17 REMARK 500 1 VAL A 91 -41.42 -131.37 REMARK 500 1 SER A 92 57.11 -93.49 REMARK 500 1 ASP A 104 -83.38 -86.40 REMARK 500 1 GLU A 105 -75.52 -92.40 REMARK 500 1 SER A 115 46.98 -90.30 REMARK 500 1 GLN A 116 92.71 179.24 REMARK 500 1 VAL B 316 138.97 -170.11 REMARK 500 2 SER A 3 -61.10 -124.06 REMARK 500 2 GLU A 4 69.48 -174.74 REMARK 500 2 THR A 29 35.02 -95.41 REMARK 500 2 GLN A 43 -63.39 -169.45 REMARK 500 2 PRO A 55 154.10 -47.00 REMARK 500 2 PHE A 79 115.89 -169.46 REMARK 500 2 VAL A 91 -40.03 -131.36 REMARK 500 2 SER A 92 58.17 -90.95 REMARK 500 2 ASP A 104 -84.02 -81.48 REMARK 500 2 GLU A 105 -75.70 -92.55 REMARK 500 2 SER A 115 46.83 -90.75 REMARK 500 2 GLN A 116 92.42 -179.99 REMARK 500 2 SER B 315 179.34 61.45 REMARK 500 2 GLU B 326 117.08 -164.60 REMARK 500 3 LYS A 5 -175.04 55.28 REMARK 500 3 THR A 29 33.28 -94.63 REMARK 500 3 GLU A 41 76.16 -106.92 REMARK 500 3 GLN A 43 -43.28 -161.87 REMARK 500 3 PRO A 55 155.72 -47.94 REMARK 500 3 PHE A 79 116.70 -170.41 REMARK 500 3 VAL A 91 -41.83 -131.21 REMARK 500 3 SER A 92 57.04 -92.81 REMARK 500 3 ASP A 104 -83.45 -89.43 REMARK 500 3 GLU A 105 -75.80 -92.41 REMARK 500 3 SER A 115 49.43 -96.09 REMARK 500 3 GLN A 116 93.91 178.79 REMARK 500 4 SER A 3 -70.00 -113.31 REMARK 500 4 GLU A 4 77.73 -160.70 REMARK 500 4 LYS A 5 166.53 63.17 REMARK 500 4 HIS A 27 76.23 -117.54 REMARK 500 4 THR A 29 33.65 -94.50 REMARK 500 4 GLU A 41 79.09 -108.60 REMARK 500 4 LYS A 42 55.51 -99.84 REMARK 500 4 GLN A 43 -41.79 -155.58 REMARK 500 4 PHE A 79 117.97 -170.10 REMARK 500 4 VAL A 91 -41.37 -131.31 REMARK 500 REMARK 500 THIS ENTRY HAS 247 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36772 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF LC3B IN COMPLEX WITH HBX BH3-LIKE MOTIF DBREF 9VUY A 1 119 UNP Q9GZQ8 MLP3B_HUMAN 1 119 DBREF 9VUY B 316 327 UNP Q913A9 X_HBVC7 116 127 SEQADV 9VUY GLY B 314 UNP Q913A9 EXPRESSION TAG SEQADV 9VUY SER B 315 UNP Q913A9 EXPRESSION TAG SEQRES 1 A 119 MET PRO SER GLU LYS THR PHE LYS GLN ARG ARG THR PHE SEQRES 2 A 119 GLU GLN ARG VAL GLU ASP VAL ARG LEU ILE ARG GLU GLN SEQRES 3 A 119 HIS PRO THR LYS ILE PRO VAL ILE ILE GLU ARG TYR LYS SEQRES 4 A 119 GLY GLU LYS GLN LEU PRO VAL LEU ASP LYS THR LYS PHE SEQRES 5 A 119 LEU VAL PRO ASP HIS VAL ASN MET SER GLU LEU ILE LYS SEQRES 6 A 119 ILE ILE ARG ARG ARG LEU GLN LEU ASN ALA ASN GLN ALA SEQRES 7 A 119 PHE PHE LEU LEU VAL ASN GLY HIS SER MET VAL SER VAL SEQRES 8 A 119 SER THR PRO ILE SER GLU VAL TYR GLU SER GLU LYS ASP SEQRES 9 A 119 GLU ASP GLY PHE LEU TYR MET VAL TYR ALA SER GLN GLU SEQRES 10 A 119 THR PHE SEQRES 1 B 14 GLY SER VAL PHE LYS ASP TRP GLU GLU LEU GLY GLU GLU SEQRES 2 B 14 ILE HELIX 1 AA1 THR A 6 ARG A 11 1 6 HELIX 2 AA2 THR A 12 HIS A 27 1 16 HELIX 3 AA3 ASN A 59 GLN A 72 1 14 HELIX 4 AA4 PRO A 94 GLU A 102 1 9 SHEET 1 AA1 5 PHE A 80 VAL A 83 0 SHEET 2 AA1 5 LEU A 109 ALA A 114 -1 O VAL A 112 N LEU A 82 SHEET 3 AA1 5 LYS A 30 ARG A 37 1 N ILE A 34 O LEU A 109 SHEET 4 AA1 5 LYS A 51 PRO A 55 -1 O VAL A 54 N ILE A 31 SHEET 5 AA1 5 GLU B 321 GLU B 322 1 O GLU B 321 N LEU A 53 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 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL MASTER 168 0 0 4 5 0 0 6 1105 2 0 12 END