HEADER PROTEIN BINDING 24-NOV-14 4X1M TITLE STRUCTURAL BASIS FOR MUTATION-INDUCED DESTABILIZATION OF PROFILIN 1 IN TITLE 2 ALS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROFILIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EPIDIDYMIS TISSUE PROTEIN LI 184A,PROFILIN I; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PFN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS ALS, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR T.V.SILVAS,S.M.D.SHANDILYA,C.A.SCHIFFER REVDAT 7 27-SEP-23 4X1M 1 REMARK REVDAT 6 18-DEC-19 4X1M 1 REMARK REVDAT 5 25-APR-18 4X1M 1 JRNL REVDAT 4 22-NOV-17 4X1M 1 REMARK REVDAT 3 13-SEP-17 4X1M 1 SOURCE KEYWDS REMARK REVDAT 2 17-JUN-15 4X1M 1 TITLE JRNL REVDAT 1 10-JUN-15 4X1M 0 JRNL AUTH S.BOOPATHY,T.V.SILVAS,M.TISCHBEIN,S.JANSEN,S.M.SHANDILYA, JRNL AUTH 2 J.A.ZITZEWITZ,J.E.LANDERS,B.L.GOODE,C.A.SCHIFFER,D.A.BOSCO JRNL TITL STRUCTURAL BASIS FOR MUTATION-INDUCED DESTABILIZATION OF JRNL TITL 2 PROFILIN 1 IN ALS. JRNL REF PROC. NATL. ACAD. SCI. V. 112 7984 2015 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 26056300 JRNL DOI 10.1073/PNAS.1424108112 REMARK 2 REMARK 2 RESOLUTION. 2.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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) : 2.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 6422 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.640 REMARK 3 FREE R VALUE TEST SET COUNT : 298 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 19.2831 - 2.7330 0.99 3100 135 0.1983 0.1930 REMARK 3 2 2.7330 - 2.1702 1.00 3024 163 0.1926 0.2528 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.400 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 : 0.003 935 REMARK 3 ANGLE : 0.668 1271 REMARK 3 CHIRALITY : 0.026 154 REMARK 3 PLANARITY : 0.003 161 REMARK 3 DIHEDRAL : 12.151 320 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 4X1M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000204808. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6468 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.170 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.09500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 18.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1FIK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PFN1 CRYSTALS WERE GROWN BY HANGING REMARK 280 DROP VAPOR DIFFUSION AFTER MIXING THE PFN1 PROTEIN WITH A 1:1 REMARK 280 RATIO OF RESERVOIR SOLUTION AT 298K FOR E117G. RESERVOIR REMARK 280 SOLUTION FOR E117G CONTAINED 50 MM KH2PO4, 41% (WT/VOL) PEG 8, REMARK 280 000 AND 100 MM MES, PH 6.0, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 36.82500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.85600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.82500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.85600 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: 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 1 REMARK 465 ALA A 2 REMARK 465 PHE A 59 REMARK 465 TYR A 60 REMARK 465 VAL A 61 REMARK 465 ASN A 62 REMARK 465 ASP A 81 REMARK 465 GLY A 82 REMARK 465 THR A 93 REMARK 465 GLY A 94 REMARK 465 GLY A 95 REMARK 465 TYR A 140 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 LYS A 38 CG CD CE NZ REMARK 470 LYS A 54 CG CD CE NZ REMARK 470 SER A 58 OG REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 80 CG CD OE1 NE2 REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 91 CG CD CE NZ REMARK 470 SER A 92 OG REMARK 470 THR A 98 OG1 CG2 REMARK 470 ASP A 107 CG OD1 OD2 REMARK 470 LYS A 108 CG CD CE NZ 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 O HOH A 228 O HOH A 231 1.87 REMARK 500 O HOH A 279 O HOH A 289 2.02 REMARK 500 O HOH A 270 O HOH A 273 2.10 REMARK 500 O HOH A 273 O HOH A 280 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 236 O HOH A 236 2856 1.83 REMARK 500 O HOH A 201 O HOH A 232 4755 2.15 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 ASP A 27 -68.39 67.77 REMARK 500 LYS A 38 -138.82 -104.93 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 288 DISTANCE = 6.75 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4X1L RELATED DB: PDB REMARK 900 RELATED ID: 4X25 RELATED DB: PDB DBREF 4X1M A 1 140 UNP P07737 PROF1_HUMAN 1 140 SEQADV 4X1M GLY A 117 UNP P07737 GLU 117 ENGINEERED MUTATION SEQRES 1 A 140 MET ALA GLY TRP ASN ALA TYR ILE ASP ASN LEU MET ALA SEQRES 2 A 140 ASP GLY THR CYS GLN ASP ALA ALA ILE VAL GLY TYR LYS SEQRES 3 A 140 ASP SER PRO SER VAL TRP ALA ALA VAL PRO GLY LYS THR SEQRES 4 A 140 PHE VAL ASN ILE THR PRO ALA GLU VAL GLY VAL LEU VAL SEQRES 5 A 140 GLY LYS ASP ARG SER SER PHE TYR VAL ASN GLY LEU THR SEQRES 6 A 140 LEU GLY GLY GLN LYS CYS SER VAL ILE ARG ASP SER LEU SEQRES 7 A 140 LEU GLN ASP GLY GLU PHE SER MET ASP LEU ARG THR LYS SEQRES 8 A 140 SER THR GLY GLY ALA PRO THR PHE ASN VAL THR VAL THR SEQRES 9 A 140 LYS THR ASP LYS THR LEU VAL LEU LEU MET GLY LYS GLY SEQRES 10 A 140 GLY VAL HIS GLY GLY LEU ILE ASN LYS LYS CYS TYR GLU SEQRES 11 A 140 MET ALA SER HIS LEU ARG ARG SER GLN TYR FORMUL 2 HOH *94(H2 O) HELIX 1 AA1 TRP A 4 ALA A 13 1 10 HELIX 2 AA2 THR A 39 ILE A 43 5 5 HELIX 3 AA3 THR A 44 GLY A 53 1 10 HELIX 4 AA4 HIS A 120 ARG A 137 1 18 SHEET 1 AA1 7 SER A 30 ALA A 34 0 SHEET 2 AA1 7 CYS A 17 GLY A 24 -1 N ILE A 22 O ALA A 33 SHEET 3 AA1 7 THR A 109 GLY A 115 -1 O LEU A 110 N VAL A 23 SHEET 4 AA1 7 ASN A 100 LYS A 105 -1 N THR A 104 O VAL A 111 SHEET 5 AA1 7 SER A 85 THR A 90 -1 N LEU A 88 O VAL A 101 SHEET 6 AA1 7 GLN A 69 ASP A 76 -1 N SER A 72 O ARG A 89 SHEET 7 AA1 7 LEU A 64 LEU A 66 -1 N LEU A 64 O CYS A 71 CRYST1 73.650 31.712 60.539 90.00 122.03 90.00 C 1 2 1 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 0.013578 0.000000 0.008494 0.00000 SCALE2 0.000000 0.031534 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019484 0.00000