HEADER METAL BINDING PROTEIN 06-OCT-22 8B9Q TITLE MOLECULAR STRUCTURE OF CU(II)-BOUND AMYLOID-BETA MONOMER IMPLICATED IN TITLE 2 INHIBITION OF PEPTIDE SELF-ASSEMBLY IN ALZHEIMER'S DISEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA A4 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMYLOID-BETA PEPTIDE, ALZHEIMER'S DISEASE, COPPER ION, PARAMAGNETIC KEYWDS 2 NMR, AGGREGATION KINETICS, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR A.ABELEIN,S.CIOFI-BAFFONI,R.KUMAR,A.GIACHETTI,M.PICCIOLI,H.BIVERSTAL REVDAT 1 08-FEB-23 8B9Q 0 JRNL AUTH A.ABELEIN,S.CIOFI-BAFFONI,C.MORMAN,R.KUMAR,A.GIACHETTI, JRNL AUTH 2 M.PICCIOLI,H.BIVERSTAL JRNL TITL MOLECULAR STRUCTURE OF CU(II)-BOUND AMYLOID-BETA MONOMER JRNL TITL 2 IMPLICATED IN INHIBITION OF PEPTIDE SELF-ASSEMBLY IN JRNL TITL 3 ALZHEIMER'S DISEASE. JRNL REF JACS AU V. 2 2571 2022 JRNL REFN ESSN 2691-3704 JRNL PMID 36465548 JRNL DOI 10.1021/JACSAU.2C00438 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8B9Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDB ON 02-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1292125856. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 281 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1013,25 MBAR REMARK 210 SAMPLE CONTENTS : 10 MM NO HEPES, 10 % D2 D2O, 100 REMARK 210 UM NO COPPER, 75 UM [U-100% 13C; REMARK 210 U-100% 15N] AMYLOID BETA, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 950 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.98.13, NMRFAM-SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-5 REMARK 465 RES C SSSEQI REMARK 465 VAL A 24 REMARK 465 GLY A 25 REMARK 465 SER A 26 REMARK 465 ASN A 27 REMARK 465 LYS A 28 REMARK 465 GLY A 29 REMARK 465 ALA A 30 REMARK 465 ILE A 31 REMARK 465 ILE A 32 REMARK 465 GLY A 33 REMARK 465 LEU A 34 REMARK 465 MET A 35 REMARK 465 VAL A 36 REMARK 465 GLY A 37 REMARK 465 GLY A 38 REMARK 465 VAL A 39 REMARK 465 VAL A 40 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. = 3.7 DEGREES REMARK 500 2 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.1 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 PHE A 4 49.11 -85.94 REMARK 500 1 ARG A 5 78.28 -66.64 REMARK 500 1 SER A 8 -19.93 59.96 REMARK 500 1 TYR A 10 31.91 -154.24 REMARK 500 1 GLU A 11 -61.74 -129.38 REMARK 500 1 VAL A 12 47.46 -89.77 REMARK 500 1 HIS A 13 75.15 -59.20 REMARK 500 1 GLN A 15 148.72 62.06 REMARK 500 1 LYS A 16 -66.77 55.58 REMARK 500 1 PHE A 20 -70.98 -158.18 REMARK 500 2 ALA A 2 -110.27 -87.24 REMARK 500 2 GLU A 3 -1.09 -59.65 REMARK 500 2 ARG A 5 -37.00 -159.17 REMARK 500 2 HIS A 6 -149.96 -153.48 REMARK 500 2 ASP A 7 -92.73 -156.09 REMARK 500 2 TYR A 10 -9.19 -59.11 REMARK 500 2 VAL A 12 82.66 63.27 REMARK 500 2 LEU A 17 67.73 37.82 REMARK 500 2 ALA A 21 -31.77 61.10 REMARK 500 3 ALA A 2 157.99 72.65 REMARK 500 3 PHE A 4 64.48 -64.45 REMARK 500 3 HIS A 6 33.48 -67.85 REMARK 500 3 PHE A 20 53.85 -152.32 REMARK 500 3 GLU A 22 -19.48 59.56 REMARK 500 4 ALA A 2 -2.40 -144.40 REMARK 500 4 HIS A 6 -54.74 -156.39 REMARK 500 4 SER A 8 177.74 65.40 REMARK 500 4 TYR A 10 26.34 -67.43 REMARK 500 4 VAL A 12 47.83 -71.69 REMARK 500 4 HIS A 14 147.08 51.45 REMARK 500 4 PHE A 20 55.40 -141.03 REMARK 500 4 GLU A 22 -43.98 -138.61 REMARK 500 5 ALA A 2 -152.85 -67.56 REMARK 500 5 GLU A 3 -24.17 63.73 REMARK 500 5 ARG A 5 88.21 27.43 REMARK 500 5 HIS A 6 -89.54 -142.05 REMARK 500 5 TYR A 10 -78.02 -72.65 REMARK 500 5 GLU A 11 145.60 54.01 REMARK 500 5 HIS A 13 -60.56 -157.33 REMARK 500 5 HIS A 14 -111.87 -155.36 REMARK 500 5 GLN A 15 -37.30 -159.08 REMARK 500 5 VAL A 18 -17.94 -151.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 13 HIS A 14 1 139.33 REMARK 500 HIS A 6 ASP A 7 2 148.48 REMARK 500 HIS A 6 ASP A 7 3 -136.50 REMARK 500 HIS A 13 HIS A 14 4 -137.36 REMARK 500 ARG A 5 HIS A 6 5 -140.29 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 3 TYR A 10 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 101 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 1 N REMARK 620 2 ASP A 1 O 80.2 REMARK 620 3 HIS A 6 NE2 169.5 93.1 REMARK 620 4 HIS A 13 ND1 84.7 157.0 104.0 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34762 RELATED DB: BMRB REMARK 900 MOLECULAR STRUCTURE OF CU(II)-BOUND AMYLOID-BETA MONOMER IMPLICATED REMARK 900 IN INHIBITION OF PEPTIDE SELF-ASSEMBLY IN ALZHEIMER'S DISEASE DBREF 8B9Q A 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 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 CU A 101 1 HETNAM CU COPPER (II) ION FORMUL 2 CU CU 2+ LINK N ASP A 1 CU CU A 101 1555 1555 1.99 LINK O ASP A 1 CU CU A 101 1555 1555 2.15 LINK NE2 HIS A 6 CU CU A 101 1555 1555 2.03 LINK ND1 HIS A 13 CU CU A 101 1555 1555 2.14 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