HEADER SUGAR BINDING PROTEIN 23-JAN-01 1HZ3 TITLE ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE (RESIDUES 10-35) COMPND MOL_ID: 1; COMPND 2 MOLECULE: A-BETA AMYLOID; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 10-35; COMPND 5 SYNONYM: BETA-AMYLOID A4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE IS TAKEN FROM THE A-BETA PEPTIDE, WHICH SOURCE 4 OCCURS NATURALLY IN HOMO SAPIENS (HUMAN). THE PEPTIDE WAS SOURCE 5 SYNTHESIZED BY MERRIFIELD SOLID-PHASE METHODOLOGY. KEYWDS COLLAPSED COIL, HYDROPHOBIC CLUSTER, HYDROPHOBIC PATCH, SUGAR BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR S.ZHANG,K.IWATA,M.J.LACHENMANN,J.W.PENG,S.LI,E.R.STIMSON,Y.LU, AUTHOR 2 A.M.FELIX,J.E.MAGGIO,J.P.LEE REVDAT 5 22-MAY-24 1HZ3 1 REMARK REVDAT 4 23-FEB-22 1HZ3 1 REMARK REVDAT 3 24-FEB-09 1HZ3 1 VERSN REVDAT 2 01-APR-03 1HZ3 1 JRNL REVDAT 1 31-JAN-01 1HZ3 0 JRNL AUTH S.ZHANG,K.IWATA,M.J.LACHENMANN,J.W.PENG,S.LI,E.R.STIMSON, JRNL AUTH 2 Y.LU,A.M.FELIX,J.E.MAGGIO,J.P.LEE JRNL TITL THE ALZHEIMER'S PEPTIDE A BETA ADOPTS A COLLAPSED COIL JRNL TITL 2 STRUCTURE IN WATER. JRNL REF J.STRUCT.BIOL. V. 130 130 2000 JRNL REFN ISSN 1047-8477 JRNL PMID 10940221 JRNL DOI 10.1006/JSBI.2000.4288 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.P.LEE,E.R.STIMSON,J.R.GHILARDI,P.W.MANTYH,Y.A.LU, REMARK 1 AUTH 2 A.M.FELIX,W.LLANOS,A.BEHBIN,M.CUMMINGS,M.VAN CRIEKINGE, REMARK 1 AUTH 3 W.TIMMS,J.E.MAGGIO REMARK 1 TITL 1H NMR OF A-BETA AMYLOID PEPTIDE CONGENERS IN WATER REMARK 1 TITL 2 SOLUTION. CONFORMATIONAL CHANGES CORRELATE WITH PLAQUE REMARK 1 TITL 3 COMPETENCE. REMARK 1 REF BIOCHEMISTRY V. 34 5191 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH F.MASSI,J.W.PENG,J.P.LEE,J.E.STRAUB REMARK 1 TITL SIMULATION STUDY OF THE STRUCTURE AND DYNAMICS OF THE REMARK 1 TITL 2 ALZHEIMER'S AMYLOID PEPTIDE CONGENER IN SOLUTION. REMARK 1 REF BIOPHYS.J. V. 80 31 2001 REMARK 1 REFN ISSN 0006-3495 REMARK 1 REFERENCE 3 REMARK 1 AUTH F.MASSI,J.E.STRAUB REMARK 1 TITL ENERGY LANDSCAPE THEORY FOR ALZHEIMER'S AMYLOID BETA-PEPTIDE REMARK 1 TITL 2 FIBRIL ELONGATION REMARK 1 REF PROTEINS V. 42 217 2001 REMARK 1 REFN ISSN 0887-3585 REMARK 1 DOI 10.1002/1097-0134(20010201)42:2<217::AID-PROT90>3.0.CO;2-N REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 5.3B, DISCOVER 3.0 REMARK 3 AUTHORS : VARIAN ASSOCIATES (VNMR), MSI, INC. (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 84 SEQUENTIAL, 66 MEDIUM- (I TO I+2 OR I+3) AND 32 LONG-RANGE REMARK 3 NOE-DERIVED DISTANCE CONSTRAINTS. REMARK 4 REMARK 4 1HZ3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-01. REMARK 100 THE DEPOSITION ID IS D_1000012702. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 5.6 REMARK 210 IONIC STRENGTH : <1MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 300UM A-BETA(10-35); 90% H2O, REMARK 210 10% D2O; 300UM A-BETA(1-40) U- REMARK 210 15N; 90% H2O, 10% D2O; 300 UM A- REMARK 210 BETA(10-35) 2H-VAL12, -LEU17, - REMARK 210 VAL18, -PHE19, -ILE32 AND -LEU34; REMARK 210 15N-PHE19, -VAL24, -GLY25 AND - REMARK 210 GLY29; 13C-VAL24; 13C-ALA21 BETA REMARK 210 METHYL; 13C-ALA30 BETA METHYL; REMARK 210 13C-MET35 DELTA METHYL; 300 UM A- REMARK 210 BETA(10-35) 2H-VAL12, -LEU17, - REMARK 210 PHE19, -VAL24, -ILE31 AND -LEU34; REMARK 210 15N-VAL 18, -PHE20, -GLY25, - REMARK 210 GLY29 AND -GLY33; 13C-VAL24; 13C- REMARK 210 ALA21 BETA METHYL; 13C-ALA30 REMARK 210 BETA METHYL; 13C-MET35 DELTA REMARK 210 METHYL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 15N EDITED REMARK 210 NOESY-HMQC; 13C EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DGII REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, AND RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1, 9 REMARK 210 REMARK 210 REMARK: MANY OBSERVED INTRA-RESIDUE NOE-BASED DISTANCE CONSTRAINTS REMARK 210 WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS. 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: 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 O GLY A 20 HXT MET A 26 1.54 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 1 MET A 26 C MET A 26 OXT 0.145 REMARK 500 2 HIS A 4 CG HIS A 4 CD2 0.061 REMARK 500 2 HIS A 5 CG HIS A 5 CD2 0.064 REMARK 500 2 MET A 26 C MET A 26 OXT 0.144 REMARK 500 3 HIS A 4 CG HIS A 4 CD2 0.058 REMARK 500 3 MET A 26 C MET A 26 OXT 0.143 REMARK 500 4 MET A 26 C MET A 26 OXT 0.144 REMARK 500 5 HIS A 4 CG HIS A 4 CD2 0.060 REMARK 500 5 HIS A 5 CG HIS A 5 CD2 0.058 REMARK 500 5 MET A 26 C MET A 26 OXT 0.145 REMARK 500 6 HIS A 4 CG HIS A 4 CD2 0.054 REMARK 500 6 MET A 26 C MET A 26 OXT 0.143 REMARK 500 7 HIS A 4 CG HIS A 4 CD2 0.055 REMARK 500 7 MET A 26 C MET A 26 OXT 0.144 REMARK 500 8 HIS A 4 CG HIS A 4 CD2 0.059 REMARK 500 8 MET A 26 C MET A 26 OXT 0.143 REMARK 500 9 HIS A 4 CG HIS A 4 CD2 0.061 REMARK 500 9 MET A 26 C MET A 26 OXT 0.142 REMARK 500 10 HIS A 4 CG HIS A 4 CD2 0.062 REMARK 500 10 MET A 26 C MET A 26 OXT 0.143 REMARK 500 11 MET A 26 C MET A 26 OXT 0.140 REMARK 500 12 HIS A 4 CG HIS A 4 CD2 0.057 REMARK 500 12 HIS A 5 CG HIS A 5 CD2 0.055 REMARK 500 12 MET A 26 C MET A 26 OXT 0.144 REMARK 500 13 HIS A 4 CG HIS A 4 CD2 0.056 REMARK 500 13 HIS A 5 CG HIS A 5 CD2 0.054 REMARK 500 13 MET A 26 C MET A 26 OXT 0.145 REMARK 500 14 HIS A 4 CG HIS A 4 CD2 0.056 REMARK 500 14 MET A 26 C MET A 26 OXT 0.142 REMARK 500 15 MET A 26 C MET A 26 OXT 0.145 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 ALA A 12 N - CA - CB ANGL. DEV. = -8.6 DEGREES REMARK 500 1 ALA A 21 N - CA - CB ANGL. DEV. = -9.4 DEGREES REMARK 500 2 ALA A 12 N - CA - CB ANGL. DEV. = -8.6 DEGREES REMARK 500 2 ALA A 21 N - CA - CB ANGL. DEV. = -10.7 DEGREES REMARK 500 3 ALA A 21 N - CA - CB ANGL. DEV. = -9.3 DEGREES REMARK 500 4 ALA A 12 N - CA - CB ANGL. DEV. = -10.5 DEGREES REMARK 500 4 ALA A 21 N - CA - CB ANGL. DEV. = -9.6 DEGREES REMARK 500 7 ALA A 12 N - CA - CB ANGL. DEV. = -10.6 DEGREES REMARK 500 7 ALA A 21 N - CA - CB ANGL. DEV. = -9.2 DEGREES REMARK 500 8 ALA A 12 N - CA - CB ANGL. DEV. = -9.2 DEGREES REMARK 500 8 ALA A 21 N - CA - CB ANGL. DEV. = -8.8 DEGREES REMARK 500 12 ALA A 21 N - CA - CB ANGL. DEV. = -9.6 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 VAL A 3 -51.99 69.42 REMARK 500 1 HIS A 4 -34.19 71.53 REMARK 500 1 HIS A 5 162.46 64.43 REMARK 500 1 LYS A 7 -64.68 -138.08 REMARK 500 1 LEU A 8 0.91 -152.57 REMARK 500 1 VAL A 9 99.06 -68.27 REMARK 500 1 ALA A 12 -90.30 -149.27 REMARK 500 1 ASP A 14 31.93 -86.51 REMARK 500 1 VAL A 15 -27.88 158.16 REMARK 500 1 ASN A 18 70.77 -174.44 REMARK 500 1 ALA A 21 -37.28 -147.49 REMARK 500 1 ILE A 23 90.85 68.63 REMARK 500 2 GLU A 2 -79.38 -93.09 REMARK 500 2 HIS A 5 115.49 -5.21 REMARK 500 2 GLN A 6 -92.94 -141.64 REMARK 500 2 LYS A 7 -39.62 -165.74 REMARK 500 2 ALA A 12 -102.27 -141.95 REMARK 500 2 ASP A 14 44.86 -91.41 REMARK 500 2 VAL A 15 -33.17 150.68 REMARK 500 2 ASN A 18 63.27 -169.59 REMARK 500 2 ALA A 21 -52.53 -142.51 REMARK 500 2 ILE A 23 81.58 64.90 REMARK 500 3 VAL A 3 106.57 -58.05 REMARK 500 3 HIS A 5 133.17 -29.53 REMARK 500 3 GLN A 6 -85.31 -158.43 REMARK 500 3 LYS A 7 -20.59 -169.45 REMARK 500 3 ALA A 12 -95.32 -98.54 REMARK 500 3 VAL A 15 -27.81 168.05 REMARK 500 3 ASN A 18 78.62 -173.78 REMARK 500 3 LYS A 19 70.43 -104.65 REMARK 500 3 ALA A 21 -50.96 -152.80 REMARK 500 3 ILE A 23 71.73 62.84 REMARK 500 3 LEU A 25 -87.30 -106.30 REMARK 500 4 GLU A 2 -56.83 -150.50 REMARK 500 4 HIS A 5 170.22 91.46 REMARK 500 4 GLN A 6 -73.82 122.52 REMARK 500 4 LYS A 7 -46.68 -153.99 REMARK 500 4 ALA A 12 -82.91 -139.72 REMARK 500 4 ASP A 14 25.98 -78.21 REMARK 500 4 VAL A 15 -27.27 164.91 REMARK 500 4 ASN A 18 72.34 -171.39 REMARK 500 4 ALA A 21 -39.54 -147.51 REMARK 500 4 ILE A 23 81.89 69.72 REMARK 500 5 HIS A 5 132.64 1.07 REMARK 500 5 GLN A 6 68.41 67.82 REMARK 500 5 LYS A 7 -53.43 -124.01 REMARK 500 5 LEU A 8 -47.13 -173.36 REMARK 500 5 VAL A 9 101.64 -16.25 REMARK 500 5 ALA A 12 -86.36 -145.94 REMARK 500 5 VAL A 15 -20.20 176.51 REMARK 500 REMARK 500 THIS ENTRY HAS 155 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 PHE A 10 0.08 SIDE CHAIN REMARK 500 4 PHE A 10 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PEPTIDE RESIDUES ARE NUMBERED 1-26 AS THEY WERE REMARK 999 DESIGNATED IN THE DISTANCE-GEOMETRY CALCULATION. REMARK 999 THIS CORRESPONDS TO RESIDUES 10-35 OF THE "HUMAN REMARK 999 AMYLOID PEPTIDE ABETA." ABETA IS A 40-43 RESIDUE REMARK 999 PEPTIDE DERIVED FROM THE HUMAN AMYLOID PRECURSOR REMARK 999 PROTEIN (APP) (ACCESSION QRHUA4). REMARK 999 RESIDUE #10 IN ABETA CORRESPONDS TO RESIDUE #681 REMARK 999 IN APP, AND RESIDUE #35 IN ABETA CORRESPONDS TO REMARK 999 RESIDUE #706 IN APP. DBREF 1HZ3 A 1 26 UNP P05067 A4_HUMAN 681 706 SEQRES 1 A 26 TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA GLU SEQRES 2 A 26 ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU MET 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