HEADER UNKNOWN FUNCTION 18-JAN-04 1S4T TITLE SOLUTION STRUCTURE OF SYNTHETIC 21MER PEPTIDE SPANNING REGION 135-155 TITLE 2 (IN HUMAN NUMBERING) OF SHEEP PRION PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PRP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS PEPTIDE HAS BEEN CHEMICALLY SYNTHESIZED. THE SOURCE 4 SEQUENCE OCCURS NATURALLY IN SHEEP. KEYWDS PRION, HELIX, UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.A.KOZIN,C.LEPAGE,G.HUI BON HOA,H.RABESONA,A.K.MAZUR,A.BLOND, AUTHOR 2 M.CHEMINANT,T.HAERTLE,P.DEBEY,S.REBUFFAT REVDAT 3 02-MAR-22 1S4T 1 REMARK REVDAT 2 24-FEB-09 1S4T 1 VERSN REVDAT 1 27-JAN-04 1S4T 0 JRNL AUTH S.A.KOZIN,C.LEPAGE,G.HUI BON HOA,H.RABESONA,A.K.MAZUR, JRNL AUTH 2 A.BLOND,M.CHEMINANT,T.HAERTLE,P.DEBEY,S.REBUFFAT JRNL TITL SPECIFIC RECOGNITION BETWEEN SURFACE LOOP 2 (132-143) AND JRNL TITL 2 HELIX 1 (144-154) WITHIN SHEEP PRION PROTEIN FROM IN VITRO JRNL TITL 3 STUDIES OF SYNTHETIC PEPTIDES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 1.3, ICMDY 2.3 REMARK 3 AUTHORS : BRUKER (XWINNMR), MAZUR, A.K. (ICMDY) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 134 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS. REMARK 4 REMARK 4 1S4T COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021367. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 324 REMARK 210 PH : 2.3 REMARK 210 IONIC STRENGTH : ND REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 5 MM REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AURELIA 2.5.9, ICMDY 2.3 REMARK 210 METHOD USED : MOLECULAR DYNAMICS WITH AMBER99 REMARK 210 ALL-ATOM FORCE FIELD PARAMETERS REMARK 210 BY USING THE VARIABLE TARGET REMARK 210 FUNCTION APPROACH IN THE TORSION REMARK 210 ANGLE SPACE WITH THE STANDARD REMARK 210 GEOMETRY OF AMINO ACIDS AND REMARK 210 PEPTIDE BONDS. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED CONFORMER MODELS REMARK 210 ARE THE 20 STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS AND REMARK 210 THE LOWESTT ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HG SER A 135 OD1 ASP A 144 1.50 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 LEU A 138 28.94 -141.26 REMARK 500 1 ILE A 139 110.58 -12.74 REMARK 500 1 HIS A 140 64.80 -113.07 REMARK 500 1 PHE A 141 126.27 -35.56 REMARK 500 1 ASN A 143 -19.14 -143.65 REMARK 500 1 ARG A 151 51.52 -92.84 REMARK 500 1 GLU A 152 33.54 -77.39 REMARK 500 1 ASN A 153 13.86 -169.63 REMARK 500 2 ILE A 139 116.76 36.38 REMARK 500 2 HIS A 140 48.61 -143.02 REMARK 500 2 PHE A 141 125.33 -31.33 REMARK 500 2 ASN A 143 -11.80 -152.21 REMARK 500 2 ASP A 144 68.30 62.04 REMARK 500 2 ARG A 151 56.12 -102.30 REMARK 500 2 GLU A 152 32.35 -86.67 REMARK 500 2 ASN A 153 8.60 -163.95 REMARK 500 3 ILE A 139 112.24 26.15 REMARK 500 3 PHE A 141 126.37 -24.18 REMARK 500 3 ASN A 143 -21.09 -150.24 REMARK 500 3 ARG A 151 47.41 -92.31 REMARK 500 3 GLU A 152 40.80 -87.03 REMARK 500 3 ASN A 153 -41.98 -154.13 REMARK 500 4 ILE A 139 118.56 19.68 REMARK 500 4 PHE A 141 126.39 -27.12 REMARK 500 4 ASN A 143 -4.73 -147.81 REMARK 500 4 GLU A 152 38.41 -75.45 REMARK 500 4 ASN A 153 9.68 -152.20 REMARK 500 5 LEU A 138 34.21 -140.87 REMARK 500 5 ILE A 139 104.86 -13.58 REMARK 500 5 HIS A 140 58.59 -105.85 REMARK 500 5 PHE A 141 125.30 -36.51 REMARK 500 5 ASN A 143 -9.51 -143.56 REMARK 500 5 GLU A 152 33.91 -75.39 REMARK 500 5 ASN A 153 -4.66 -143.97 REMARK 500 6 ILE A 139 113.13 27.83 REMARK 500 6 PHE A 141 125.01 -32.87 REMARK 500 6 ASN A 143 -12.54 -148.85 REMARK 500 6 ARG A 151 54.68 -92.98 REMARK 500 6 GLU A 152 36.42 -79.46 REMARK 500 6 ASN A 153 41.21 -159.56 REMARK 500 7 ILE A 139 118.32 28.93 REMARK 500 7 PHE A 141 124.60 -30.87 REMARK 500 7 ASN A 143 -6.71 -142.83 REMARK 500 7 ARG A 151 53.37 -94.78 REMARK 500 7 GLU A 152 37.75 -83.32 REMARK 500 7 ASN A 153 34.18 -150.02 REMARK 500 8 ILE A 139 111.61 21.54 REMARK 500 8 PHE A 141 125.92 -33.13 REMARK 500 8 GLU A 152 33.55 -78.00 REMARK 500 8 ASN A 153 26.21 -175.70 REMARK 500 REMARK 500 THIS ENTRY HAS 133 RAMACHANDRAN OUTLIERS. 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 LEU A 138 ILE A 139 1 -111.01 REMARK 500 LEU A 138 ILE A 139 2 -127.21 REMARK 500 PHE A 141 GLY A 142 2 -37.18 REMARK 500 LEU A 138 ILE A 139 3 -123.69 REMARK 500 PHE A 141 GLY A 142 3 -32.52 REMARK 500 LEU A 138 ILE A 139 4 -111.68 REMARK 500 PHE A 141 GLY A 142 4 -30.93 REMARK 500 LEU A 138 ILE A 139 5 -117.95 REMARK 500 PHE A 141 GLY A 142 5 -31.51 REMARK 500 LEU A 138 ILE A 139 6 -119.58 REMARK 500 PHE A 141 GLY A 142 6 -38.83 REMARK 500 LEU A 138 ILE A 139 7 -122.00 REMARK 500 PHE A 141 GLY A 142 7 -34.66 REMARK 500 LEU A 138 ILE A 139 8 -118.24 REMARK 500 PHE A 141 GLY A 142 8 -35.12 REMARK 500 LEU A 138 ILE A 139 9 -126.34 REMARK 500 PHE A 141 GLY A 142 9 -31.88 REMARK 500 LEU A 138 ILE A 139 10 -119.98 REMARK 500 PHE A 141 GLY A 142 10 -33.52 REMARK 500 LEU A 138 ILE A 139 11 -133.85 REMARK 500 PHE A 141 GLY A 142 11 -33.30 REMARK 500 LEU A 138 ILE A 139 12 -108.43 REMARK 500 LEU A 138 ILE A 139 13 -127.84 REMARK 500 PHE A 141 GLY A 142 13 -36.78 REMARK 500 LEU A 138 ILE A 139 14 -100.33 REMARK 500 ASN A 143 ASP A 144 14 144.21 REMARK 500 LEU A 138 ILE A 139 15 -124.88 REMARK 500 LEU A 138 ILE A 139 16 -128.24 REMARK 500 PHE A 141 GLY A 142 16 -37.59 REMARK 500 LEU A 138 ILE A 139 17 -117.98 REMARK 500 PHE A 141 GLY A 142 17 -38.74 REMARK 500 LEU A 138 ILE A 139 18 -130.03 REMARK 500 PHE A 141 GLY A 142 18 -34.26 REMARK 500 LEU A 138 ILE A 139 19 -103.44 REMARK 500 LEU A 138 ILE A 139 20 -128.29 REMARK 500 PHE A 141 GLY A 142 20 -35.11 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 ARG A 136 0.08 SIDE CHAIN REMARK 500 7 ARG A 136 0.08 SIDE CHAIN REMARK 500 8 ARG A 151 0.08 SIDE CHAIN REMARK 500 9 ARG A 148 0.09 SIDE CHAIN REMARK 500 19 ARG A 151 0.13 SIDE CHAIN REMARK 500 20 ARG A 148 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 10041 RELATED DB: BMRB REMARK 900 PROTON CHEMICAL SHIFT ASSIGNMENTS OF THE PEPTIDE REMARK 900 RELATED ID: 1G04 RELATED DB: PDB REMARK 900 NMR STRUCTURE (IN 10 MM PHOSPHATE BUFFER, PH 6.5) OF A SHEEP PRION- REMARK 900 DERIVED PEPTIDE WHERE THE HELIX H1 REGION IS IN AN EXTENDED REMARK 900 CONFORMATION. REMARK 900 RELATED ID: 1M25 RELATED DB: PDB REMARK 900 NMR STRUCTURE (IN 90 % TFE) OF A SHEEP PRION-DERIVED PEPTIDE WHERE REMARK 900 THE HELIX H1 REGION ADOPTS NATIVE-LIKE HELICAL CONFORMATION. DBREF 1S4T A 135 155 UNP P23907 PRIO_SHEEP 138 158 SEQRES 1 A 21 SER ARG PRO LEU ILE HIS PHE GLY ASN ASP TYR GLU ASP SEQRES 2 A 21 ARG TYR TYR ARG GLU ASN MET TYR HELIX 1 1 TYR A 145 TYR A 150 5 6 CISPEP 1 PHE A 141 GLY A 142 1 -28.63 CISPEP 2 PHE A 141 GLY A 142 12 -26.77 CISPEP 3 PHE A 141 GLY A 142 14 -20.29 CISPEP 4 PHE A 141 GLY A 142 15 -29.63 CISPEP 5 PHE A 141 GLY A 142 19 -28.53 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