HEADER LIPID BINDING PROTEIN 05-MAY-15 4ZNN TITLE MICROED STRUCTURE OF THE SEGMENT, GVVHGVTTVA, FROM THE A53T FAMILIAL TITLE 2 MUTANT OF PARKINSON'S DISEASE PROTEIN, ALPHA-SYNUCLEIN RESIDUES 47-56 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-SYNUCLEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NON-A BETA COMPONENT OF AD AMYLOID,NON-A4 COMPONENT OF COMPND 5 AMYLOID PRECURSOR,NACP; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 OTHER_DETAILS: SYNTHETIC PEPTIDE GVVHGVTTVA CORRESPONDING TO SEGMENT SOURCE 7 47-56 OF HUMAN ALPHA-SYNUCLEIN KEYWDS AMYLOID, ALPHA-SYNUCLEIN, PARKINSON'S DISEASE, TOXIC CORE, NACORE, KEYWDS 2 LIPID BINDING PROTEIN EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR J.A.RODRIGUEZ,M.IVANOVA,M.R.SAWAYA,D.CASCIO,F.REYES,D.SHI,L.JOHNSON, AUTHOR 2 E.GUENTHER,S.SANGWAN,J.HATTNE,B.NANNENGA,A.S.BREWSTER, AUTHOR 3 M.MESSERSCHMIDT,S.BOUTET,N.K.SAUTER,T.GONEN,D.S.EISENBERG REVDAT 8 04-MAR-26 4ZNN 1 REMARK REVDAT 7 06-MAR-24 4ZNN 1 REMARK REVDAT 6 18-DEC-19 4ZNN 1 REMARK REVDAT 5 06-SEP-17 4ZNN 1 REMARK REVDAT 4 30-NOV-16 4ZNN 1 REMARK REVDAT 3 07-OCT-15 4ZNN 1 JRNL REVDAT 2 23-SEP-15 4ZNN 1 JRNL REVDAT 1 09-SEP-15 4ZNN 0 JRNL AUTH J.A.RODRIGUEZ,M.I.IVANOVA,M.R.SAWAYA,D.CASCIO,F.E.REYES, JRNL AUTH 2 D.SHI,S.SANGWAN,E.L.GUENTHER,L.M.JOHNSON,M.ZHANG,L.JIANG, JRNL AUTH 3 M.A.ARBING,B.L.NANNENGA,J.HATTNE,J.WHITELEGGE,A.S.BREWSTER, JRNL AUTH 4 M.MESSERSCHMIDT,S.BOUTET,N.K.SAUTER,T.GONEN,D.S.EISENBERG JRNL TITL STRUCTURE OF THE TOXIC CORE OF ALPHA-SYNUCLEIN FROM JRNL TITL 2 INVISIBLE CRYSTALS. JRNL REF NATURE V. 525 486 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26352473 JRNL DOI 10.1038/NATURE15368 REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.7 REMARK 3 NUMBER OF REFLECTIONS : 1006 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 112 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 66 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.08000 REMARK 3 B22 (A**2) : -1.13000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.112 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.491 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4ZNN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000209579. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : 20-APR-15 REMARK 240 TEMPERATURE (KELVIN) : 100.0 REMARK 240 PH : 7.00 REMARK 240 NUMBER OF CRYSTALS USED : 1 REMARK 240 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 240 DETECTOR TYPE : NULL REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 1120 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 240 RESOLUTION RANGE LOW (A) : 16.500 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 86.9 REMARK 240 DATA REDUNDANCY : 3.700 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.41 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.48 REMARK 240 COMPLETENESS FOR SHELL (%) : 58.5 REMARK 240 DATA REDUNDANCY IN SHELL : NULL REMARK 240 R MERGE FOR SHELL (I) : 0.78000 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : PHASER 2.5.6 REMARK 240 STARTING MODEL : IDEAL MODEL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 2.35500 REMARK 290 SMTRY3 2 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: DECAMERIC 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 4.71000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 9.42000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 14.13000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 18.84000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 -2.49379 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 2.35500 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 32.93572 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 -2.49379 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 7.06500 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 32.93572 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 -2.49379 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 11.77500 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 32.93572 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 9 -1.000000 0.000000 0.000000 -2.49379 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 16.48500 REMARK 350 BIOMT3 9 0.000000 0.000000 -1.000000 32.93572 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 -2.49379 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 21.19500 REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 32.93572 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RIL RELATED DB: PDB REMARK 900 ANOTHER SEGMENT FROM ALPHA-SYNUCLEIN REMARK 900 RELATED ID: EMD-3001 RELATED DB: EMDB DBREF 4ZNN A 47 56 UNP P37840 SYUA_HUMAN 47 56 SEQADV 4ZNN THR A 53 UNP P37840 ALA 53 ENGINEERED MUTATION SEQRES 1 A 10 GLY VAL VAL HIS GLY VAL THR THR VAL ALA FORMUL 2 HOH *4(H2 O) CRYST1 17.930 4.710 33.030 90.00 94.33 90.00 P 1 21 1 2 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 0.055772 0.000000 0.004219 0.00000 SCALE2 0.000000 0.212314 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030362 0.00000 ATOM 1 N GLY A 47 -6.815 -0.668 1.607 1.00 19.60 N ATOM 2 CA GLY A 47 -5.714 0.002 2.373 1.00 18.55 C ATOM 3 C GLY A 47 -4.357 -0.673 2.588 1.00 15.73 C ATOM 4 O GLY A 47 -4.212 -1.870 2.492 1.00 15.28 O ATOM 5 N VAL A 48 -3.381 0.125 2.953 1.00 16.06 N ATOM 6 CA VAL A 48 -2.062 -0.390 3.274 1.00 17.19 C ATOM 7 C VAL A 48 -1.636 0.175 4.600 1.00 15.56 C ATOM 8 O VAL A 48 -1.744 1.356 4.862 1.00 16.09 O ATOM 9 CB VAL A 48 -0.993 -0.045 2.197 1.00 16.98 C ATOM 10 CG1 VAL A 48 0.390 -0.488 2.640 1.00 18.97 C ATOM 11 CG2 VAL A 48 -1.378 -0.662 0.897 1.00 21.79 C ATOM 12 N VAL A 49 -1.095 -0.700 5.415 1.00 16.25 N ATOM 13 CA VAL A 49 -0.572 -0.311 6.669 1.00 17.10 C ATOM 14 C VAL A 49 0.840 -0.854 6.792 1.00 13.92 C ATOM 15 O VAL A 49 1.027 -2.022 6.720 1.00 14.77 O ATOM 16 CB VAL A 49 -1.411 -0.913 7.797 1.00 18.21 C ATOM 17 CG1 VAL A 49 -0.727 -0.645 9.123 1.00 24.67 C ATOM 18 CG2 VAL A 49 -2.800 -0.349 7.789 1.00 21.98 C ATOM 19 N HIS A 50 1.810 0.002 7.023 1.00 14.97 N ATOM 20 CA HIS A 50 3.191 -0.429 7.101 1.00 14.81 C ATOM 21 C HIS A 50 3.911 0.258 8.229 1.00 12.78 C ATOM 22 O HIS A 50 4.064 1.478 8.228 1.00 14.27 O ATOM 23 CB HIS A 50 3.871 -0.103 5.748 1.00 17.54 C ATOM 24 CG HIS A 50 5.247 -0.643 5.581 1.00 20.10 C ATOM 25 ND1 HIS A 50 5.861 -0.689 4.353 1.00 31.24 N ATOM 26 CD2 HIS A 50 6.108 -1.197 6.448 1.00 23.34 C ATOM 27 CE1 HIS A 50 7.059 -1.227 4.482 1.00 31.67 C ATOM 28 NE2 HIS A 50 7.239 -1.523 5.751 1.00 27.12 N ATOM 29 N GLY A 51 4.364 -0.527 9.189 1.00 13.20 N ATOM 30 CA GLY A 51 5.067 0.020 10.326 1.00 11.38 C ATOM 31 C GLY A 51 4.271 0.817 11.296 1.00 11.23 C ATOM 32 O GLY A 51 4.359 2.033 11.367 1.00 14.14 O ATOM 33 N VAL A 52 3.492 0.104 12.073 1.00 13.14 N ATOM 34 CA VAL A 52 2.585 0.677 13.085 1.00 12.89 C ATOM 35 C VAL A 52 3.006 0.047 14.361 1.00 12.85 C ATOM 36 O VAL A 52 2.958 -1.169 14.515 1.00 14.15 O ATOM 37 CB VAL A 52 1.127 0.330 12.827 1.00 15.29 C ATOM 38 CG1 VAL A 52 0.248 0.675 14.038 1.00 16.63 C ATOM 39 CG2 VAL A 52 0.674 1.047 11.596 1.00 16.11 C ATOM 40 N THR A 53 3.481 0.887 15.262 1.00 14.70 N ATOM 41 CA THR A 53 4.163 0.392 16.442 1.00 16.60 C ATOM 42 C THR A 53 3.424 0.965 17.631 1.00 12.84 C ATOM 43 O THR A 53 3.136 2.110 17.612 1.00 13.55 O ATOM 44 CB THR A 53 5.688 0.750 16.389 1.00 19.42 C ATOM 45 OG1 THR A 53 6.264 0.130 15.236 1.00 17.84 O ATOM 46 CG2 THR A 53 6.420 0.210 17.569 1.00 22.98 C ATOM 47 N THR A 54 3.173 0.129 18.647 1.00 13.49 N ATOM 48 CA THR A 54 2.559 0.516 19.903 1.00 12.98 C ATOM 49 C THR A 54 3.350 -0.122 21.014 1.00 12.94 C ATOM 50 O THR A 54 3.366 -1.339 21.140 1.00 17.14 O ATOM 51 CB THR A 54 1.138 -0.021 19.983 1.00 18.49 C ATOM 52 OG1 THR A 54 0.393 0.394 18.824 1.00 23.95 O ATOM 53 CG2 THR A 54 0.486 0.501 21.167 1.00 24.15 C ATOM 54 N VAL A 55 4.067 0.688 21.768 1.00 13.39 N ATOM 55 CA VAL A 55 4.888 0.205 22.851 1.00 13.49 C ATOM 56 C VAL A 55 4.350 0.769 24.174 1.00 14.87 C ATOM 57 O VAL A 55 4.161 1.981 24.269 1.00 12.81 O ATOM 58 CB VAL A 55 6.362 0.614 22.652 1.00 15.66 C ATOM 59 CG1 VAL A 55 7.152 0.297 23.874 1.00 17.11 C ATOM 60 CG2 VAL A 55 6.953 -0.121 21.455 1.00 18.23 C ATOM 61 N ALA A 56 4.065 -0.120 25.151 1.00 15.89 N ATOM 62 CA ALA A 56 3.720 0.313 26.515 1.00 22.36 C ATOM 63 C ALA A 56 4.941 0.140 27.420 1.00 30.33 C ATOM 64 O ALA A 56 5.714 -0.809 27.287 1.00 50.34 O ATOM 65 CB ALA A 56 2.499 -0.422 27.062 1.00 18.64 C ATOM 66 OXT ALA A 56 5.250 0.955 28.294 1.00 45.80 O TER 67 ALA A 56 HETATM 68 O HOH A 101 5.798 2.348 13.663 1.00 16.49 O HETATM 69 O HOH A 102 0.282 -1.835 17.069 1.00 19.45 O HETATM 70 O HOH A 103 3.490 -2.329 2.715 1.00 23.99 O HETATM 71 O HOH A 104 4.229 0.250 1.542 1.00 38.40 O MASTER 194 0 0 0 0 0 0 6 70 1 0 1 END