HEADER DE NOVO PROTEIN 14-MAR-22 7UBF TITLE SOLUTION NMR STRUCTURE OF 8-RESIDUE ROSETTA-DESIGNED CYCLIC PEPTIDE TITLE 2 D8.21 IN 50% D6-DMSO AND 50% WATER WITH CIS/TRANS SWITCHING (CC TITLE 3 CONFORMATION, 50%) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIC PEPTIDE D8.21 DVA-MLE-DPR-LEU-DVA-MLE-DPR-LEU; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS CYCLIC PEPTIDE, NON NATURAL AMINO ACIDS, CIS/TRANS, SWITCH PEPTIDES, KEYWDS 2 DE NOVO DESIGN, MEMBRANE PERMEABILITY, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.A.RAMELOT,R.TEJERO,G.T.MONTELIONE REVDAT 2 28-SEP-22 7UBF 1 JRNL REVDAT 1 14-SEP-22 7UBF 0 JRNL AUTH G.BHARDWAJ,J.O'CONNOR,S.RETTIE,Y.H.HUANG,T.A.RAMELOT, JRNL AUTH 2 V.K.MULLIGAN,G.G.ALPKILIC,J.PALMER,A.K.BERA,M.J.BICK, JRNL AUTH 3 M.DI PIAZZA,X.LI,P.HOSSEINZADEH,T.W.CRAVEN,R.TEJERO,A.LAUKO, JRNL AUTH 4 R.CHOI,C.GLYNN,L.DONG,R.GRIFFIN,W.C.VAN VOORHIS,J.RODRIGUEZ, JRNL AUTH 5 L.STEWART,G.T.MONTELIONE,D.CRAIK,D.BAKER JRNL TITL ACCURATE DE NOVO DESIGN OF MEMBRANE-TRAVERSING MACROCYCLES. JRNL REF CELL V. 185 3520 2022 JRNL REFN ISSN 1097-4172 JRNL PMID 36041435 JRNL DOI 10.1016/J.CELL.2022.07.019 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.13 REMARK 3 AUTHORS : GUNTERT , MUMENTHALER, AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THIS IS CONFORMATION A (TT) OF THE SAME REMARK 3 8-RESIDUE CYCLIC PEPTIDE PRESENT IN THE SAME NMR SAMPLE IN 50% REMARK 3 D6-DMSO AND 50% WATER. TT SYMMETRIC CONFORMATION HAS TRANS DPR3 REMARK 3 AND TRANS DPR7 (7UBF, 50%). CC SYMMETRIC CONFORMATION HAS CIS REMARK 3 DPR3 AND CIS DPR7 (50%). REMARK 4 REMARK 4 7UBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000263688. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 0.0 REMARK 210 IONIC STRENGTH : NA REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 6 MG/L PEPTIDE, 0.03 % TMS, 50% REMARK 210 H2O / 50% DMSO; 6 MG/ML PEPTIDE, REMARK 210 0.03 % TMS, 50% D2O/50% DMSO REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1D 1H; 2D 1H-1H NOESY; 2D 1H-1H REMARK 210 TOCSY; 2D 1H-1H COSY; 2D 1H-1H REMARK 210 ROESY; 2D 1H-13C HSQC; 2D 1H-15N REMARK 210 SOFAST; 2D 1H-13C HSQC-TOCSY; 1H- REMARK 210 13C HMBC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFAM-SPARKY V1.370, NMRPIPE REMARK 210 10.9, PDBSTAT 5.21.6, CYANA REMARK 210 3.98.13 REMARK 210 METHOD USED : NA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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 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 19 DPR A 3 N - CA - CB ANGL. DEV. = -7.5 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 10 MLE A 2 78.12 -116.07 REMARK 500 10 MLE A 6 78.17 -116.16 REMARK 500 11 MLE A 2 75.92 -116.16 REMARK 500 11 DVA A 5 -148.18 172.94 REMARK 500 11 MLE A 6 76.34 -116.86 REMARK 500 16 DVA A 5 -144.57 179.38 REMARK 500 19 DPR A 3 -54.70 115.21 REMARK 500 19 LEU A 4 51.00 -99.98 REMARK 500 19 DPR A 7 -53.42 112.76 REMARK 500 20 DVA A 5 -142.92 179.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31000 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF 8-RESIDUE ROSETTA-DESIGNED CYCLIC PEPTIDE REMARK 900 D8.21 IN 50% D6-DMSO AND 50% WATER WITH CIS/TRANS SWITCHING REMARK 900 RELATED ID: 31022 RELATED DB: BMRB REMARK 900 CC CONFORMATION (50%) REMARK 900 RELATED ID: 8CUN RELATED DB: PDB REMARK 900 CC CONFORMATION (50%) DBREF 7UBF A 1 8 PDB 7UBF 7UBF 1 8 SEQRES 1 A 8 DVA MLE DPR LEU DVA MLE DPR LEU HET DVA A 1 16 HET MLE A 2 22 HET DPR A 3 14 HET DVA A 5 16 HET MLE A 6 22 HET DPR A 7 14 HETNAM DVA D-VALINE HETNAM MLE N-METHYLLEUCINE HETNAM DPR D-PROLINE FORMUL 1 DVA 2(C5 H11 N O2) FORMUL 1 MLE 2(C7 H15 N O2) FORMUL 1 DPR 2(C5 H9 N O2) LINK C DVA A 1 N MLE A 2 1555 1555 1.33 LINK N DVA A 1 C LEU A 8 1555 1555 1.34 LINK C MLE A 2 N DPR A 3 1555 1555 1.33 LINK C DPR A 3 N LEU A 4 1555 1555 1.33 LINK C LEU A 4 N DVA A 5 1555 1555 1.33 LINK C DVA A 5 N MLE A 6 1555 1555 1.33 LINK C MLE A 6 N DPR A 7 1555 1555 1.33 LINK C DPR A 7 N LEU A 8 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 HETATM 1 N DVA A 1 -0.062 -3.156 -0.042 1.00 13.34 N HETATM 2 CA DVA A 1 0.705 -3.159 -1.293 1.00 75.42 C HETATM 3 CB DVA A 1 0.834 -4.592 -1.809 1.00 64.10 C HETATM 4 CG1 DVA A 1 -0.558 -5.175 -2.054 1.00 4.42 C HETATM 5 CG2 DVA A 1 1.624 -4.593 -3.119 1.00 23.31 C HETATM 6 C DVA A 1 2.077 -2.589 -1.043 1.00 21.51 C HETATM 7 O DVA A 1 2.672 -2.819 0.008 1.00 50.25 O HETATM 8 H1 DVA A 1 0.417 -3.127 0.813 1.00 73.41 H HETATM 9 HA DVA A 1 0.189 -2.551 -2.037 1.00 40.13 H HETATM 10 HB DVA A 1 1.357 -5.198 -1.070 1.00 25.33 H HETATM 11 HG11 DVA A 1 -1.140 -4.487 -2.665 1.00 44.53 H HETATM 12 HG12 DVA A 1 -0.465 -6.130 -2.571 1.00 24.43 H HETATM 13 HG13 DVA A 1 -1.061 -5.329 -1.100 1.00 21.42 H HETATM 14 HG21 DVA A 1 2.574 -4.083 -2.971 1.00 5.42 H HETATM 15 HG22 DVA A 1 1.810 -5.621 -3.430 1.00 52.44 H HETATM 16 HG23 DVA A 1 1.051 -4.079 -3.889 1.00 52.23 H HETATM 17 N MLE A 2 2.586 -1.838 -2.014 1.00 64.11 N HETATM 18 CN MLE A 2 2.054 -1.444 -3.325 1.00 55.14 C HETATM 19 CA MLE A 2 3.915 -1.224 -1.895 1.00 1.21 C HETATM 20 CB MLE A 2 4.901 -1.963 -2.800 1.00 52.52 C HETATM 21 CG MLE A 2 6.325 -1.743 -2.288 1.00 15.21 C HETATM 22 CD1 MLE A 2 7.206 -2.923 -2.707 1.00 12.20 C HETATM 23 CD2 MLE A 2 6.889 -0.452 -2.885 1.00 55.21 C HETATM 24 C MLE A 2 3.838 0.223 -2.309 1.00 40.20 C HETATM 25 O MLE A 2 4.194 0.575 -3.433 1.00 10.55 O HETATM 26 HN1 MLE A 2 1.670 -0.425 -3.272 1.00 21.54 H HETATM 27 HN2 MLE A 2 2.848 -1.494 -4.069 1.00 73.11 H HETATM 28 HN3 MLE A 2 1.248 -2.122 -3.608 1.00 50.24 H HETATM 29 HA MLE A 2 4.254 -1.288 -0.861 1.00 63.43 H HETATM 30 HB2 MLE A 2 4.672 -3.027 -2.792 1.00 74.04 H HETATM 31 HB3 MLE A 2 4.817 -1.581 -3.817 1.00 22.54 H HETATM 32 HG MLE A 2 6.314 -1.667 -1.202 1.00 20.22 H HETATM 33 HD11 MLE A 2 6.917 -3.810 -2.144 1.00 12.22 H HETATM 34 HD12 MLE A 2 7.078 -3.111 -3.773 1.00 51.33 H HETATM 35 HD13 MLE A 2 8.250 -2.687 -2.504 1.00 54.14 H HETATM 36 HD21 MLE A 2 7.974 -0.519 -2.937 1.00 15.54 H HETATM 37 HD22 MLE A 2 6.484 -0.308 -3.886 1.00 63.10 H HETATM 38 HD23 MLE A 2 6.608 0.392 -2.254 1.00 42.32 H HETATM 39 N DPR A 3 3.371 1.069 -1.397 1.00 31.21 N HETATM 40 CA DPR A 3 3.245 2.511 -1.677 1.00 0.24 C HETATM 41 CB DPR A 3 3.123 3.188 -0.323 1.00 14.43 C HETATM 42 CG DPR A 3 2.259 2.146 0.434 1.00 64.21 C HETATM 43 CD DPR A 3 2.906 0.814 -0.018 1.00 21.11 C HETATM 44 C DPR A 3 2.055 2.760 -2.568 1.00 14.40 C HETATM 45 O DPR A 3 1.986 3.775 -3.261 1.00 32.22 O HETATM 46 HA DPR A 3 4.153 2.877 -2.156 1.00 50.40 H HETATM 47 HB2 DPR A 3 4.093 3.309 0.160 1.00 2.31 H HETATM 48 HB3 DPR A 3 2.603 4.143 -0.392 1.00 34.23 H HETATM 49 HG2 DPR A 3 2.347 2.277 1.513 1.00 20.21 H HETATM 50 HG3 DPR A 3 1.216 2.202 0.120 1.00 25.23 H HETATM 51 HD2 DPR A 3 2.169 0.011 -0.008 1.00 0.52 H HETATM 52 HD3 DPR A 3 3.749 0.564 0.626 1.00 55.54 H