HEADER VIRAL PROTEIN 21-MAR-17 5V8A TITLE CRYSTAL STRUCTURE OF INFLUENZA A VIRUS MATRIX PROTEIN M1 (NLS-88R, PH TITLE 2 7.3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRIX PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: M1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS (STRAIN A/WILSON-SMITH/1933 SOURCE 3 H1N1); SOURCE 4 ORGANISM_TAXID: 381518; SOURCE 5 STRAIN: A/WILSON-SMITH/1933 H1N1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: NICO21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLAZMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS INFLUENZA A, MATRIX PROTEIN, NLS-88R MUTANT, PH 7.3, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.N.MUSAYEV,M.K.SAFO,U.R.DESAI,H.XIE,P.D.MOSIER,Q.ZHOU,M.-J.CHIANG, AUTHOR 2 M.KOSIKOVA REVDAT 5 04-OCT-23 5V8A 1 JRNL REVDAT 4 04-DEC-19 5V8A 1 REMARK REVDAT 3 20-DEC-17 5V8A 1 JRNL REVDAT 2 27-SEP-17 5V8A 1 REMARK REVDAT 1 19-APR-17 5V8A 0 JRNL AUTH M.J.CHIANG,F.N.MUSAYEV,M.KOSIKOVA,Z.LIN,Y.GAO,P.D.MOSIER, JRNL AUTH 2 B.ALTHUFAIRI,Z.YE,Q.ZHOU,U.R.DESAI,H.XIE,M.K.SAFO JRNL TITL MAINTAINING PH-DEPENDENT CONFORMATIONAL FLEXIBILITY OF M1 IS JRNL TITL 2 CRITICAL FOR EFFICIENT INFLUENZA A VIRUS REPLICATION. JRNL REF EMERG MICROBES INFECT V. 6 E108 2017 JRNL REFN ESSN 2222-1751 JRNL PMID 29209052 JRNL DOI 10.1038/EMI.2017.96 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 2177 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.275 REMARK 3 R VALUE (WORKING SET) : 0.272 REMARK 3 FREE R VALUE : 0.321 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.470 REMARK 3 FREE R VALUE TEST SET COUNT : 119 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 21.9263 - 5.1130 0.94 405 29 0.2083 0.2771 REMARK 3 2 5.1130 - 4.0668 0.94 413 25 0.2506 0.2526 REMARK 3 3 4.0668 - 3.5552 0.95 419 21 0.2918 0.3895 REMARK 3 4 3.5552 - 3.2313 0.95 414 24 0.3730 0.4895 REMARK 3 5 3.2313 - 3.0003 0.94 407 20 0.3974 0.4339 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) : 0.520 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 42.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 73.06 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 : 0.003 1145 REMARK 3 ANGLE : 0.595 1549 REMARK 3 CHIRALITY : 0.023 189 REMARK 3 PLANARITY : 0.005 193 REMARK 3 DIHEDRAL : 13.517 419 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5V8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000227032. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5419 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2187 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 28.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 2.830 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.97 REMARK 200 R MERGE FOR SHELL (I) : 0.51200 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: PHENIX REMARK 200 STARTING MODEL: 1EA3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 21.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 10 MG/ML IN REMARK 280 K2HPO4/KH2PO4, 0.2M NACL, 10BME, PH 7.2. RESERVOIR SOLUTION: REMARK 280 0.2M NAF, 20% PEG-3350, PH 7.3, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET 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 HIS A 1 REMARK 465 GLU A 71 REMARK 465 ARG A 72 REMARK 465 GLY A 73 REMARK 465 LEU A 74 REMARK 465 GLN A 75 REMARK 465 ARG A 76 REMARK 465 GLY A 86 REMARK 465 ASN A 87 REMARK 465 ARG A 88 REMARK 465 HIS A 159 REMARK 465 ARG A 160 REMARK 465 SER A 161 REMARK 465 HIS A 162 REMARK 465 ARG A 163 REMARK 465 GLN A 164 REMARK 465 MET A 165 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 ASP A 38 94.02 -64.11 REMARK 500 THR A 67 -75.51 -86.94 REMARK 500 VAL A 68 125.99 -29.24 REMARK 500 PRO A 90 -95.04 -114.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5V6G RELATED DB: PDB REMARK 900 RELATED ID: 5V7B RELATED DB: PDB REMARK 900 RELATED ID: 5V7S RELATED DB: PDB DBREF 5V8A A 2 165 UNP P05777 M1_I33A0 2 165 SEQADV 5V8A MET A -5 UNP P05777 EXPRESSION TAG SEQADV 5V8A HIS A -4 UNP P05777 EXPRESSION TAG SEQADV 5V8A HIS A -3 UNP P05777 EXPRESSION TAG SEQADV 5V8A HIS A -2 UNP P05777 EXPRESSION TAG SEQADV 5V8A HIS A -1 UNP P05777 EXPRESSION TAG SEQADV 5V8A HIS A 0 UNP P05777 EXPRESSION TAG SEQADV 5V8A HIS A 1 UNP P05777 EXPRESSION TAG SEQADV 5V8A ARG A 88 UNP P05777 GLY 88 ENGINEERED MUTATION SEQADV 5V8A SER A 101 UNP P05777 ARG 101 ENGINEERED MUTATION SEQADV 5V8A SER A 105 UNP P05777 ARG 105 ENGINEERED MUTATION SEQRES 1 A 171 MET HIS HIS HIS HIS HIS HIS SER LEU LEU THR GLU VAL SEQRES 2 A 171 GLU THR TYR VAL LEU SER ILE VAL PRO SER GLY PRO LEU SEQRES 3 A 171 LYS ALA GLU ILE ALA GLN ARG LEU GLU ASP VAL PHE ALA SEQRES 4 A 171 GLY LYS ASN THR ASP LEU GLU VAL LEU MET GLU TRP LEU SEQRES 5 A 171 LYS THR ARG PRO ILE LEU SER PRO LEU THR LYS GLY ILE SEQRES 6 A 171 LEU GLY PHE VAL PHE THR LEU THR VAL PRO SER GLU ARG SEQRES 7 A 171 GLY LEU GLN ARG ARG ARG PHE VAL GLN ASN ALA LEU ASN SEQRES 8 A 171 GLY ASN ARG ASP PRO ASN ASN MET ASP LYS ALA VAL LYS SEQRES 9 A 171 LEU TYR SER LYS LEU LYS SER GLU ILE THR PHE HIS GLY SEQRES 10 A 171 ALA LYS GLU ILE ALA LEU SER TYR SER ALA GLY ALA LEU SEQRES 11 A 171 ALA SER CYS MET GLY LEU ILE TYR ASN ARG MET GLY ALA SEQRES 12 A 171 VAL THR THR GLU VAL ALA PHE GLY LEU VAL CYS ALA THR SEQRES 13 A 171 CYS GLU GLN ILE ALA ASP SER GLN HIS ARG SER HIS ARG SEQRES 14 A 171 GLN MET FORMUL 2 HOH *2(H2 O) HELIX 1 AA1 LEU A 3 LEU A 12 1 10 HELIX 2 AA2 PRO A 19 PHE A 32 1 14 HELIX 3 AA3 ASP A 38 THR A 48 1 11 HELIX 4 AA4 SER A 53 VAL A 68 1 16 HELIX 5 AA5 ARG A 78 ASN A 85 1 8 HELIX 6 AA6 ASN A 91 LYS A 104 1 14 HELIX 7 AA7 THR A 108 LEU A 117 1 10 HELIX 8 AA8 SER A 120 ASN A 133 1 14 HELIX 9 AA9 THR A 139 ALA A 155 1 17 CRYST1 27.664 33.341 36.151 112.18 100.38 94.21 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 0.036148 0.002662 0.008372 0.00000 SCALE2 0.000000 0.030075 0.013060 0.00000 SCALE3 0.000000 0.000000 0.030659 0.00000