HEADER PROTEIN FIBRIL 23-APR-19 6RHY TITLE STRUCTURE OF PORE-FORMING AMYLOID-BETA TETRAMERS COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: ABPP,APPI,APP,ALZHEIMER DISEASE AMYLOID PROTEIN,AMYLOID COMPND 5 PRECURSOR PROTEIN,BETA-AMYLOID PRECURSOR PROTEIN,CEREBRAL VASCULAR COMPND 6 AMYLOID PEPTIDE,CVAP,PREA4,PROTEASE NEXIN-II,PN-II; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: APP, A4, AD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMYLOID, ALZHEIMER'S DISEASE, MEMBRANE PORE, OLIGOMER, PROTEIN FIBRIL EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR B.BARDIAUX,S.CIUDAD,N.CARULLA REVDAT 4 19-JUN-24 6RHY 1 REMARK REVDAT 3 14-JUN-23 6RHY 1 JRNL REVDAT 2 08-JUL-20 6RHY 1 JRNL REVDAT 1 25-SEP-19 6RHY 0 JRNL AUTH S.CIUDAD,E.PUIG,T.BOTZANOWSKI,M.MEIGOONI,A.S.ARANGO,J.DO, JRNL AUTH 2 M.MAYZEL,M.BAYOUMI,S.CHAIGNEPAIN,G.MAGLIA,S.CIANFERANI, JRNL AUTH 3 V.OREKHOV,E.TAJKHORSHID,B.BARDIAUX,N.CARULLA JRNL TITL A BETA (1-42) TETRAMER AND OCTAMER STRUCTURES REVEAL EDGE JRNL TITL 2 CONDUCTIVITY PORES AS A MECHANISM FOR MEMBRANE DAMAGE. JRNL REF NAT COMMUN V. 11 3014 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32541820 JRNL DOI 10.1038/S41467-020-16566-1 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.CIUDAD,E.PUIG,T.BOTZANOWSKI,M.MEIGOONI,A.S.ARANGO,J.DO, REMARK 1 AUTH 2 M.MAYZEL,M.BAYOUMI,S.CHAIGNEPAIN,G.MAGLIA,S.CIANFERANI, REMARK 1 AUTH 3 V.OREKHOV,E.TAJKHORSHID,B.BARDIAUX,N.CARULLA REMARK 1 TITL ABETA(1-42) TETRAMER AND OCTAMER STRUCTURES REVEAL EDGE REMARK 1 TITL 2 PORES AS A MECHANISM FOR MEMBRANE DAMAGE REMARK 1 REF BIORXIV 2019 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/759472 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA, CNS REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), BRUNGER, REMARK 3 ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6RHY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101515. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310.15; 310.15 REMARK 210 PH : 8.5; 9.5 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-15N] AMYLOID-BETA A4 REMARK 210 PROTEIN, 10 MM [U-2H] TRIS-D11, REMARK 210 28.5 MM [U-2H] DPC-D38, 90% H2O/ REMARK 210 10% D2O; 1 MM [U-13C; U-15N; U- REMARK 210 2H] AMYLOID-BETA A4 PROTEIN, 10 REMARK 210 MM [U-2H] TRIS-D11, 28.5 MM [U- REMARK 210 2H] DPC-D38, 90% H2O/10% D2O; 1 REMARK 210 MM [U-2H,13C,15N]-ILE-[13CH3]D1, REMARK 210 ALA-[13CH3], LEU/VAL-[13CH3]PROR REMARK 210 AMYLOID-BETA A4 PROTEIN, 10 MM REMARK 210 [U-2H] TRIS-D11, 28.5 MM [U-2H] REMARK 210 DPC-D38, 90% H2O/10% D2O; 1 MM REMARK 210 [U-2H,15N]-ILE-[13CH3]D1, ALA- REMARK 210 [13CH3], LEU/VAL-[13CH3]PROR REMARK 210 AMYLOID-BETA A4 PROTEIN, 10 MM REMARK 210 [U-2H] TRIS-D11, 28.5 MM [U-2H] REMARK 210 DPC-D38, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N TROSY; 3D HNCA; 3D REMARK 210 HNCO; 3D HN(CO)CA; 3D HNCACB; 3D REMARK 210 HN(COCA)CB; 3D 13C-HMQC-[1H,1H]- REMARK 210 NOESY-13C-HMQC; 3D (HME)CME([C] REMARK 210 CA)CO; 3D (HME)CME([C]CA)NH; 3D REMARK 210 HME(CME[C]CA)NH; 3D (H)C-TOCSY-C- REMARK 210 TOCSY-(C)H; 3D HM-CMHM NOESY; 3D REMARK 210 CM-CMHM NOESY; 3D HM-NH NOESY; REMARK 210 3D CM-NH NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TALOS, TOPSPIN, CCPNMR ANALYSIS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 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 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 OE2 GLU C 11 HE2 HIS C 13 1.59 REMARK 500 OE2 GLU A 11 HE2 HIS A 13 1.59 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 GLU B 22 179.17 63.48 REMARK 500 1 LYS B 28 -52.99 71.51 REMARK 500 1 GLU D 22 179.37 63.26 REMARK 500 1 LYS D 28 -52.34 71.94 REMARK 500 2 GLU A 3 79.31 62.34 REMARK 500 2 ARG A 5 94.41 57.09 REMARK 500 2 SER A 8 114.51 -168.01 REMARK 500 2 ARG B 5 -52.55 -131.71 REMARK 500 2 VAL B 24 28.85 -147.45 REMARK 500 2 ASN B 27 70.74 69.56 REMARK 500 2 GLU C 3 79.30 61.53 REMARK 500 2 ARG C 5 94.63 56.72 REMARK 500 2 SER C 8 114.43 -168.31 REMARK 500 2 ARG D 5 -52.73 -131.67 REMARK 500 2 VAL D 24 28.73 -147.70 REMARK 500 2 ASN D 27 70.56 69.45 REMARK 500 3 HIS A 6 57.94 -96.25 REMARK 500 3 SER A 26 -46.46 -170.85 REMARK 500 3 ASN A 27 63.68 -158.96 REMARK 500 3 LYS B 16 -36.16 -143.86 REMARK 500 3 HIS C 6 57.11 -96.34 REMARK 500 3 SER C 26 -46.72 -170.21 REMARK 500 3 ASN C 27 63.20 -158.70 REMARK 500 3 LYS D 16 -36.22 -143.90 REMARK 500 4 ARG A 5 43.13 -78.58 REMARK 500 4 ARG C 5 43.64 -78.47 REMARK 500 5 LYS B 16 77.03 -112.22 REMARK 500 5 VAL B 24 -75.35 -119.27 REMARK 500 5 LYS D 16 76.86 -112.37 REMARK 500 5 VAL D 24 -75.26 -119.33 REMARK 500 6 GLU A 22 -76.86 68.40 REMARK 500 6 ASP A 23 -76.01 -139.31 REMARK 500 6 VAL A 24 61.15 64.61 REMARK 500 6 ASN A 27 36.60 -151.38 REMARK 500 6 GLU C 22 -77.15 69.06 REMARK 500 6 ASP C 23 -75.70 -138.87 REMARK 500 6 VAL C 24 61.44 64.29 REMARK 500 6 ASN C 27 36.30 -151.01 REMARK 500 7 PHE A 4 113.72 -166.52 REMARK 500 7 ASN A 27 78.96 -151.06 REMARK 500 7 ASP B 7 -65.79 -97.61 REMARK 500 7 GLN B 15 -69.46 -139.01 REMARK 500 7 ASN B 27 101.43 -168.29 REMARK 500 7 PHE C 4 113.79 -166.94 REMARK 500 7 ASN C 27 79.51 -151.17 REMARK 500 7 ASP D 7 -66.04 -97.36 REMARK 500 7 GLN D 15 -69.15 -139.50 REMARK 500 7 ASN D 27 101.43 -167.45 REMARK 500 8 HIS A 6 -58.91 -154.51 REMARK 500 8 GLU B 3 65.83 68.13 REMARK 500 REMARK 500 THIS ENTRY HAS 134 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34396 RELATED DB: BMRB REMARK 900 STRUCTURE OF PORE-FORMING AMYLOID-BETA TETRAMERS DBREF 6RHY A 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 6RHY B 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 6RHY C 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 6RHY D 1 42 UNP P05067 A4_HUMAN 672 713 SEQRES 1 A 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 A 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 A 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 A 42 VAL ILE ALA SEQRES 1 B 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 B 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 B 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 B 42 VAL ILE ALA SEQRES 1 C 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 C 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 C 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 C 42 VAL ILE ALA SEQRES 1 D 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 D 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 D 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 D 42 VAL ILE ALA HELIX 1 AA1 LEU B 17 PHE B 20 1 4 HELIX 2 AA2 LEU D 17 PHE D 20 1 4 SHEET 1 AA1 6 TYR A 10 ALA A 21 0 SHEET 2 AA1 6 GLY A 29 ILE A 41 -1 O ALA A 30 N ALA A 21 SHEET 3 AA1 6 ALA B 30 ILE B 41 -1 O ALA B 30 N ILE A 41 SHEET 4 AA1 6 ALA D 30 ILE D 41 -1 O MET D 35 N GLY B 37 SHEET 5 AA1 6 GLY C 29 ILE C 41 -1 N ILE C 41 O ALA D 30 SHEET 6 AA1 6 TYR C 10 ALA C 21 -1 N ALA C 21 O ALA C 30 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