HEADER PROTEIN FIBRIL 19-JUN-13 2M9R TITLE 3D NMR STRUCTURE OF A COMPLEX BETWEEN THE AMYLOID BETA PEPTIDE (1-40) TITLE 2 AND THE POLYPHENOL EPSILON-VINIFERIN GLUCOSIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 672-711; 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 PEPTIDE, PROTEIN FIBRIL EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR J.MONTI,T.RICHARD REVDAT 1 11-SEP-13 2M9R 0 JRNL AUTH T.RICHARD,Y.PAPASTAMOULIS,W.T.PIERRE,J.P.MONTI JRNL TITL 3D NMR STRUCTURE OF A COMPLEX BETWEEN THE AMYLOID BETA JRNL TITL 2 PEPTIDE (1-40) AND THE POLYPHENOL EPSILON-VINIFERIN JRNL TITL 3 GLUCOSIDE: IMPLICATIONS IN ALZHEIMER'S DISEASE. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1830 5068 2013 JRNL REFN ISSN 0006-3002 JRNL PMID 23830862 JRNL DOI 10.1016/J.BBAGEN.2013.06.031 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : INSIGHTII REMARK 3 AUTHORS : ACCELRYS SOFTWARE INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THIS FAMILY REPRESENTS THE TURN IN THE REMARK 3 N-TERMINUS GLY9-LYS16 OBTAINED BY AN INDEPENDENT SUPERIMPOSITION REMARK 3 RELATIVE TO THE TURN IN THE C-TERMINUS. REMARK 4 REMARK 4 2M9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-13. REMARK 100 THE RCSB ID CODE IS RCSB103387. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM AMYLOID PEPTIDE, 100% DMSO- REMARK 210 D6 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : INSIGHTII REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 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: MONOMERIC 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 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 3 HIS A 13 CG HIS A 13 CD2 0.054 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 1 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 HIS A 6 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 1 HIS A 13 ND1 - CE1 - NE2 ANGL. DEV. = 8.5 DEGREES REMARK 500 1 HIS A 14 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 2 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 HIS A 6 ND1 - CE1 - NE2 ANGL. DEV. = 8.8 DEGREES REMARK 500 2 HIS A 13 ND1 - CE1 - NE2 ANGL. DEV. = 8.7 DEGREES REMARK 500 2 HIS A 14 ND1 - CE1 - NE2 ANGL. DEV. = 8.7 DEGREES REMARK 500 3 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 HIS A 6 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 3 HIS A 13 ND1 - CE1 - NE2 ANGL. DEV. = 8.5 DEGREES REMARK 500 3 HIS A 14 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 4 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 HIS A 6 ND1 - CE1 - NE2 ANGL. DEV. = 8.7 DEGREES REMARK 500 4 HIS A 13 ND1 - CE1 - NE2 ANGL. DEV. = 8.3 DEGREES REMARK 500 4 HIS A 14 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 5 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 HIS A 6 ND1 - CE1 - NE2 ANGL. DEV. = 8.7 DEGREES REMARK 500 5 HIS A 13 ND1 - CE1 - NE2 ANGL. DEV. = 8.7 DEGREES REMARK 500 5 HIS A 14 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 6 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 HIS A 6 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 6 HIS A 13 ND1 - CE1 - NE2 ANGL. DEV. = 8.7 DEGREES REMARK 500 6 HIS A 14 ND1 - CE1 - NE2 ANGL. DEV. = 8.8 DEGREES REMARK 500 7 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 7 HIS A 6 ND1 - CE1 - NE2 ANGL. DEV. = 8.7 DEGREES REMARK 500 7 HIS A 13 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 7 HIS A 14 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 8 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 8 HIS A 6 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 8 HIS A 13 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 8 HIS A 14 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 9 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 9 HIS A 6 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 9 HIS A 13 ND1 - CE1 - NE2 ANGL. DEV. = 8.5 DEGREES REMARK 500 9 HIS A 14 ND1 - CE1 - NE2 ANGL. DEV. = 8.5 DEGREES REMARK 500 10 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 10 HIS A 6 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 10 HIS A 13 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 10 HIS A 14 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 11 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 11 HIS A 6 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 11 HIS A 13 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 11 HIS A 14 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 12 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 12 HIS A 6 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 12 HIS A 13 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 12 HIS A 14 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 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 ASP A 7 -55.01 -133.25 REMARK 500 2 LEU A 17 140.94 -173.11 REMARK 500 2 ILE A 32 -40.64 -138.20 REMARK 500 2 VAL A 39 -81.75 -130.04 REMARK 500 3 ASP A 7 -66.59 -127.46 REMARK 500 3 LEU A 17 96.74 -62.38 REMARK 500 3 ASP A 23 96.69 -170.46 REMARK 500 3 ASN A 27 -50.61 -168.43 REMARK 500 3 ILE A 32 -57.22 -140.75 REMARK 500 3 VAL A 39 -63.73 -133.26 REMARK 500 4 ALA A 2 -52.01 -123.09 REMARK 500 5 LEU A 17 145.21 -179.81 REMARK 500 6 ASP A 7 -56.09 -134.19 REMARK 500 6 VAL A 18 104.06 -59.60 REMARK 500 6 ASP A 23 98.72 -170.93 REMARK 500 8 LEU A 17 131.77 -170.49 REMARK 500 8 ASP A 23 -41.58 -142.53 REMARK 500 9 VAL A 18 95.81 -67.67 REMARK 500 9 ASN A 27 98.10 -67.45 REMARK 500 10 LEU A 17 146.27 -179.71 REMARK 500 11 LEU A 17 145.07 -179.25 REMARK 500 12 ASP A 23 98.19 -160.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 23Y A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 23Y A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19309 RELATED DB: BMRB REMARK 900 RELATED ID: 2M9S RELATED DB: PDB DBREF 2M9R A 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 HET 23Y A 101 77 HET 23Y A 102 77 HETNAM 23Y (2S,3S)-3-(3,5-DIHYDROXYPHENYL)-2-(4-HYDROXYPHENYL)-4- HETNAM 2 23Y [(E)-2-(4-HYDROXYPHENYL)ETHENYL]-2,3-DIHYDRO-1- HETNAM 3 23Y BENZOFURAN-6-YL BETA-D-GLUCOPYRANOSIDE HETSYN 23Y POLYPHENOL EPSILON-VINIFERIN GLUCOSIDE FORMUL 2 23Y 2(C34 H32 O11) SITE 1 AC1 3 TYR A 10 GLN A 15 PHE A 19 SITE 1 AC2 2 LYS A 28 GLY A 29 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