HEADER LIPID BINDING PROTEIN 26-JUL-25 9W1U TITLE CRYSTAL STRUCTURE OF MUTANT APO LC3B 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 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MAP1LC3B, MAP1ALC3, MAP1LC3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ATG8-ORTHOLOG, AUTOPHAGY, ENGINEERED LC3B, APO STATE, LIPID BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.MATHUR,R.K.PAL,B.K.BISWAL,L.THUKRAL REVDAT 1 29-JUL-26 9W1U 0 JRNL AUTH D.GAHLOT,J.CASTIN,S.MATHUR,D.DAS,A.KUMAR,A.ARUN,C.GAIN, JRNL AUTH 2 M.SHARMA,R.K.PAL,N.JAIN,B.K.BISWAL,R.SINGH,L.THUKRAL JRNL TITL A NOVEL LIPID-TRIGGERED ALLOSTERIC SITE MODULATES LC3-LIR JRNL TITL 2 RECEPTOR BINDING ACTIVITY JRNL REF BIORXIV 2026 JRNL REFN ISSN 2692-8205 JRNL DOI 10.64898/2026.03.10.710726 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.2_5419: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 17447 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 855 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.2400 - 2.9100 1.00 2834 160 0.1557 0.1705 REMARK 3 2 2.9100 - 2.3100 1.00 2791 138 0.2042 0.2555 REMARK 3 3 2.3100 - 2.0200 0.98 2708 157 0.2170 0.2581 REMARK 3 4 2.0200 - 1.8300 0.97 2692 145 0.2731 0.3021 REMARK 3 5 1.8300 - 1.7000 1.00 2783 120 0.1938 0.2484 REMARK 3 6 1.7000 - 1.6000 1.00 2784 135 0.2146 0.2738 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1072 REMARK 3 ANGLE : 0.963 1448 REMARK 3 CHIRALITY : 0.059 158 REMARK 3 PLANARITY : 0.007 190 REMARK 3 DIHEDRAL : 16.383 424 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 18.3707 21.3101 1.9689 REMARK 3 T TENSOR REMARK 3 T11: 0.1257 T22: 0.1331 REMARK 3 T33: 0.1270 T12: 0.0054 REMARK 3 T13: -0.0163 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 1.2128 L22: 1.0276 REMARK 3 L33: 1.2892 L12: 0.0097 REMARK 3 L13: 0.0798 L23: -0.3204 REMARK 3 S TENSOR REMARK 3 S11: 0.0146 S12: 0.0036 S13: -0.0676 REMARK 3 S21: -0.0284 S22: 0.0072 S23: 0.0439 REMARK 3 S31: -0.0044 S32: 0.0351 S33: 0.0001 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9W1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300062003. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17653 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 18.50 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 53.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2ZJD REMARK 200 REMARK 200 REMARK: HEXAGONAL SHAPED CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM AMMONIUM SULPHATE 25% PEG 4000 REMARK 280 100 MM SODIUM ACETATE PH 4.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.20200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.10100 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.15150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 7.05050 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.25250 REMARK 290 REMARK 290 REMARK: NULL 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 SER A 3 REMARK 465 MET A 123 REMARK 465 ALA A 124 REMARK 465 VAL A 125 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 4 CG CD OE1 OE2 REMARK 470 ARG A 24 NE CZ NH1 NH2 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 ASN A 84 -141.73 51.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 85 HIS A 86 -146.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 445 DISTANCE = 6.12 ANGSTROMS DBREF 9W1U A 1 125 UNP Q9CQV6 MLP3B_MOUSE 1 125 SEQADV 9W1U HIS A -5 UNP Q9CQV6 EXPRESSION TAG SEQADV 9W1U HIS A -4 UNP Q9CQV6 EXPRESSION TAG SEQADV 9W1U HIS A -3 UNP Q9CQV6 EXPRESSION TAG SEQADV 9W1U HIS A -2 UNP Q9CQV6 EXPRESSION TAG SEQADV 9W1U HIS A -1 UNP Q9CQV6 EXPRESSION TAG SEQADV 9W1U HIS A 0 UNP Q9CQV6 EXPRESSION TAG SEQADV 9W1U LYS A 64 UNP Q9CQV6 ILE 64 ENGINEERED MUTATION SEQADV 9W1U ASP A 89 UNP Q9CQV6 VAL 89 ENGINEERED MUTATION SEQADV 9W1U PHE A 91 UNP Q9CQV6 VAL 91 ENGINEERED MUTATION SEQRES 1 A 131 HIS HIS HIS HIS HIS HIS MET PRO SER GLU LYS THR PHE SEQRES 2 A 131 LYS GLN ARG ARG SER PHE GLU GLN ARG VAL GLU ASP VAL SEQRES 3 A 131 ARG LEU ILE ARG GLU GLN HIS PRO THR LYS ILE PRO VAL SEQRES 4 A 131 ILE ILE GLU ARG TYR LYS GLY GLU LYS GLN LEU PRO VAL SEQRES 5 A 131 LEU ASP LYS THR LYS PHE LEU VAL PRO ASP HIS VAL ASN SEQRES 6 A 131 MET SER GLU LEU LYS LYS ILE ILE ARG ARG ARG LEU GLN SEQRES 7 A 131 LEU ASN ALA ASN GLN ALA PHE PHE LEU LEU VAL ASN GLY SEQRES 8 A 131 HIS SER MET ASP SER PHE SER THR PRO ILE SER GLU VAL SEQRES 9 A 131 TYR GLU SER GLU ARG ASP GLU ASP GLY PHE LEU TYR MET SEQRES 10 A 131 VAL TYR ALA SER GLN GLU THR PHE GLY THR ALA MET ALA SEQRES 11 A 131 VAL HET EDO A 201 4 HET EDO A 202 4 HET EDO A 203 4 HET ACT A 204 4 HET CL A 205 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 3(C2 H6 O2) FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 CL CL 1- FORMUL 7 HOH *145(H2 O) HELIX 1 AA1 THR A 6 ARG A 11 1 6 HELIX 2 AA2 SER A 12 HIS A 27 1 16 HELIX 3 AA3 ASN A 59 GLN A 72 1 14 HELIX 4 AA4 PRO A 94 ARG A 103 1 10 SHEET 1 AA1 4 LYS A 51 PRO A 55 0 SHEET 2 AA1 4 LYS A 30 ARG A 37 -1 N VAL A 33 O PHE A 52 SHEET 3 AA1 4 LEU A 109 ALA A 114 1 O LEU A 109 N ILE A 34 SHEET 4 AA1 4 PHE A 80 VAL A 83 -1 N LEU A 82 O VAL A 112 CRYST1 74.056 74.056 42.303 90.00 90.00 120.00 P 65 6 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 0.013503 0.007796 0.000000 0.00000 SCALE2 0.000000 0.015592 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023639 0.00000 CONECT 1033 1034 1035 CONECT 1034 1033 CONECT 1035 1033 1036 CONECT 1036 1035 CONECT 1037 1038 1039 CONECT 1038 1037 CONECT 1039 1037 1040 CONECT 1040 1039 CONECT 1041 1042 1043 CONECT 1042 1041 CONECT 1043 1041 1044 CONECT 1044 1043 CONECT 1045 1046 1047 1048 CONECT 1046 1045 CONECT 1047 1045 CONECT 1048 1045 MASTER 286 0 5 4 4 0 0 6 1146 1 16 11 END