HEADER STRUCTURAL PROTEIN 05-JUL-16 5LFY TITLE ZINC BOUND DIMER OF THE FRAGMENT OF HUMAN AMYLOID-BETA PEPTIDE WITH TITLE 2 ALZHEIMER'S DISEASE PATHOGENIC TAIWANESE MUTATION D7H COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 17-26; 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 ALZHEIMER'S DISEASE, AMYLOID-BETA PEPTIDE, ZINC COMPLEX, ZINC-BOUND KEYWDS 2 DIMER, STRUCTURAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR V.I.POLSHAKOV,A.B.MANTSYZOV,S.A.KOZIN REVDAT 4 14-JUN-23 5LFY 1 REMARK LINK REVDAT 3 08-MAY-19 5LFY 1 REMARK REVDAT 2 27-SEP-17 5LFY 1 JRNL REVDAT 1 23-AUG-17 5LFY 0 JRNL AUTH V.I.POLSHAKOV,A.B.MANTSYZOV,S.A.KOZIN,A.A.ADZHUBEI, JRNL AUTH 2 S.S.ZHOKHOV,W.VAN BEEK,A.A.KULIKOVA,M.I.INDEYKINA, JRNL AUTH 3 V.A.MITKEVICH,A.A.MAKAROV JRNL TITL A BINUCLEAR ZINC INTERACTION FOLD DISCOVERED IN THE JRNL TITL 2 HOMODIMER OF ALZHEIMER'S AMYLOID-BETA FRAGMENT WITH JRNL TITL 3 TAIWANESE MUTATION D7H. JRNL REF ANGEW. CHEM. INT. ED. ENGL. V. 56 11734 2017 JRNL REFN ESSN 1521-3773 JRNL PMID 28570778 JRNL DOI 10.1002/ANIE.201704615 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5LFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000600. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 3 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.4 MM D7H_ABETA(1-10), 2.8 MM REMARK 210 ZNCL2, 10 MM [U-99% 2D] BIS-TRIS- REMARK 210 D19, 90% H2O/10% D2O; 1.4 MM D7H_ REMARK 210 ABETA(1-10), 2.8 MM ZNCL2, 10 MM REMARK 210 [U-99% 2D] BIS-TRIS-D19, 100% REMARK 210 D2O; 0.8 MM D7H_ABETA(1-10), 0.8 REMARK 210 MM [U-99% 13C,15N]-(D1,3); [U-99% REMARK 210 15N]-(H6,H7) D7H_ABETA(1-10), REMARK 210 1.7 MM ZNCL2, 10 MM [U-99% 2D] REMARK 210 BIS-TRIS-D19, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-1H NOESY; 2D 1H-15N HSQC; 2D REMARK 210 1H-13C HSQC ALIPHATIC; 2D 1H-13C REMARK 210 HSQC AROMATIC; 2D 1H-1H ROESY; REMARK 210 2D DOSY; 2D 1H-15N HMBC; 2D 13C- REMARK 210 EDITED,13C-FILTERED NOESY; 2D 1H- REMARK 210 15N HMBC-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 : TOPSPIN, NMRPIPE, SPARKY, REMARK 210 ANGLESEARCH, PROCHECK / PROCHECK- REMARK 210 NMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 4 HIS B 7 79.81 -100.27 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 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 1 O REMARK 620 2 HIS A 6 NE2 98.7 REMARK 620 3 GLU B 3 OE1 123.2 99.3 REMARK 620 4 GLU B 3 OE2 85.9 160.9 63.3 REMARK 620 5 HIS B 7 NE2 105.0 108.8 118.9 87.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 3 OE1 REMARK 620 2 GLU A 3 OE2 59.2 REMARK 620 3 HIS A 7 NE2 119.0 98.5 REMARK 620 4 ASP B 1 O 123.1 81.3 105.0 REMARK 620 5 HIS B 6 NE2 99.2 151.7 108.6 98.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide TYR B 10 and NH2 B REMARK 800 11 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34019 RELATED DB: BMRB DBREF 5LFY A 1 10 UNP L7XE61 L7XE61_HUMAN 17 26 DBREF 5LFY B 1 10 UNP L7XE61 L7XE61_HUMAN 17 26 SEQADV 5LFY HIS A 7 UNP L7XE61 ASP 23 CONFLICT SEQADV 5LFY NH2 A 11 UNP L7XE61 AMIDATION SEQADV 5LFY HIS B 7 UNP L7XE61 ASP 23 CONFLICT SEQADV 5LFY NH2 B 11 UNP L7XE61 AMIDATION SEQRES 1 A 11 ASP ALA GLU PHE ARG HIS HIS SER GLY TYR NH2 SEQRES 1 B 11 ASP ALA GLU PHE ARG HIS HIS SER GLY TYR NH2 HET NH2 A 11 3 HET NH2 B 11 3 HET ZN A 101 1 HET ZN A 102 1 HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION FORMUL 1 NH2 2(H2 N) FORMUL 3 ZN 2(ZN 2+) HELIX 1 AA1 ALA A 2 HIS A 7 1 6 HELIX 2 AA2 ALA B 2 HIS B 7 1 6 LINK C TYR A 10 N NH2 A 11 1555 1555 1.33 LINK C TYR B 10 N NH2 B 11 1555 1555 1.33 LINK O ASP A 1 ZN ZN A 102 1555 1555 2.04 LINK OE1 GLU A 3 ZN ZN A 101 1555 1555 1.97 LINK OE2 GLU A 3 ZN ZN A 101 1555 1555 2.42 LINK NE2 HIS A 6 ZN ZN A 102 1555 1555 2.07 LINK NE2 HIS A 7 ZN ZN A 101 1555 1555 2.03 LINK ZN ZN A 101 O ASP B 1 1555 1555 2.04 LINK ZN ZN A 101 NE2 HIS B 6 1555 1555 2.06 LINK ZN ZN A 102 OE1 GLU B 3 1555 1555 1.97 LINK ZN ZN A 102 OE2 GLU B 3 1555 1555 2.21 LINK ZN ZN A 102 NE2 HIS B 7 1555 1555 2.04 SITE 1 AC1 5 GLU A 3 HIS A 7 ASP B 1 ALA B 2 SITE 2 AC1 5 HIS B 6 SITE 1 AC2 5 ASP A 1 ALA A 2 HIS A 6 GLU B 3 SITE 2 AC2 5 HIS B 7 SITE 1 AC3 1 GLY B 9 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