HEADER VIRUS 28-MAR-24 8YV6 TITLE CRYSTAL STRUCTURE OF LC3B IN COMPLEX WITH INFLUENZA A VIRUS M2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B; 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,MAP1A/MAP1B COMPND 6 LIGHT CHAIN 3 B,MAP1A/MAP1B LC3 B,MICROTUBULE-ASSOCIATED PROTEIN 1 COMPND 7 LIGHT CHAIN 3 BETA; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: MATRIX PROTEIN 2; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES 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 PHAGE ECSZW-2; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 2419741; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS; SOURCE 10 ORGANISM_TAXID: 11320; SOURCE 11 GENE: M2; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA PHAGE ECSZW-2; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 2419741 KEYWDS INFLUENZA A VIRUS, COMPLEX, LC3, VIRUS EXPDTA X-RAY DIFFRACTION AUTHOR D.MURATA,C.NOVOA,R.BEALE,M.AKUTSU REVDAT 1 13-NOV-24 8YV6 0 JRNL AUTH D.MURATA,C.NOVOA,R.BEALE,M.AKUTSU JRNL TITL CRYSTAL STRUCTURE OF LC3B IN COMPLEX WITH INFLUENZA A VIRUS JRNL TITL 2 M2 PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13599 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 666 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 2.9924 - 2.3751 1.00 2594 131 0.2387 0.2675 REMARK 3 2 2.3751 - 2.0749 1.00 2567 131 0.2535 0.3085 REMARK 3 3 2.0749 - 1.8852 1.00 2522 139 0.2558 0.2959 REMARK 3 4 1.8852 - 1.7501 1.00 2538 119 0.2786 0.2818 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.540 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 : 0.012 1093 REMARK 3 ANGLE : 1.183 1473 REMARK 3 CHIRALITY : 0.077 163 REMARK 3 PLANARITY : 0.007 192 REMARK 3 DIHEDRAL : 6.619 917 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): -3.1950 5.2474 -10.3603 REMARK 3 T TENSOR REMARK 3 T11: 0.1672 T22: 0.3011 REMARK 3 T33: 0.1748 T12: 0.0271 REMARK 3 T13: -0.0126 T23: 0.0775 REMARK 3 L TENSOR REMARK 3 L11: 4.2242 L22: 2.5721 REMARK 3 L33: 3.9686 L12: 0.7227 REMARK 3 L13: -0.4390 L23: 0.9748 REMARK 3 S TENSOR REMARK 3 S11: -0.1169 S12: -0.6693 S13: -0.1318 REMARK 3 S21: -0.0331 S22: 0.0545 S23: 0.0421 REMARK 3 S31: 0.0803 S32: 0.1703 S33: 0.0525 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 8YV6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-24. REMARK 100 THE DEPOSITION ID IS D_1300046406. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13649 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 46.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% JEFFAMINE, 0.1M HEPES, PH 7.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 17.84050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.88700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.23100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.88700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.84050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.23100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 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 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 PRO A 2 REMARK 465 SER A 3 REMARK 465 MET A 88 REMARK 465 VAL A 89 REMARK 465 MET A 121 REMARK 465 LYS A 122 REMARK 465 LEU A 123 REMARK 465 SER A 124 REMARK 465 VAL A 125 REMARK 465 LYS B 70 REMARK 465 SER B 71 REMARK 465 MET B 72 REMARK 465 ARG B 73 REMARK 465 GLU B 74 REMARK 465 GLU B 75 REMARK 465 TYR B 76 REMARK 465 ARG B 77 REMARK 465 LYS B 78 REMARK 465 GLU B 79 REMARK 465 GLN B 80 REMARK 465 GLN B 81 REMARK 465 SER B 82 REMARK 465 ALA B 83 REMARK 465 VAL B 84 REMARK 465 ASP B 85 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 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 A 38 O GLY A 120 1.96 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 ASN A 84 59.32 38.43 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YV6 A 1 125 UNP Q9GZQ8 MLP3B_HUMAN 1 125 DBREF1 8YV6 B 70 97 UNP A0A3S5G6R9_9INFA DBREF2 8YV6 B A0A3S5G6R9 70 97 SEQRES 1 A 125 MET PRO SER GLU LYS THR PHE LYS GLN ARG ARG THR PHE SEQRES 2 A 125 GLU GLN ARG VAL GLU ASP VAL ARG LEU ILE ARG GLU GLN SEQRES 3 A 125 HIS PRO THR LYS ILE PRO VAL ILE ILE GLU ARG TYR LYS SEQRES 4 A 125 GLY GLU LYS GLN LEU PRO VAL LEU ASP LYS THR LYS PHE SEQRES 5 A 125 LEU VAL PRO ASP HIS VAL ASN MET SER GLU LEU ILE LYS SEQRES 6 A 125 ILE ILE ARG ARG ARG LEU GLN LEU ASN ALA ASN GLN ALA SEQRES 7 A 125 PHE PHE LEU LEU VAL ASN GLY HIS SER MET VAL SER VAL SEQRES 8 A 125 SER THR PRO ILE SER GLU VAL TYR GLU SER GLU LYS ASP SEQRES 9 A 125 GLU ASP GLY PHE LEU TYR MET VAL TYR ALA SER GLN GLU SEQRES 10 A 125 THR PHE GLY MET LYS LEU SER VAL SEQRES 1 B 28 LYS SER MET ARG GLU GLU TYR ARG LYS GLU GLN GLN SER SEQRES 2 B 28 ALA VAL ASP ALA ASP ASP GLY HIS PHE VAL SER ILE GLU SEQRES 3 B 28 LEU GLU FORMUL 3 HOH *22(H2 O) 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 LYS A 103 1 10 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 PHE B 91 SER B 93 1 O VAL B 92 N LEU A 53 CISPEP 1 PHE A 119 GLY A 120 0 -3.19 CRYST1 35.681 38.462 93.774 90.00 90.00 90.00 P 21 21 21 4 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 0.028026 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010664 0.00000 MASTER 275 0 0 4 5 0 0 6 1069 2 0 13 END