HEADER HORMONE 11-APR-21 7ELJ TITLE PRION DERIVED TETRAPEPTIDE STABILIZES THERMOLABILE INSULIN VIA TITLE 2 CONFORMATIONAL TRAPPING COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULIN A CHAIN; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: INSULIN B CHAIN; COMPND 6 CHAIN: B; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: IS1; COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 7 ORGANISM_COMMON: BOVINE; SOURCE 8 ORGANISM_TAXID: 9913; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS INSULIN, STABILIZATION, AMYLOID, HORMONE EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR N.BANERJEE REVDAT 2 07-JUL-21 7ELJ 1 JRNL REVDAT 1 28-APR-21 7ELJ 0 JRNL AUTH M.MUKHERJEE,D.DAS,J.SARKAR,N.BANERJEE,J.JANA,J.BHAT, JRNL AUTH 2 J.REDDY G,J.BHARATAM,S.CHATTOPADHYAY,S.CHATTERJEE, JRNL AUTH 3 P.CHAKRABARTI JRNL TITL PRION-DERIVED TETRAPEPTIDE STABILIZES THERMOLABILE INSULIN JRNL TITL 2 VIA CONFORMATIONAL TRAPPING. JRNL REF ISCIENCE V. 24 02573 2021 JRNL REFN ESSN 2589-0042 JRNL PMID 34142060 JRNL DOI 10.1016/J.ISCI.2021.102573 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 3.1 REMARK 3 AUTHORS : BRUKER BIOSPIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7ELJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021671. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 2.6 REMARK 210 IONIC STRENGTH : 1 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM PROTON BOVINE INSULIN, 1 MM REMARK 210 PROTON-15N, 13C PEPTIDE, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1D 1H; 2D 1H-1H NOESY; 3D 1H-15N REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFAM-SPARKY, TOPSPIN REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 ARG C 4 CZ ARG C 4 NH2 -0.098 REMARK 500 3 TYR A 14 CZ TYR A 14 CE2 0.114 REMARK 500 3 TYR B 16 CZ TYR B 16 CE2 0.082 REMARK 500 3 TYR C 2 CZ TYR C 2 CE2 0.091 REMARK 500 3 TYR C 3 CG TYR C 3 CD1 0.084 REMARK 500 5 GLU B 13 CG GLU B 13 CD 0.094 REMARK 500 5 TYR C 3 CE1 TYR C 3 CZ 0.081 REMARK 500 6 TYR A 14 CE1 TYR A 14 CZ 0.081 REMARK 500 8 PHE B 1 CG PHE B 1 CD2 0.114 REMARK 500 8 ARG B 22 CZ ARG B 22 NH2 -0.082 REMARK 500 REMARK 500 REMARK: NULL 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 LEU A 13 CB - CA - C ANGL. DEV. = 11.6 DEGREES REMARK 500 1 TYR B 16 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 PHE B 24 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 PHE B 24 CB - CG - CD1 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 PHE B 25 CB - CG - CD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 TYR C 2 CB - CG - CD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 TYR C 2 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 VAL A 3 CG1 - CB - CG2 ANGL. DEV. = -9.6 DEGREES REMARK 500 2 CYS A 7 CA - CB - SG ANGL. DEV. = -11.9 DEGREES REMARK 500 2 VAL B 2 CA - CB - CG2 ANGL. DEV. = 9.4 DEGREES REMARK 500 2 TYR B 16 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 ARG B 22 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 VAL C 1 CG1 - CB - CG2 ANGL. DEV. = -9.7 DEGREES REMARK 500 2 TYR C 2 CB - CG - CD2 ANGL. DEV. = 9.0 DEGREES REMARK 500 2 TYR C 2 CB - CG - CD1 ANGL. DEV. = -9.3 DEGREES REMARK 500 2 TYR C 3 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 3 VAL A 10 CA - CB - CG2 ANGL. DEV. = 11.8 DEGREES REMARK 500 3 LEU A 13 CB - CG - CD2 ANGL. DEV. = 11.8 DEGREES REMARK 500 3 TYR A 14 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 3 TYR A 19 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 PHE B 1 CB - CG - CD1 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 VAL B 18 CA - CB - CG2 ANGL. DEV. = -9.7 DEGREES REMARK 500 3 TYR B 26 CB - CG - CD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 3 TYR B 26 CG - CD1 - CE1 ANGL. DEV. = -7.4 DEGREES REMARK 500 3 TYR B 26 CD1 - CE1 - CZ ANGL. DEV. = 6.2 DEGREES REMARK 500 3 VAL C 1 CA - CB - CG2 ANGL. DEV. = 9.7 DEGREES REMARK 500 3 TYR C 2 CB - CG - CD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 3 ARG C 4 NH1 - CZ - NH2 ANGL. DEV. = -7.6 DEGREES REMARK 500 3 ARG C 4 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 4 TYR A 19 CZ - CE2 - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 4 PHE B 1 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 4 VAL B 2 CA - CB - CG2 ANGL. DEV. = 10.2 DEGREES REMARK 500 4 TYR C 3 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 4 ARG C 4 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 TYR A 14 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 5 TYR A 14 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 TYR A 19 CG - CD2 - CE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 5 TYR B 16 CG - CD2 - CE2 ANGL. DEV. = 5.6 DEGREES REMARK 500 5 ARG B 22 NH1 - CZ - NH2 ANGL. DEV. = -7.0 DEGREES REMARK 500 5 ARG B 22 NE - CZ - NH1 ANGL. DEV. = 8.7 DEGREES REMARK 500 5 VAL C 1 CA - CB - CG2 ANGL. DEV. = 9.8 DEGREES REMARK 500 5 ARG C 4 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ILE A 2 CA - CB - CG1 ANGL. DEV. = 12.2 DEGREES REMARK 500 6 CYS A 6 CA - CB - SG ANGL. DEV. = 8.6 DEGREES REMARK 500 6 TYR A 14 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 6 TYR A 19 CZ - CE2 - CD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 6 PHE B 1 CZ - CE2 - CD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 6 LEU B 11 CB - CG - CD1 ANGL. DEV. = 12.6 DEGREES REMARK 500 6 TYR B 16 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 6 TYR B 16 CZ - CE2 - CD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 72 ANGLE DEVIATIONS. 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 1 ALA A 8 -31.34 -138.80 REMARK 500 1 TYR C 2 145.94 72.67 REMARK 500 1 TYR C 3 170.81 61.55 REMARK 500 2 GLN A 5 -75.69 -69.06 REMARK 500 2 ALA A 8 -20.12 -143.15 REMARK 500 2 LYS B 29 100.12 -56.45 REMARK 500 2 TYR C 2 154.79 67.81 REMARK 500 2 TYR C 3 176.39 52.16 REMARK 500 3 LYS B 29 97.01 -65.55 REMARK 500 3 TYR C 2 145.42 75.05 REMARK 500 3 TYR C 3 171.70 64.12 REMARK 500 4 CYS A 7 40.96 -96.49 REMARK 500 4 ALA A 8 -28.22 -173.57 REMARK 500 4 CYS B 7 150.19 -40.00 REMARK 500 4 TYR C 2 146.42 72.90 REMARK 500 4 TYR C 3 156.52 62.30 REMARK 500 5 ALA A 8 -27.51 -144.81 REMARK 500 5 TYR C 2 145.25 78.07 REMARK 500 5 TYR C 3 154.20 69.30 REMARK 500 6 ALA A 8 -44.20 -144.43 REMARK 500 6 TYR C 2 146.22 76.06 REMARK 500 6 TYR C 3 157.85 57.94 REMARK 500 7 GLN A 5 -66.23 -94.27 REMARK 500 7 THR B 27 73.08 -109.49 REMARK 500 7 TYR C 2 149.25 60.41 REMARK 500 7 TYR C 3 157.51 64.53 REMARK 500 8 CYS B 7 152.17 -49.48 REMARK 500 8 GLU B 21 -9.96 -52.82 REMARK 500 8 THR B 27 71.87 -116.95 REMARK 500 8 TYR C 2 144.36 74.11 REMARK 500 8 TYR C 3 166.97 72.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CYS A 11 SER A 12 2 146.59 REMARK 500 CYS A 20 ASN A 21 2 147.75 REMARK 500 PRO B 28 LYS B 29 2 145.79 REMARK 500 ALA A 8 SER A 9 3 -148.27 REMARK 500 PRO B 28 LYS B 29 3 144.68 REMARK 500 CYS A 11 SER A 12 4 148.55 REMARK 500 CYS A 20 ASN A 21 4 145.04 REMARK 500 CYS A 20 ASN A 21 5 145.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 TYR A 19 0.07 SIDE CHAIN REMARK 500 2 ARG C 4 0.12 SIDE CHAIN REMARK 500 3 TYR C 2 0.08 SIDE CHAIN REMARK 500 4 TYR B 26 0.11 SIDE CHAIN REMARK 500 5 TYR C 3 0.07 SIDE CHAIN REMARK 500 6 PHE B 1 0.08 SIDE CHAIN REMARK 500 7 TYR B 16 0.09 SIDE CHAIN REMARK 500 8 TYR A 19 0.08 SIDE CHAIN REMARK 500 8 TYR C 2 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 6 HIS B 10 -10.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36417 RELATED DB: BMRB REMARK 900 PRION DERIVED TETRAPEPTIDE STABILIZES THERMOLABILE INSULIN VIA REMARK 900 CONFORMATIONAL TRAPPING DBREF 7ELJ A 1 21 UNP P01317 INS_BOVIN 85 105 DBREF 7ELJ B 1 30 UNP P01317 INS_BOVIN 25 54 DBREF 7ELJ C 1 4 PDB 7ELJ 7ELJ 1 4 SEQRES 1 A 21 GLY ILE VAL GLU GLN CYS CYS ALA SER VAL CYS SER LEU SEQRES 2 A 21 TYR GLN LEU GLU ASN TYR CYS ASN SEQRES 1 B 30 PHE VAL ASN GLN HIS LEU CYS GLY SER HIS LEU VAL GLU SEQRES 2 B 30 ALA LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE PHE TYR SEQRES 3 B 30 THR PRO LYS ALA SEQRES 1 C 4 VAL TYR TYR ARG HELIX 1 AA1 ILE A 2 CYS A 7 1 6 HELIX 2 AA2 SER A 12 TYR A 19 1 8 HELIX 3 AA3 CYS B 7 GLY B 20 1 14 HELIX 4 AA4 GLU B 21 GLY B 23 5 3 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