HEADER PROTEIN FIBRIL 03-MAY-17 5VOS TITLE VGSNKGAIIGL FROM AMYLOID BETA DETERMINED BY MICROED COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VGSNKGAIIGL PEPTIDE (RESIDUES 24-34, UNP RESIDUES 7-17); COMPND 5 ENGINEERED: 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 KEYWDS AMYLOID, STERIC ZIPPER, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR J.A.RODRIGUEZ,M.R.SAWAYA,D.CASCIO,D.S.EISENBERG,S.L.GRINER,T.GONEN REVDAT 8 13-MAR-24 5VOS 1 REMARK REVDAT 7 30-JUN-21 5VOS 1 REMARK REVDAT 6 20-NOV-19 5VOS 1 REMARK REVDAT 5 06-JUN-18 5VOS 1 REMARK REVDAT 4 25-APR-18 5VOS 1 REMARK REVDAT 3 07-MAR-18 5VOS 1 JRNL REVDAT 2 10-JAN-18 5VOS 1 JRNL REVDAT 1 03-JAN-18 5VOS 0 JRNL AUTH P.KROTEE,S.L.GRINER,M.R.SAWAYA,D.CASCIO,J.A.RODRIGUEZ,D.SHI, JRNL AUTH 2 S.PHILIPP,K.MURRAY,L.SAELICES,J.LEE,P.SEIDLER,C.G.GLABE, JRNL AUTH 3 L.JIANG,T.GONEN,D.S.EISENBERG JRNL TITL COMMON FIBRILLAR SPINES OF AMYLOID-BETA AND HUMAN ISLET JRNL TITL 2 AMYLOID POLYPEPTIDE REVEALED BY MICROELECTRON DIFFRACTION JRNL TITL 3 AND STRUCTURE-BASED INHIBITORS. JRNL REF J. BIOL. CHEM. V. 293 2888 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29282295 JRNL DOI 10.1074/JBC.M117.806109 REMARK 2 REMARK 2 RESOLUTION. 1.42 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.5 REMARK 3 NUMBER OF REFLECTIONS : 1014 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) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 113 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 72 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 1 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.04000 REMARK 3 B22 (A**2) : -1.30000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.83000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.115 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.871 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 5VOS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227781. 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 : 17-APR-15 REMARK 240 TEMPERATURE (KELVIN) : 100.0 REMARK 240 PH : 4.00 REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 1129 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 240 RESOLUTION RANGE LOW (A) : 32.960 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 85.5 REMARK 240 DATA REDUNDANCY : 5.175 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.42 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.49 REMARK 240 COMPLETENESS FOR SHELL (%) : 47.5 REMARK 240 DATA REDUNDANCY IN SHELL : 2.57 REMARK 240 R MERGE FOR SHELL (I) : 0.49600 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : PHASER REMARK 240 STARTING MODEL : NULL 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 2.36500 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 4.73000 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 9.46000 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 -4.73000 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 -9.46000 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 1.30947 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 2.36500 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 98.87845 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 1.30947 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 7.09500 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 98.87845 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 1.30947 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 11.82500 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 98.87845 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 9 -1.000000 0.000000 0.000000 1.30947 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 -2.36500 REMARK 350 BIOMT3 9 0.000000 0.000000 -1.000000 98.87845 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 1.30947 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 -7.09500 REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 98.87845 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KNZ RELATED DB: PDB REMARK 900 HOMOLOGOUS SEQUENCE FROM HIAPP REMARK 900 RELATED ID: EMD-8720 RELATED DB: EMDB REMARK 900 VGSNKGAIIGL FROM AMYLOID BETA DETERMINED BY MICROED DBREF 5VOS A 24 34 UNP L7XCZ9 L7XCZ9_HUMAN 7 17 SEQRES 1 A 11 VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU FORMUL 2 HOH *(H2 O) CRYST1 18.780 4.730 33.470 90.00 100.02 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 0.053248 0.000000 0.009405 0.00000 SCALE2 0.000000 0.211416 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030340 0.00000 ATOM 1 N VAL A 24 9.585 -0.410 36.450 1.00 18.03 N ATOM 2 CA VAL A 24 8.348 -1.211 36.293 1.00 17.53 C ATOM 3 C VAL A 24 7.375 -0.492 35.356 1.00 13.69 C ATOM 4 O VAL A 24 7.456 0.703 35.197 1.00 13.25 O ATOM 5 CB VAL A 24 7.754 -1.499 37.685 1.00 18.06 C ATOM 6 CG1 VAL A 24 7.607 -0.226 38.435 1.00 20.35 C ATOM 7 CG2 VAL A 24 6.389 -2.147 37.632 1.00 20.65 C ATOM 8 N GLY A 25 6.514 -1.238 34.667 1.00 10.67 N ATOM 9 CA GLY A 25 5.526 -0.630 33.774 1.00 8.87 C ATOM 10 C GLY A 25 4.452 0.077 34.545 1.00 7.23 C ATOM 11 O GLY A 25 4.229 1.277 34.381 1.00 7.12 O ATOM 12 N SER A 26 3.788 -0.685 35.396 1.00 6.65 N ATOM 13 CA SER A 26 2.693 -0.181 36.209 1.00 6.64 C ATOM 14 C SER A 26 2.872 -0.705 37.612 1.00 5.64 C ATOM 15 O SER A 26 3.074 -1.883 37.788 1.00 6.33 O ATOM 16 CB SER A 26 1.346 -0.647 35.627 1.00 7.02 C ATOM 17 OG SER A 26 0.268 -0.552 36.548 1.00 9.40 O ATOM 18 N ASN A 27 2.853 0.174 38.607 1.00 5.63 N ATOM 19 CA ASN A 27 2.808 -0.290 39.974 1.00 5.53 C ATOM 20 C ASN A 27 1.560 0.286 40.581 1.00 5.96 C ATOM 21 O ASN A 27 1.388 1.485 40.533 1.00 5.61 O ATOM 22 CB ASN A 27 4.049 0.167 40.769 1.00 5.80 C ATOM 23 CG ASN A 27 4.150 -0.487 42.128 1.00 5.69 C ATOM 24 OD1 ASN A 27 4.076 -1.673 42.244 1.00 7.13 O ATOM 25 ND2 ASN A 27 4.303 0.300 43.162 1.00 5.70 N ATOM 26 N LYS A 28 0.679 -0.562 41.111 1.00 6.74 N ATOM 27 CA LYS A 28 -0.613 -0.107 41.660 1.00 7.37 C ATOM 28 C LYS A 28 -0.782 -0.694 43.024 1.00 6.35 C ATOM 29 O LYS A 28 -0.649 -1.891 43.181 1.00 5.98 O ATOM 30 CB LYS A 28 -1.793 -0.608 40.818 1.00 10.05 C ATOM 31 CG LYS A 28 -1.881 -0.124 39.397 1.00 13.08 C ATOM 32 CD LYS A 28 -3.221 -0.537 38.789 1.00 15.61 C ATOM 33 CE LYS A 28 -3.518 0.245 37.539 1.00 21.38 C ATOM 34 NZ LYS A 28 -4.708 -0.310 36.806 1.00 21.78 N ATOM 35 N GLY A 29 -1.073 0.130 44.016 1.00 6.55 N ATOM 36 CA GLY A 29 -1.202 -0.406 45.339 1.00 6.36 C ATOM 37 C GLY A 29 -2.292 0.271 46.105 1.00 5.27 C ATOM 38 O GLY A 29 -2.486 1.454 46.005 1.00 5.35 O ATOM 39 N ALA A 30 -2.955 -0.515 46.917 1.00 5.46 N ATOM 40 CA ALA A 30 -3.876 -0.026 47.906 1.00 5.33 C ATOM 41 C ALA A 30 -3.483 -0.651 49.233 1.00 4.81 C ATOM 42 O ALA A 30 -3.435 -1.861 49.368 1.00 4.77 O ATOM 43 CB ALA A 30 -5.269 -0.446 47.531 1.00 6.37 C ATOM 44 N ILE A 31 -3.163 0.187 50.196 1.00 5.04 N ATOM 45 CA ILE A 31 -2.776 -0.287 51.534 1.00 5.15 C ATOM 46 C ILE A 31 -3.720 0.384 52.484 1.00 5.10 C ATOM 47 O ILE A 31 -3.595 1.576 52.788 1.00 4.42 O ATOM 48 CB ILE A 31 -1.338 0.064 51.912 1.00 5.73 C ATOM 49 CG1 ILE A 31 -0.381 -0.576 50.912 1.00 6.26 C ATOM 50 CG2 ILE A 31 -1.041 -0.460 53.290 1.00 5.92 C ATOM 51 CD1 ILE A 31 1.064 -0.295 51.191 1.00 6.96 C ATOM 52 N ILE A 32 -4.675 -0.399 52.928 1.00 5.76 N ATOM 53 CA ILE A 32 -5.861 0.141 53.495 1.00 6.89 C ATOM 54 C ILE A 32 -6.082 -0.515 54.857 1.00 6.63 C ATOM 55 O ILE A 32 -6.137 -1.709 54.942 1.00 6.46 O ATOM 56 CB ILE A 32 -7.089 -0.100 52.574 1.00 9.87 C ATOM 57 CG1 ILE A 32 -6.804 0.449 51.176 1.00 10.65 C ATOM 58 CG2 ILE A 32 -8.335 0.500 53.214 1.00 12.70 C ATOM 59 CD1 ILE A 32 -7.938 1.062 50.419 1.00 16.92 C ATOM 60 N GLY A 33 -6.206 0.306 55.895 1.00 9.17 N ATOM 61 CA GLY A 33 -6.577 -0.150 57.226 1.00 12.74 C ATOM 62 C GLY A 33 -7.997 0.265 57.540 1.00 13.72 C ATOM 63 O GLY A 33 -8.306 1.453 57.515 1.00 13.74 O ATOM 64 N LEU A 34 -8.849 -0.728 57.792 1.00 22.20 N ATOM 65 CA LEU A 34 -10.201 -0.529 58.315 1.00 28.84 C ATOM 66 C LEU A 34 -10.331 -1.076 59.764 1.00 27.99 C ATOM 67 O LEU A 34 -11.207 -0.671 60.546 1.00 28.91 O ATOM 68 CB LEU A 34 -11.250 -1.196 57.388 1.00 34.49 C ATOM 69 CG LEU A 34 -11.866 -0.323 56.286 1.00 38.09 C ATOM 70 CD1 LEU A 34 -10.749 0.182 55.404 1.00 42.18 C ATOM 71 CD2 LEU A 34 -12.895 -1.058 55.438 1.00 40.02 C ATOM 72 OXT LEU A 34 -9.592 -1.961 60.205 1.00 30.29 O TER 73 LEU A 34 HETATM 74 O HOH A 101 -0.080 -2.580 37.756 1.00 15.91 O MASTER 195 0 0 0 0 0 0 6 73 1 0 1 END