HEADER UNKNOWN FUNCTION 24-JUL-23 8PXS TITLE SHORT RNA BINDING TO PEPTIDE AMYLOIDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-R(P*GP*UP*CP*A)-3'); COMPND 7 CHAIN: R; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 4 ORGANISM_TAXID: 562; SOURCE 5 OTHER_DETAILS: ARTIFICIALLY DESIGNED; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 9 ORGANISM_TAXID: 562; SOURCE 10 OTHER_DETAILS: ARTIFICIALLY DESIGNED KEYWDS AMYLOIDS, RNA, GENETIC CODE, ORIGIN OF LIFE, UNKNOWN FUNCTION EXPDTA SOLID-STATE NMR NUMMDL 10 AUTHOR S.K.ROUT,R.CADALBERT,N.SCHRODER,T.WIEGAND,J.ZEHNDER,O.GAMPP, AUTHOR 2 P.GUNTERT,D.KRINGLER,C.KREUTZ,A.KNORLEIN,J.HALL,J.GREENWALD,R.RIEK REVDAT 1 18-OCT-23 8PXS 0 JRNL AUTH S.K.ROUT,R.CADALBERT,N.SCHRODER,J.WANG,J.ZEHNDER,O.GAMPP, JRNL AUTH 2 T.WIEGAND,P.GUNTERT,D.KLINGLER,C.KREUTZ,A.KNORLEIN,J.HALL, JRNL AUTH 3 J.GREENWALD,R.RIEK JRNL TITL AN ANALYSIS OF NUCLEOTIDE-AMYLOID INTERACTIONS REVEALS JRNL TITL 2 SELECTIVE BINDING TO CODON-SIZED RNA. JRNL REF J.AM.CHEM.SOC. V. 145 21915 2023 JRNL REFN ESSN 1520-5126 JRNL PMID 37782045 JRNL DOI 10.1021/JACS.3C06287 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.15 REMARK 3 AUTHORS : P. GUNTERT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8PXS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292132146. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 272 REMARK 210 PH : 3 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 10 NA [U-13C; U-15N] VAL-ALA-GLN REMARK 210 -ALA-GLN-ILE-ASN-ILE, 1.5 NA [U- REMARK 210 13C; U-15N] RNA (5'-R(P*GP*UP*CP* REMARK 210 A)-3'), 100% D2O; 10 NA MIXED REMARK 210 VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE, REMARK 210 1.5 NA [U-13C; U-15N] RNA (5'- REMARK 210 R(P*GP*UP*CP*A)-3'), 100% D2O; REMARK 210 10 NA MIXED VAL-ALA-GLN-ALA-GLN- REMARK 210 ILE-ASN-ILE, 1.5 NA [U-13C; U- REMARK 210 15N] RNA (5'-R(P*GP*UP*CP*A)-3'), REMARK 210 100% D2O; 10 NA [U-13C; U-15N] REMARK 210 VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE, REMARK 210 1.5 NA RNA (5'-R(P*GP*UP*CP*A)-3' REMARK 210 ), 100% D2O; 10 NA [U-13C; U-15N] REMARK 210 VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE, REMARK 210 1.5 NA SPECIFICLY LABELED RNA REMARK 210 (5'-R(P*GP*UP*CP*A)-3'), 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DARR 20 MS; DARR 150 MS; NCA; REMARK 210 NCO; PAR 8 MS; PDSD; DARR 450 MS; REMARK 210 CHHC; PAIN 6 MS; CHHP; 31P PDSD; REMARK 210 31P DP REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 4000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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, B, C, R, D, E, F, G, H, I, REMARK 350 AND CHAINS: J 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: 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 G R 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G R 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G R 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 U R 2 O4' - C4' - C3' ANGL. DEV. = -8.5 DEGREES REMARK 500 1 U R 2 C1' - O4' - C4' ANGL. DEV. = 7.7 DEGREES REMARK 500 1 C R 3 O4' - C4' - C3' ANGL. DEV. = -10.9 DEGREES REMARK 500 1 A R 4 C1' - O4' - C4' ANGL. DEV. = 6.2 DEGREES REMARK 500 2 G R 1 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES REMARK 500 2 G R 1 C1' - O4' - C4' ANGL. DEV. = 8.1 DEGREES REMARK 500 2 G R 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 2 G R 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 G R 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 U R 2 O4' - C4' - C3' ANGL. DEV. = -7.5 DEGREES REMARK 500 2 U R 2 C1' - O4' - C4' ANGL. DEV. = 8.1 DEGREES REMARK 500 2 C R 3 C1' - O4' - C4' ANGL. DEV. = 5.0 DEGREES REMARK 500 2 A R 4 O4' - C4' - C3' ANGL. DEV. = -6.6 DEGREES REMARK 500 2 A R 4 C1' - O4' - C4' ANGL. DEV. = 8.2 DEGREES REMARK 500 3 G R 1 O4' - C4' - C3' ANGL. DEV. = -9.6 DEGREES REMARK 500 3 G R 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 3 G R 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 G R 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 3 U R 2 O4' - C4' - C3' ANGL. DEV. = -10.8 DEGREES REMARK 500 3 C R 3 O4' - C4' - C3' ANGL. DEV. = -11.1 DEGREES REMARK 500 3 A R 4 C1' - O4' - C4' ANGL. DEV. = 7.2 DEGREES REMARK 500 4 G R 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 4 G R 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 4 G R 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 4 U R 2 O4' - C4' - C3' ANGL. DEV. = -9.3 DEGREES REMARK 500 4 U R 2 C1' - O4' - C4' ANGL. DEV. = 7.1 DEGREES REMARK 500 4 C R 3 O4' - C4' - C3' ANGL. DEV. = -10.9 DEGREES REMARK 500 4 A R 4 C1' - O4' - C4' ANGL. DEV. = 8.1 DEGREES REMARK 500 5 G R 1 C1' - O4' - C4' ANGL. DEV. = 6.7 DEGREES REMARK 500 5 G R 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 5 G R 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 5 G R 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 5 U R 2 C1' - O4' - C4' ANGL. DEV. = 8.2 DEGREES REMARK 500 5 C R 3 O4' - C4' - C3' ANGL. DEV. = -10.5 DEGREES REMARK 500 5 A R 4 C1' - O4' - C4' ANGL. DEV. = 6.2 DEGREES REMARK 500 6 G R 1 O4' - C4' - C3' ANGL. DEV. = -8.4 DEGREES REMARK 500 6 G R 1 C1' - O4' - C4' ANGL. DEV. = 7.7 DEGREES REMARK 500 6 G R 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 6 G R 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 6 G R 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 6 C R 3 C1' - O4' - C4' ANGL. DEV. = 5.5 DEGREES REMARK 500 6 A R 4 C1' - O4' - C4' ANGL. DEV. = 4.9 DEGREES REMARK 500 7 G R 1 O4' - C4' - C3' ANGL. DEV. = -11.0 DEGREES REMARK 500 7 G R 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 7 G R 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 7 G R 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 7 U R 2 O4' - C4' - C3' ANGL. DEV. = -8.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 73 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34838 RELATED DB: BMRB REMARK 900 SHORT RNA BINDING TO PEPTIDE AMYLOIDS DBREF 8PXS A 1 9 PDB 8PXS 8PXS 1 9 DBREF 8PXS B 1 9 PDB 8PXS 8PXS 1 9 DBREF 8PXS C 1 9 PDB 8PXS 8PXS 1 9 DBREF 8PXS R 1 4 PDB 8PXS 8PXS 1 4 DBREF 8PXS D 1 9 PDB 8PXS 8PXS 1 9 DBREF 8PXS E 1 9 PDB 8PXS 8PXS 1 9 DBREF 8PXS F 1 9 PDB 8PXS 8PXS 1 9 DBREF 8PXS G 1 9 PDB 8PXS 8PXS 1 9 DBREF 8PXS H 1 9 PDB 8PXS 8PXS 1 9 DBREF 8PXS I 1 9 PDB 8PXS 8PXS 1 9 DBREF 8PXS J 1 9 PDB 8PXS 8PXS 1 9 SEQRES 1 A 9 VAL ALA GLN ALA GLN ILE ASN ILE NH2 SEQRES 1 B 9 VAL ALA GLN ALA GLN ILE ASN ILE NH2 SEQRES 1 C 9 VAL ALA GLN ALA GLN ILE ASN ILE NH2 SEQRES 1 R 4 G U C A SEQRES 1 D 9 VAL ALA GLN ALA GLN ILE ASN ILE NH2 SEQRES 1 E 9 VAL ALA GLN ALA GLN ILE ASN ILE NH2 SEQRES 1 F 9 VAL ALA GLN ALA GLN ILE ASN ILE NH2 SEQRES 1 G 9 VAL ALA GLN ALA GLN ILE ASN ILE NH2 SEQRES 1 H 9 VAL ALA GLN ALA GLN ILE ASN ILE NH2 SEQRES 1 I 9 VAL ALA GLN ALA GLN ILE ASN ILE NH2 SEQRES 1 J 9 VAL ALA GLN ALA GLN ILE ASN ILE NH2 HET NH2 A 9 3 HET NH2 B 9 3 HET NH2 C 9 3 HET NH2 D 9 3 HET NH2 E 9 3 HET NH2 F 9 3 HET NH2 G 9 3 HET NH2 H 9 3 HET NH2 I 9 3 HET NH2 J 9 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 10(H2 N) SHEET 1 AA1 5 ALA A 2 ASN A 7 0 SHEET 2 AA1 5 ALA B 2 ASN B 7 1 O GLN B 5 N ALA A 4 SHEET 3 AA1 5 ALA C 2 ASN C 7 1 O GLN C 5 N ILE B 6 SHEET 4 AA1 5 ALA D 2 ASN D 7 1 O GLN D 5 N ALA C 4 SHEET 5 AA1 5 ALA E 2 ASN E 7 1 O GLN E 5 N ILE D 6 SHEET 1 AA2 5 ALA F 2 ASN F 7 0 SHEET 2 AA2 5 ALA G 2 ASN G 7 1 O GLN G 5 N ALA F 4 SHEET 3 AA2 5 ALA H 2 ASN H 7 1 O GLN H 5 N ALA G 4 SHEET 4 AA2 5 ALA I 2 ASN I 7 1 O GLN I 5 N ALA H 4 SHEET 5 AA2 5 ALA J 2 ASN J 7 1 O GLN J 5 N ALA I 4 LINK C ILE A 8 N NH2 A 9 1555 1555 1.33 LINK C ILE B 8 N NH2 B 9 1555 1555 1.33 LINK C ILE C 8 N NH2 C 9 1555 1555 1.33 LINK C ILE D 8 N NH2 D 9 1555 1555 1.33 LINK C ILE E 8 N NH2 E 9 1555 1555 1.33 LINK C ILE F 8 N NH2 F 9 1555 1555 1.33 LINK C ILE G 8 N NH2 G 9 1555 1555 1.33 LINK C ILE H 8 N NH2 H 9 1555 1555 1.33 LINK C ILE I 8 N NH2 I 9 1555 1555 1.33 LINK C ILE J 8 N NH2 J 9 1555 1555 1.33 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