HEADER PROTEIN FIBRIL 05-FEB-13 2M4J TITLE 40-RESIDUE BETA-AMYLOID FIBRIL DERIVED FROM ALZHEIMER'S DISEASE BRAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I; COMPND 4 FRAGMENT: UNP RESIDUES 672-711; COMPND 5 SYNONYM: ABPP, APPI, APP, ALZHEIMER DISEASE AMYLOID PROTEIN, CEREBRAL COMPND 6 VASCULAR AMYLOID PEPTIDE, CVAP, PREA4, PROTEASE NEXIN-II, PN-II, N- COMPND 7 APP, SOLUBLE APP-ALPHA, S-APP-ALPHA, SOLUBLE APP-BETA, S-APP-BETA, COMPND 8 C99, BETA-AMYLOID PROTEIN 42, BETA-APP42, BETA-AMYLOID PROTEIN 40, COMPND 9 BETA-APP40, C83, P3(42), P3(40), C80, GAMMA-SECRETASE C-TERMINAL COMPND 10 FRAGMENT 59, AMYLOID INTRACELLULAR DOMAIN 59, AICD-59, AID(59), COMPND 11 GAMMA-CTF(59), GAMMA-SECRETASE C-TERMINAL FRAGMENT 57, AMYLOID COMPND 12 INTRACELLULAR DOMAIN 57, AICD-57, AID(57), GAMMA-CTF(57), GAMMA- COMPND 13 SECRETASE C-TERMINAL FRAGMENT 50, AMYLOID INTRACELLULAR DOMAIN 50, COMPND 14 AICD-50, AID(50), GAMMA-CTF(50), C31 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS AMYLOID, ALZHEIMER'S DISEASE, SOLID STATE NMR, PROTEIN FIBRIL EXPDTA SOLID-STATE NMR NUMMDL 20 AUTHOR J.LU,W.QIANG,S.C.MEREDITH,W.YAU,C.D.SCHWEITERS,R.TYCKO REVDAT 4 14-JUN-23 2M4J 1 REMARK REVDAT 3 05-FEB-14 2M4J 1 REVDAT 2 02-OCT-13 2M4J 1 JRNL REVDAT 1 25-SEP-13 2M4J 0 JRNL AUTH J.X.LU,W.QIANG,W.M.YAU,C.D.SCHWIETERS,S.C.MEREDITH,R.TYCKO JRNL TITL MOLECULAR STRUCTURE OF BETA-AMYLOID FIBRILS IN ALZHEIMER'S JRNL TITL 2 DISEASE BRAIN TISSUE. JRNL REF CELL(CAMBRIDGE,MASS.) V. 154 1257 2013 JRNL REFN ISSN 0092-8674 JRNL PMID 24034249 JRNL DOI 10.1016/J.CELL.2013.08.035 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INCLUDES "NON-CRYSTALLOGRAPHIC" REMARK 3 SYMMETRY, 3-FOLD ROTATIONAL SYMMETRY, AND TRANSLATIONAL SYMMETRY REMARK 3 RESTRAINTS. THREE STAGES OF ANNEALING, STARTING WITH RANDOM REMARK 3 CONFIGURATION OF NINE BETA-AMYLOID PEPTIDE MOLECULES. SEE REMARK 3 PUBLICATION FOR FULL DETAILS. REMARK 4 REMARK 4 2M4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000103199. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1-2 MG SELECTIVELY AND UNIFORMLY REMARK 210 LABELED SAMPLES BETA-AMYLOID REMARK 210 PEPTIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 13C-13C WITH FPRFDR; 2D AND REMARK 210 3D NCACX; 2D NCOCX; 3D NCOCX; 2D REMARK 210 NCACX; 2D 13C-13C WITH SPIN REMARK 210 DIFFUSION; 2D 13C-13C WITH RAD; REMARK 210 2D 13C-13C WITH PAR; 2D 15N-13C REMARK 210 TEDOR; 15N- AND 13C-BARE; 13C REMARK 210 PITHIRDS-CT REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : INFINITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 600 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO VIOLATIONS, LOW RESTRAINT REMARK 210 ENERGY, AND MAXIMUM STRUCTURAL REMARK 210 DIVERSITY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 THESE RECORDS ARE MEANINGLESS. 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: NONAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 18 SER D 26 CA SER D 26 CB 0.103 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 18 SER D 26 CA - C - O ANGL. DEV. = -12.8 DEGREES REMARK 500 18 SER D 26 CA - C - N ANGL. DEV. = 16.1 DEGREES REMARK 500 19 ALA D 21 CB - CA - C ANGL. DEV. = 9.5 DEGREES REMARK 500 20 VAL D 24 CB - CA - C ANGL. DEV. = 12.4 DEGREES 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 1 SER A 8 -168.91 -163.24 REMARK 500 1 HIS A 14 97.39 -164.53 REMARK 500 1 LYS A 16 95.68 -169.77 REMARK 500 1 PHE A 20 74.83 53.45 REMARK 500 1 ALA A 21 -77.77 -79.94 REMARK 500 1 SER A 26 -168.01 -61.19 REMARK 500 1 SER B 8 -168.51 -162.56 REMARK 500 1 HIS B 14 97.33 -164.65 REMARK 500 1 LYS B 16 95.63 -170.22 REMARK 500 1 PHE B 20 74.79 53.10 REMARK 500 1 ALA B 21 -78.01 -79.98 REMARK 500 1 SER B 26 -167.74 -61.18 REMARK 500 1 SER C 8 -168.71 -162.99 REMARK 500 1 HIS C 14 97.31 -164.85 REMARK 500 1 LYS C 16 95.81 -170.06 REMARK 500 1 PHE C 20 74.77 53.28 REMARK 500 1 ALA C 21 -78.23 -79.96 REMARK 500 1 SER C 26 -168.18 -61.59 REMARK 500 1 HIS D 14 104.37 -165.04 REMARK 500 1 LYS D 16 104.59 -166.03 REMARK 500 1 PHE D 20 71.69 55.65 REMARK 500 1 ALA D 21 -73.03 -81.92 REMARK 500 1 SER D 26 -170.71 -57.72 REMARK 500 1 SER E 8 -168.25 -163.68 REMARK 500 1 HIS E 14 97.15 -164.32 REMARK 500 1 LYS E 16 94.67 -169.77 REMARK 500 1 PHE E 20 73.57 54.47 REMARK 500 1 ALA E 21 -78.46 -78.27 REMARK 500 1 SER E 26 -167.48 -61.81 REMARK 500 1 SER F 8 -168.33 -163.60 REMARK 500 1 HIS F 14 97.26 -163.94 REMARK 500 1 LYS F 16 94.71 -169.50 REMARK 500 1 PHE F 20 74.08 54.41 REMARK 500 1 ALA F 21 -78.42 -78.40 REMARK 500 1 SER F 26 -167.63 -62.24 REMARK 500 1 SER G 8 -166.23 -160.11 REMARK 500 1 HIS G 14 97.63 -165.22 REMARK 500 1 LYS G 16 94.37 -170.32 REMARK 500 1 PHE G 20 73.43 54.40 REMARK 500 1 ALA G 21 -77.86 -77.49 REMARK 500 1 SER G 26 -167.73 -62.93 REMARK 500 1 SER H 8 -166.52 -160.39 REMARK 500 1 HIS H 14 97.33 -165.22 REMARK 500 1 LYS H 16 94.22 -170.31 REMARK 500 1 PHE H 20 73.63 54.55 REMARK 500 1 ALA H 21 -77.98 -77.33 REMARK 500 1 SER H 26 -167.63 -63.77 REMARK 500 1 SER I 8 -166.63 -160.41 REMARK 500 1 HIS I 14 97.41 -165.05 REMARK 500 1 LYS I 16 94.02 -170.36 REMARK 500 REMARK 500 THIS ENTRY HAS 1062 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 18 GLY D 25 13.39 REMARK 500 19 PHE D 19 -13.55 REMARK 500 20 GLY D 25 10.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19009 RELATED DB: BMRB DBREF 2M4J A 1 40 UNP P05067 A4_HUMAN 672 711 DBREF 2M4J B 1 40 UNP P05067 A4_HUMAN 672 711 DBREF 2M4J C 1 40 UNP P05067 A4_HUMAN 672 711 DBREF 2M4J D 1 40 UNP P05067 A4_HUMAN 672 711 DBREF 2M4J E 1 40 UNP P05067 A4_HUMAN 672 711 DBREF 2M4J F 1 40 UNP P05067 A4_HUMAN 672 711 DBREF 2M4J G 1 40 UNP P05067 A4_HUMAN 672 711 DBREF 2M4J H 1 40 UNP P05067 A4_HUMAN 672 711 DBREF 2M4J I 1 40 UNP P05067 A4_HUMAN 672 711 SEQRES 1 A 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 A 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 A 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 A 40 VAL SEQRES 1 B 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 B 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 B 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 B 40 VAL SEQRES 1 C 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 C 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 C 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 C 40 VAL SEQRES 1 D 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 D 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 D 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 D 40 VAL SEQRES 1 E 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 E 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 E 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 E 40 VAL SEQRES 1 F 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 F 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 F 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 F 40 VAL SEQRES 1 G 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 G 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 G 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 G 40 VAL SEQRES 1 H 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 H 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 H 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 H 40 VAL SEQRES 1 I 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 I 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 I 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 I 40 VAL SHEET 1 A 3 VAL A 12 HIS A 13 0 SHEET 2 A 3 VAL D 12 HIS D 13 1 O VAL D 12 N HIS A 13 SHEET 3 A 3 VAL G 12 HIS G 13 1 O VAL G 12 N HIS D 13 SHEET 1 B 3 VAL A 18 PHE A 19 0 SHEET 2 B 3 VAL D 18 PHE D 19 1 O VAL D 18 N PHE A 19 SHEET 3 B 3 VAL G 18 PHE G 19 1 O VAL G 18 N PHE D 19 SHEET 1 C 3 MET A 35 VAL A 36 0 SHEET 2 C 3 MET D 35 VAL D 36 1 O MET D 35 N VAL A 36 SHEET 3 C 3 MET G 35 VAL G 36 1 O MET G 35 N VAL D 36 SHEET 1 D 3 VAL B 12 HIS B 13 0 SHEET 2 D 3 VAL E 12 HIS E 13 1 O VAL E 12 N HIS B 13 SHEET 3 D 3 VAL H 12 HIS H 13 1 O VAL H 12 N HIS E 13 SHEET 1 E 3 VAL B 18 PHE B 19 0 SHEET 2 E 3 VAL E 18 PHE E 19 1 O VAL E 18 N PHE B 19 SHEET 3 E 3 VAL H 18 PHE H 19 1 O VAL H 18 N PHE E 19 SHEET 1 F 3 MET B 35 VAL B 36 0 SHEET 2 F 3 MET E 35 VAL E 36 1 O MET E 35 N VAL B 36 SHEET 3 F 3 MET H 35 VAL H 36 1 O MET H 35 N VAL E 36 SHEET 1 G 3 VAL C 12 HIS C 13 0 SHEET 2 G 3 VAL F 12 HIS F 13 1 O VAL F 12 N HIS C 13 SHEET 3 G 3 VAL I 12 HIS I 13 1 O VAL I 12 N HIS F 13 SHEET 1 H 3 VAL C 18 PHE C 19 0 SHEET 2 H 3 VAL F 18 PHE F 19 1 O VAL F 18 N PHE C 19 SHEET 3 H 3 VAL I 18 PHE I 19 1 O VAL I 18 N PHE F 19 SHEET 1 I 3 MET C 35 VAL C 36 0 SHEET 2 I 3 MET F 35 VAL F 36 1 O MET F 35 N VAL C 36 SHEET 3 I 3 MET I 35 VAL I 36 1 O MET I 35 N VAL F 36 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1