HEADER DE NOVO PROTEIN 09-MAY-22 7UZL TITLE SOLUTION NMR STRUCTURE OF 9-RESIDUE ROSETTA-DESIGNED CYCLIC PEPTIDE TITLE 2 D9.16 IN CDCL3 WITH CIS/TRANS SWITCHING (B-TC CONFORMATION) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIC PEPTIDE D9.16 DPR-MAA-ALA-DVA-MLE-LEU-LEU-PRO-DLE; 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 7UZL 1 JRNL REVDAT 1 14-SEP-22 7UZL 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 B (TC) OF THE SAME REMARK 3 9-RESIDUE CYCLIC PEPTIDE PRESENT IN THE SAME NMR SAMPLE IN REMARK 3 CDCL3. TT CONFORMATION HAS TRANS DPR-1 AND TRANS DPR-8. TC REMARK 3 CONFORMATION HAS TRANS DPR-1 AND CIS DPR-8 REMARK 4 REMARK 4 7UZL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265192. 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 CHLOROFORM REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1D 1H; 2D 1H-15N SOFAST; 2D 1H REMARK 210 -13C HSQC-ED; 2D 1H-13C HMBC; 2D REMARK 210 1H-1H NOESY; 2D 1H-1H ROESY; 2D REMARK 210 1H-1H DQF-COSY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HSQC-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFAM-SPARKY V.1.370 BY 3.19, REMARK 210 NMRPIPE 10.9, TOPSPIN 4.0.9, 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 1 LEU A 7 159.57 -45.57 REMARK 500 2 LEU A 7 160.64 -46.13 REMARK 500 3 LEU A 7 161.60 -49.21 REMARK 500 4 LEU A 7 161.66 -49.73 REMARK 500 5 LEU A 7 159.71 -47.00 REMARK 500 6 MAA A 2 54.36 -114.40 REMARK 500 6 ALA A 3 60.64 -119.49 REMARK 500 6 LEU A 7 162.46 -46.46 REMARK 500 7 LEU A 7 159.81 -47.57 REMARK 500 8 LEU A 7 159.88 -46.32 REMARK 500 9 LEU A 7 162.40 -49.83 REMARK 500 10 MAA A 2 51.31 -114.75 REMARK 500 10 LEU A 7 160.66 -47.61 REMARK 500 11 ALA A 3 43.77 -101.28 REMARK 500 11 LEU A 7 161.97 -48.56 REMARK 500 12 LEU A 7 162.32 -46.49 REMARK 500 13 ALA A 3 49.70 -106.66 REMARK 500 14 LEU A 7 162.26 -46.17 REMARK 500 15 ALA A 3 48.71 -106.49 REMARK 500 15 LEU A 7 160.79 -49.47 REMARK 500 16 LEU A 7 160.33 -47.32 REMARK 500 17 LEU A 7 161.43 -45.77 REMARK 500 18 ALA A 3 64.62 -117.46 REMARK 500 18 LEU A 7 160.89 -45.13 REMARK 500 19 DVA A 4 -106.71 51.96 REMARK 500 19 LEU A 7 160.61 -45.58 REMARK 500 20 LEU A 7 161.95 -45.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31001 RELATED DB: BMRB REMARK 900 CONFORMATION A-TT REMARK 900 RELATED ID: 7UBG RELATED DB: PDB REMARK 900 CONFORMATION A-TT REMARK 900 RELATED ID: 31019 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF 9-RESIDUE ROSETTA-DESIGNED CYCLIC PEPTIDE REMARK 900 D9.16 IN CDCL3 WITH CIS/TRANS SWITCHING (B-TC CONFORMATION) DBREF 7UZL A 1 9 PDB 7UZL 7UZL 1 9 SEQRES 1 A 9 DPR MAA ALA DVA MLE LEU LEU PRO DLE HET DPR A 1 14 HET MAA A 2 13 HET DVA A 4 16 HET MLE A 5 22 HET DLE A 9 19 HETNAM DPR D-PROLINE HETNAM MAA N-METHYL-L-ALANINE HETNAM DVA D-VALINE HETNAM MLE N-METHYLLEUCINE HETNAM DLE D-LEUCINE FORMUL 1 DPR C5 H9 N O2 FORMUL 1 MAA C4 H9 N O2 FORMUL 1 DVA C5 H11 N O2 FORMUL 1 MLE C7 H15 N O2 FORMUL 1 DLE C6 H13 N O2 LINK C DPR A 1 N MAA A 2 1555 1555 1.33 LINK N DPR A 1 C DLE A 9 1555 1555 1.37 LINK C MAA A 2 N ALA A 3 1555 1555 1.33 LINK C ALA A 3 N DVA A 4 1555 1555 1.33 LINK C DVA A 4 N MLE A 5 1555 1555 1.33 LINK C MLE A 5 N LEU A 6 1555 1555 1.33 LINK C PRO A 8 N DLE A 9 1555 1555 1.33 CISPEP 1 LEU A 7 PRO A 8 1 -0.04 CISPEP 2 LEU A 7 PRO A 8 2 -0.14 CISPEP 3 LEU A 7 PRO A 8 3 -0.09 CISPEP 4 LEU A 7 PRO A 8 4 -0.23 CISPEP 5 LEU A 7 PRO A 8 5 -0.17 CISPEP 6 LEU A 7 PRO A 8 6 -0.13 CISPEP 7 LEU A 7 PRO A 8 7 -0.07 CISPEP 8 LEU A 7 PRO A 8 8 -0.17 CISPEP 9 LEU A 7 PRO A 8 9 -0.22 CISPEP 10 LEU A 7 PRO A 8 10 -0.15 CISPEP 11 LEU A 7 PRO A 8 11 -0.17 CISPEP 12 LEU A 7 PRO A 8 12 -0.17 CISPEP 13 LEU A 7 PRO A 8 13 -0.17 CISPEP 14 LEU A 7 PRO A 8 14 -0.23 CISPEP 15 LEU A 7 PRO A 8 15 -0.10 CISPEP 16 LEU A 7 PRO A 8 16 -0.11 CISPEP 17 LEU A 7 PRO A 8 17 -0.20 CISPEP 18 LEU A 7 PRO A 8 18 -0.27 CISPEP 19 LEU A 7 PRO A 8 19 -0.06 CISPEP 20 LEU A 7 PRO A 8 20 -0.06 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 DPR A 1 1.996 -0.150 3.825 1.00 65.12 N HETATM 2 CA DPR A 1 2.821 -1.354 4.030 1.00 60.32 C HETATM 3 CB DPR A 1 3.902 -0.931 5.087 1.00 33.05 C HETATM 4 CG DPR A 1 3.693 0.583 5.354 1.00 43.15 C HETATM 5 CD DPR A 1 2.204 0.764 4.967 1.00 14.24 C HETATM 6 C DPR A 1 3.406 -1.805 2.717 1.00 23.22 C HETATM 7 O DPR A 1 4.190 -1.087 2.097 1.00 72.31 O HETATM 8 HA DPR A 1 2.214 -2.150 4.462 1.00 23.40 H HETATM 9 HB2 DPR A 1 3.750 -1.508 6.000 1.00 33.42 H HETATM 10 HB3 DPR A 1 4.894 -1.116 4.674 1.00 42.22 H HETATM 11 HG2 DPR A 1 3.855 0.821 6.405 1.00 0.51 H HETATM 12 HG3 DPR A 1 4.339 1.185 4.714 1.00 52.20 H HETATM 13 HD2 DPR A 1 2.013 1.795 4.667 1.00 14.32 H HETATM 14 HD3 DPR A 1 1.558 0.485 5.800 1.00 5.21 H HETATM 15 N MAA A 2 3.025 -3.003 2.284 1.00 1.44 N HETATM 16 CM MAA A 2 2.115 -4.004 2.857 1.00 33.24 C HETATM 17 CA MAA A 2 3.522 -3.558 1.020 1.00 3.00 C HETATM 18 CB MAA A 2 4.493 -4.704 1.311 1.00 1.03 C HETATM 19 C MAA A 2 2.365 -4.076 0.208 1.00 2.42 C HETATM 20 O MAA A 2 2.371 -5.222 -0.239 1.00 2.11 O HETATM 21 HM1 MAA A 2 1.088 -3.747 2.605 1.00 3.31 H HETATM 22 HM2 MAA A 2 2.354 -4.985 2.453 1.00 44.13 H HETATM 23 HM3 MAA A 2 2.230 -4.019 3.942 1.00 64.32 H HETATM 24 HA MAA A 2 4.039 -2.779 0.459 1.00 24.11 H HETATM 25 HB1 MAA A 2 3.936 -5.635 1.402 1.00 61.54 H HETATM 26 HB2 MAA A 2 5.212 -4.787 0.498 1.00 74.51 H HETATM 27 HB3 MAA A 2 5.022 -4.504 2.243 1.00 50.52 H