HEADER DE NOVO PROTEIN 18-MAY-22 8CWA TITLE SOLUTION NMR STRUCTURE OF 8-RESIDUE ROSETTA-DESIGNED CYCLIC PEPTIDE TITLE 2 D8.21 IN CDCL3 WITH CIS/TRANS SWITCHING (TC CONFORMATION, 53%) 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 8CWA 1 JRNL REVDAT 1 14-SEP-22 8CWA 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 P., MUMENTHALER, AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THIS IS CONFORMATION A (TC) OF THE SAME REMARK 3 8-RESIDUE CYCLIC PEPTIDE PRESENT IN THE SAME NMR SAMPLE. TT REMARK 3 SYMMETRIC CONFORMATION HAS TRANS DPR3 AND TRANS DPR7 (47%). TC REMARK 3 CONFORMATION HAS TRANS DPR3 AND CIS DPR7 (53%). REMARK 4 REMARK 4 8CWA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265531. 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/ML PEPTIDE, 0.03 % TMS, REMARK 210 CDCL3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1D 1H; 2D 1H-15N HSQC; 2D 1H-13C REMARK 210 HSQC-ED; 2D 1H-1H NOESY; 2D 1H- REMARK 210 1H ROESY; 2D 1H-1H COSY; 2D 1H- REMARK 210 1H TOCSY; 2D 1H-13C HMBC; 2D 1H- REMARK 210 13C HSQC-TOCSY 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 1.37, TOPSPIN 3.5, REMARK 210 PDBSTAT 5.21.6, CYANA 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: 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 5 MLE A 6 74.10 -161.62 REMARK 500 10 LEU A 4 -56.02 -131.60 REMARK 500 11 LEU A 4 -54.12 -131.26 REMARK 500 12 LEU A 4 -54.07 -131.26 REMARK 500 13 LEU A 4 -52.25 -131.18 REMARK 500 14 DPR A 3 -46.51 78.67 REMARK 500 14 LEU A 4 -77.52 -65.54 REMARK 500 14 DVA A 5 57.63 129.12 REMARK 500 14 MLE A 6 66.37 23.82 REMARK 500 15 LEU A 4 -81.93 -64.83 REMARK 500 15 DVA A 5 54.27 137.61 REMARK 500 15 MLE A 6 69.00 36.98 REMARK 500 16 LEU A 4 -81.50 -64.79 REMARK 500 16 DVA A 5 54.15 136.53 REMARK 500 16 MLE A 6 68.76 37.03 REMARK 500 17 LEU A 4 -81.33 -64.80 REMARK 500 17 DVA A 5 54.41 136.63 REMARK 500 17 MLE A 6 68.91 37.02 REMARK 500 18 LEU A 4 -82.63 -66.99 REMARK 500 18 DVA A 5 55.04 141.71 REMARK 500 18 MLE A 6 69.25 37.53 REMARK 500 19 MLE A 2 170.16 60.51 REMARK 500 20 MLE A 2 167.82 60.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31003 RELATED DB: BMRB REMARK 900 A-TT CONFORMATION REMARK 900 RELATED ID: 7UBI RELATED DB: PDB REMARK 900 A-TT CONFORMATION REMARK 900 RELATED ID: 31023 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF 8-RESIDUE ROSETTA-DESIGNED CYCLIC PEPTIDE REMARK 900 D8.21 IN CDCL3 WITH CIS/TRANS SWITCHING (TC CONFORMATION, 53%) DBREF 8CWA A 1 8 PDB 8CWA 8CWA 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 1.36 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 CISPEP 1 MLE A 6 DPR A 7 1 -0.02 CISPEP 2 MLE A 6 DPR A 7 2 0.08 CISPEP 3 MLE A 6 DPR A 7 3 -0.09 CISPEP 4 MLE A 6 DPR A 7 4 -0.08 CISPEP 5 MLE A 6 DPR A 7 5 0.10 CISPEP 6 MLE A 6 DPR A 7 6 -0.10 CISPEP 7 MLE A 6 DPR A 7 7 0.00 CISPEP 8 MLE A 6 DPR A 7 8 -0.08 CISPEP 9 MLE A 6 DPR A 7 9 0.04 CISPEP 10 MLE A 6 DPR A 7 10 -0.05 CISPEP 11 MLE A 6 DPR A 7 11 0.02 CISPEP 12 MLE A 6 DPR A 7 12 0.01 CISPEP 13 MLE A 6 DPR A 7 13 0.10 CISPEP 14 MLE A 6 DPR A 7 14 0.00 CISPEP 15 MLE A 6 DPR A 7 15 0.02 CISPEP 16 MLE A 6 DPR A 7 16 0.09 CISPEP 17 MLE A 6 DPR A 7 17 0.02 CISPEP 18 MLE A 6 DPR A 7 18 0.03 CISPEP 19 MLE A 6 DPR A 7 19 -0.08 CISPEP 20 MLE A 6 DPR A 7 20 -0.03 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 -1.806 -1.073 -1.821 1.00 72.00 N HETATM 2 CA DVA A 1 -1.027 -1.132 -3.065 1.00 3.15 C HETATM 3 CB DVA A 1 -0.726 -2.591 -3.409 1.00 4.43 C HETATM 4 CG1 DVA A 1 -0.651 -3.416 -2.123 1.00 52.04 C HETATM 5 CG2 DVA A 1 -1.838 -3.145 -4.303 1.00 64.44 C HETATM 6 C DVA A 1 0.264 -0.380 -2.886 1.00 22.53 C HETATM 7 O DVA A 1 1.174 -0.845 -2.200 1.00 43.53 O HETATM 8 H1 DVA A 1 -1.336 -1.111 -0.961 1.00 41.14 H HETATM 9 HA DVA A 1 -1.602 -0.681 -3.874 1.00 61.04 H HETATM 10 HB DVA A 1 0.225 -2.652 -3.936 1.00 62.35 H HETATM 11 HG11 DVA A 1 -0.057 -4.312 -2.299 1.00 31.30 H HETATM 12 HG12 DVA A 1 -0.186 -2.819 -1.337 1.00 54.24 H HETATM 13 HG13 DVA A 1 -1.656 -3.699 -1.813 1.00 12.43 H HETATM 14 HG21 DVA A 1 -1.521 -4.095 -4.730 1.00 50.52 H HETATM 15 HG22 DVA A 1 -2.740 -3.296 -3.711 1.00 23.32 H HETATM 16 HG23 DVA A 1 -2.044 -2.437 -5.106 1.00 50.22 H HETATM 17 N MLE A 2 0.351 0.793 -3.503 1.00 53.34 N HETATM 18 CN MLE A 2 -0.600 1.521 -4.355 1.00 41.12 C HETATM 19 CA MLE A 2 1.557 1.626 -3.410 1.00 33.13 C HETATM 20 CB MLE A 2 1.995 2.049 -4.812 1.00 12.43 C HETATM 21 CG MLE A 2 2.145 0.809 -5.695 1.00 54.11 C HETATM 22 CD1 MLE A 2 2.451 1.240 -7.131 1.00 42.51 C HETATM 23 CD2 MLE A 2 3.290 -0.057 -5.169 1.00 33.13 C HETATM 24 C MLE A 2 1.260 2.850 -2.585 1.00 4.35 C HETATM 25 O MLE A 2 0.100 3.163 -2.320 1.00 4.33 O HETATM 26 HN1 MLE A 2 -0.415 2.592 -4.275 1.00 24.10 H HETATM 27 HN2 MLE A 2 -0.473 1.207 -5.391 1.00 1.24 H HETATM 28 HN3 MLE A 2 -1.617 1.303 -4.031 1.00 31.14 H HETATM 29 HA MLE A 2 2.357 1.055 -2.937 1.00 5.22 H HETATM 30 HB2 MLE A 2 1.246 2.713 -5.240 1.00 11.41 H HETATM 31 HB3 MLE A 2 2.950 2.571 -4.753 1.00 21.54 H HETATM 32 HG MLE A 2 1.219 0.237 -5.678 1.00 65.20 H HETATM 33 HD11 MLE A 2 3.459 1.650 -7.181 1.00 53.23 H HETATM 34 HD12 MLE A 2 2.376 0.377 -7.794 1.00 11.31 H HETATM 35 HD13 MLE A 2 1.734 1.999 -7.444 1.00 22.23 H HETATM 36 HD21 MLE A 2 3.698 -0.654 -5.984 1.00 61.51 H HETATM 37 HD22 MLE A 2 4.071 0.583 -4.761 1.00 44.43 H HETATM 38 HD23 MLE A 2 2.916 -0.718 -4.388 1.00 2.15 H HETATM 39 N DPR A 3 2.311 3.550 -2.173 1.00 43.03 N HETATM 40 CA DPR A 3 2.155 4.770 -1.358 1.00 51.22 C HETATM 41 CB DPR A 3 3.486 5.500 -1.434 1.00 33.31 C HETATM 42 CG DPR A 3 4.469 4.299 -1.443 1.00 32.24 C HETATM 43 CD DPR A 3 3.753 3.315 -2.401 1.00 24.41 C HETATM 44 C DPR A 3 1.784 4.398 0.054 1.00 72.22 C HETATM 45 O DPR A 3 2.530 4.672 0.996 1.00 40.34 O HETATM 46 HA DPR A 3 1.385 5.408 -1.791 1.00 70.22 H HETATM 47 HB2 DPR A 3 3.578 6.080 -2.352 1.00 54.22 H HETATM 48 HB3 DPR A 3 3.655 6.129 -0.560 1.00 5.41 H HETATM 49 HG2 DPR A 3 5.441 4.593 -1.840 1.00 35.11 H HETATM 50 HG3 DPR A 3 4.570 3.871 -0.446 1.00 21.24 H HETATM 51 HD2 DPR A 3 4.013 2.286 -2.151 1.00 1.14 H HETATM 52 HD3 DPR A 3 4.015 3.534 -3.435 1.00 1.53 H