HEADER METAL BINDING PROTEIN 09-JAN-17 5UGK TITLE ZINC-BINDING STRUCTURE OF A CATALYTIC AMYLOID FROM SOLID-STATE NMR TITLE 2 SPECTROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: ILE-HIS-VAL-HIS-LEU-GLN-ILE; COMPND 3 CHAIN: A, C, E, G, I, K, O, Q, S, U, W, Y; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS AMYLOID, METAL BINDING PROTEIN EXPDTA SOLID-STATE NMR NUMMDL 20 AUTHOR M.LEE,T.WANG,O.V.MAKHLYNETS,Y.WU,N.POLIZZI,H.WU,P.M.GOSAVI, AUTHOR 2 I.V.KORENDOVYCH,W.F.DEGRADO,M.HONG REVDAT 7 15-MAY-24 5UGK 1 REMARK REVDAT 6 14-JUN-23 5UGK 1 LINK REVDAT 5 18-DEC-19 5UGK 1 REMARK REVDAT 4 27-SEP-17 5UGK 1 REMARK REVDAT 3 28-JUN-17 5UGK 1 JRNL REVDAT 2 14-JUN-17 5UGK 1 JRNL REVDAT 1 31-MAY-17 5UGK 0 JRNL AUTH M.LEE,T.WANG,O.V.MAKHLYNETS,Y.WU,N.F.POLIZZI,H.WU, JRNL AUTH 2 P.M.GOSAVI,J.STOHR,I.V.KORENDOVYCH,W.F.DEGRADO,M.HONG JRNL TITL ZINC-BINDING STRUCTURE OF A CATALYTIC AMYLOID FROM JRNL TITL 2 SOLID-STATE NMR. JRNL REF PROC. NATL. ACAD. SCI. V. 114 6191 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 28566494 JRNL DOI 10.1073/PNAS.1706179114 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5UGK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000225834. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 8 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.4 G/L [U-13C; U-15N] IVL, PH 8 REMARK 210 TRIS BUFFER; 0.4 G/L [U-13C] REMARK 210 MIXED SAMPLE, PH 8 TRIS BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 13C-13C CORRELATION SPECTRA; REMARK 210 2D 15N-13C CORRELATION SPECTRA; REMARK 210 REDOR REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : BRUKER REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, TOPSPIN, TALOS REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, E, G, I, K, O, Q, S, U, REMARK 350 AND CHAINS: W, Y 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 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 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 2 NE2 REMARK 620 2 HIS A 4 ND1 129.5 REMARK 620 3 HIS C 4 ND1 96.6 117.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 2 ND1 REMARK 620 2 HIS C 4 NE2 133.6 REMARK 620 3 HIS E 2 ND1 106.1 107.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS E 2 NE2 REMARK 620 2 HIS E 4 ND1 127.4 REMARK 620 3 HIS G 4 ND1 100.1 116.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN G 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS G 2 ND1 REMARK 620 2 HIS G 4 NE2 134.0 REMARK 620 3 HIS I 2 ND1 106.9 107.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN I 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS I 2 NE2 REMARK 620 2 HIS I 4 ND1 129.0 REMARK 620 3 HIS K 4 ND1 97.9 115.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN K 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS K 2 ND1 REMARK 620 2 HIS K 4 NE2 132.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN O 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS O 2 NE2 REMARK 620 2 HIS O 4 ND1 129.9 REMARK 620 3 HIS Q 4 ND1 99.2 117.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN Q 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS Q 2 ND1 REMARK 620 2 HIS Q 4 NE2 132.9 REMARK 620 3 HIS S 2 ND1 106.3 107.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN S 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS S 2 NE2 REMARK 620 2 HIS S 4 ND1 126.7 REMARK 620 3 HIS U 4 ND1 100.6 114.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN U 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS U 2 ND1 REMARK 620 2 HIS U 4 NE2 131.6 REMARK 620 3 HIS W 2 ND1 108.9 107.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN W 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS W 2 NE2 REMARK 620 2 HIS W 4 ND1 133.9 REMARK 620 3 HIS Y 4 ND1 94.9 104.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN Y 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS Y 2 ND1 REMARK 620 2 HIS Y 4 NE2 134.0 REMARK 620 N 1 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 C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN G 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN I 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN K 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN O 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN Q 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN S 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN U 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN W 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN Y 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30227 RELATED DB: BMRB REMARK 900 ZINC-BINDING STRUCTURE OF A CATALYTIC AMYLOID FROM SOLID-STATE NMR REMARK 900 SPECTROSCOPY DBREF 5UGK A 1 7 PDB 5UGK 5UGK 1 7 DBREF 5UGK C 1 7 PDB 5UGK 5UGK 1 7 DBREF 5UGK E 1 7 PDB 5UGK 5UGK 1 7 DBREF 5UGK G 1 7 PDB 5UGK 5UGK 1 7 DBREF 5UGK I 1 7 PDB 5UGK 5UGK 1 7 DBREF 5UGK K 1 7 PDB 5UGK 5UGK 1 7 DBREF 5UGK O 1 7 PDB 5UGK 5UGK 1 7 DBREF 5UGK Q 1 7 PDB 5UGK 5UGK 1 7 DBREF 5UGK S 1 7 PDB 5UGK 5UGK 1 7 DBREF 5UGK U 1 7 PDB 5UGK 5UGK 1 7 DBREF 5UGK W 1 7 PDB 5UGK 5UGK 1 7 DBREF 5UGK Y 1 7 PDB 5UGK 5UGK 1 7 SEQRES 1 A 7 ILE HIS VAL HIS LEU GLN ILE SEQRES 1 C 7 ILE HIS VAL HIS LEU GLN ILE SEQRES 1 E 7 ILE HIS VAL HIS LEU GLN ILE SEQRES 1 G 7 ILE HIS VAL HIS LEU GLN ILE SEQRES 1 I 7 ILE HIS VAL HIS LEU GLN ILE SEQRES 1 K 7 ILE HIS VAL HIS LEU GLN ILE SEQRES 1 O 7 ILE HIS VAL HIS LEU GLN ILE SEQRES 1 Q 7 ILE HIS VAL HIS LEU GLN ILE SEQRES 1 S 7 ILE HIS VAL HIS LEU GLN ILE SEQRES 1 U 7 ILE HIS VAL HIS LEU GLN ILE SEQRES 1 W 7 ILE HIS VAL HIS LEU GLN ILE SEQRES 1 Y 7 ILE HIS VAL HIS LEU GLN ILE HET ZN A 101 1 HET ZN C 101 1 HET ZN E 101 1 HET ZN G 101 1 HET ZN I 101 1 HET ZN K 101 1 HET ZN O 101 1 HET ZN Q 101 1 HET ZN S 101 1 HET ZN U 101 1 HET ZN W 101 1 HET ZN Y 101 1 HETNAM ZN ZINC ION FORMUL 13 ZN 12(ZN 2+) SHEET 1 AA1 6 HIS A 2 GLN A 6 0 SHEET 2 AA1 6 HIS C 2 GLN C 6 1 O HIS C 4 N VAL A 3 SHEET 3 AA1 6 HIS E 2 GLN E 6 1 O HIS E 2 N VAL C 3 SHEET 4 AA1 6 HIS G 2 GLN G 6 1 O HIS G 4 N VAL E 3 SHEET 5 AA1 6 HIS I 2 GLN I 6 1 O HIS I 2 N VAL G 3 SHEET 6 AA1 6 HIS K 2 GLN K 6 1 O HIS K 2 N VAL I 3 SHEET 1 AA2 6 HIS O 2 GLN O 6 0 SHEET 2 AA2 6 HIS Q 2 GLN Q 6 1 O HIS Q 4 N VAL O 3 SHEET 3 AA2 6 HIS S 2 GLN S 6 1 O HIS S 2 N VAL Q 3 SHEET 4 AA2 6 HIS U 2 GLN U 6 1 O HIS U 2 N VAL S 3 SHEET 5 AA2 6 HIS W 2 GLN W 6 1 O HIS W 2 N VAL U 3 SHEET 6 AA2 6 HIS Y 2 GLN Y 6 1 O HIS Y 2 N VAL W 3 LINK NE2 HIS A 2 ZN ZN A 101 1555 1555 2.21 LINK ND1 HIS A 4 ZN ZN A 101 1555 1555 1.92 LINK ZN ZN A 101 ND1 HIS C 4 1555 1555 2.12 LINK ND1 HIS C 2 ZN ZN C 101 1555 1555 1.89 LINK NE2 HIS C 4 ZN ZN C 101 1555 1555 2.21 LINK ZN ZN C 101 ND1 HIS E 2 1555 1555 1.91 LINK NE2 HIS E 2 ZN ZN E 101 1555 1555 2.21 LINK ND1 HIS E 4 ZN ZN E 101 1555 1555 1.94 LINK ZN ZN E 101 ND1 HIS G 4 1555 1555 2.20 LINK ND1 HIS G 2 ZN ZN G 101 1555 1555 1.89 LINK NE2 HIS G 4 ZN ZN G 101 1555 1555 2.19 LINK ZN ZN G 101 ND1 HIS I 2 1555 1555 1.90 LINK NE2 HIS I 2 ZN ZN I 101 1555 1555 2.22 LINK ND1 HIS I 4 ZN ZN I 101 1555 1555 1.91 LINK ZN ZN I 101 ND1 HIS K 4 1555 1555 2.16 LINK ND1 HIS K 2 ZN ZN K 101 1555 1555 2.06 LINK NE2 HIS K 4 ZN ZN K 101 1555 1555 2.04 LINK NE2 HIS O 2 ZN ZN O 101 1555 1555 2.21 LINK ND1 HIS O 4 ZN ZN O 101 1555 1555 1.92 LINK ZN ZN O 101 ND1 HIS Q 4 1555 1555 2.10 LINK ND1 HIS Q 2 ZN ZN Q 101 1555 1555 1.90 LINK NE2 HIS Q 4 ZN ZN Q 101 1555 1555 2.22 LINK ZN ZN Q 101 ND1 HIS S 2 1555 1555 1.93 LINK NE2 HIS S 2 ZN ZN S 101 1555 1555 2.22 LINK ND1 HIS S 4 ZN ZN S 101 1555 1555 1.95 LINK ZN ZN S 101 ND1 HIS U 4 1555 1555 2.20 LINK ND1 HIS U 2 ZN ZN U 101 1555 1555 1.92 LINK NE2 HIS U 4 ZN ZN U 101 1555 1555 2.20 LINK ZN ZN U 101 ND1 HIS W 2 1555 1555 1.95 LINK NE2 HIS W 2 ZN ZN W 101 1555 1555 2.13 LINK ND1 HIS W 4 ZN ZN W 101 1555 1555 1.94 LINK ZN ZN W 101 ND1 HIS Y 4 1555 1555 2.24 LINK ND1 HIS Y 2 ZN ZN Y 101 1555 1555 2.14 LINK NE2 HIS Y 4 ZN ZN Y 101 1555 1555 1.95 SITE 1 AC1 3 HIS A 2 HIS A 4 HIS C 4 SITE 1 AC2 3 HIS C 2 HIS C 4 HIS E 2 SITE 1 AC3 3 HIS E 2 HIS E 4 HIS G 4 SITE 1 AC4 3 HIS G 2 HIS G 4 HIS I 2 SITE 1 AC5 3 HIS I 2 HIS I 4 HIS K 4 SITE 1 AC6 2 HIS K 2 HIS K 4 SITE 1 AC7 3 HIS O 2 HIS O 4 HIS Q 4 SITE 1 AC8 3 HIS Q 2 HIS Q 4 HIS S 2 SITE 1 AC9 3 HIS S 2 HIS S 4 HIS U 4 SITE 1 AD1 3 HIS U 2 HIS U 4 HIS W 2 SITE 1 AD2 3 HIS W 2 HIS W 4 HIS Y 4 SITE 1 AD3 2 HIS Y 2 HIS Y 4 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