HEADER MEMBRANE PROTEIN 25-OCT-04 1XU0 TITLE SOLUTION STRUCTURE OF XENOPUS LEAVIS PRION PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GLOBULAR DOMAIN(RESIDUES 98-226); COMPND 5 SYNONYM: XLPRP; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 GENE: PRNP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSET KEYWDS PRION, AMPHIBIAN, POLYMORPHISM, GLYCOPROTEIN, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.R.PEREZ,K.WUTHRICH REVDAT 5 02-MAR-22 1XU0 1 REMARK SEQADV REVDAT 4 24-FEB-09 1XU0 1 VERSN REVDAT 3 25-JAN-05 1XU0 1 JRNL REVDAT 2 11-JAN-05 1XU0 1 JRNL AUTHOR REVDAT 1 04-JAN-05 1XU0 0 JRNL AUTH L.CALZOLAI,D.A.LYSEK,D.R.PEREZ,P.GUNTERT,K.WUTHRICH JRNL TITL PRION PROTEIN NMR STRUCTURES OF CHICKEN, TURTLE, AND FROG JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 651 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15647366 JRNL DOI 10.1073/PNAS.0408939102 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 6.01, OPALP REMARK 3 AUTHORS : GUNTERT, P., MUMENTHALER, C. & WUTHRICH, K. REMARK 3 (DYANA), R.KORADI,M.BILLITER,P.GUNTERT (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 2283 NOE-DERIVED DISTANCE RESTRAINTS. REMARK 4 REMARK 4 1XU0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030768. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.15 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 10MM SODIUM ACETAT REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : U-15N, U-13C; 95% H2O, 5% D2O; U REMARK 210 -15N, U-13C; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY ALIPHATIC REMARK 210 REGION; 3D_13C-SEPARATED_NOESY REMARK 210 AROMATIC REGION REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CANDID REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 97 REMARK 465 SER A 98 REMARK 465 GLY A 99 REMARK 465 TYR A 100 REMARK 465 ASN A 101 REMARK 465 LYS A 102 REMARK 465 GLN A 103 REMARK 465 TRP A 104 REMARK 465 LYS A 105 REMARK 465 PRO A 106 REMARK 465 PRO A 107 REMARK 465 LYS A 108 REMARK 465 SER A 109 REMARK 465 LYS A 110 REMARK 465 THR A 111 REMARK 465 ASN A 112 REMARK 465 MET A 113 REMARK 465 LYS A 114 REMARK 465 SER A 115 REMARK 465 VAL A 116 REMARK 465 ALA A 117 REMARK 465 ILE A 118 REMARK 465 GLY A 119 REMARK 465 ALA A 120 REMARK 465 ALA A 121 REMARK 465 ALA A 122 REMARK 465 GLY A 123 REMARK 465 ALA A 124 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 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 TYR A 153 CB - CG - CD1 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 TYR A 162 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 4 TYR A 139 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 6 TYR A 139 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 6 VAL A 209 CA - CB - CG2 ANGL. DEV. = 10.3 DEGREES REMARK 500 10 ARG A 163 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 11 CYS A 218 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 12 VAL A 209 CA - CB - CG1 ANGL. DEV. = 11.5 DEGREES REMARK 500 12 ARG A 224 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 14 TYR A 162 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 16 ARG A 167 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 167 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 18 VAL A 161 CA - CB - CG2 ANGL. DEV. = 9.3 DEGREES REMARK 500 19 ASP A 175 CB - CG - OD1 ANGL. DEV. = 5.4 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 1 VAL A 134 -81.02 -122.54 REMARK 500 1 ARG A 136 16.70 52.45 REMARK 500 1 MET A 137 -74.95 20.30 REMARK 500 1 TYR A 139 173.51 -50.79 REMARK 500 1 PHE A 141 162.41 55.33 REMARK 500 1 GLU A 169 -72.48 -101.16 REMARK 500 1 GLU A 170 6.64 53.37 REMARK 500 1 TYR A 171 42.74 -144.32 REMARK 500 1 ILE A 190 -55.38 -130.11 REMARK 500 1 SER A 200 79.29 45.85 REMARK 500 1 GLU A 201 -14.20 71.80 REMARK 500 2 LEU A 130 154.34 65.24 REMARK 500 2 ARG A 136 -10.33 70.25 REMARK 500 2 MET A 137 -69.75 34.95 REMARK 500 2 TYR A 139 175.04 -55.88 REMARK 500 2 GLN A 140 91.44 -67.75 REMARK 500 2 TYR A 166 179.91 52.52 REMARK 500 2 GLU A 169 -78.40 -69.37 REMARK 500 2 GLU A 170 -109.64 -161.59 REMARK 500 2 TYR A 171 52.68 -149.29 REMARK 500 2 ILE A 190 -60.82 -133.45 REMARK 500 2 LYS A 197 68.26 32.35 REMARK 500 2 SER A 200 88.45 44.62 REMARK 500 2 GLU A 201 -42.12 81.96 REMARK 500 3 MET A 129 14.19 -144.63 REMARK 500 3 LEU A 130 168.45 56.91 REMARK 500 3 VAL A 134 -74.29 -108.27 REMARK 500 3 ARG A 136 75.63 -105.57 REMARK 500 3 SER A 138 59.32 28.49 REMARK 500 3 TYR A 139 179.60 -52.15 REMARK 500 3 TYR A 162 64.09 -112.33 REMARK 500 3 TYR A 171 -164.90 -65.31 REMARK 500 3 VAL A 172 172.03 60.41 REMARK 500 3 ILE A 190 -49.03 -136.45 REMARK 500 3 LYS A 197 112.43 53.07 REMARK 500 3 ASN A 198 82.82 -69.80 REMARK 500 3 ASN A 199 -71.97 -137.85 REMARK 500 3 SER A 200 94.83 46.94 REMARK 500 3 GLU A 201 -22.15 74.08 REMARK 500 4 TYR A 128 111.47 67.63 REMARK 500 4 LEU A 130 135.00 77.01 REMARK 500 4 VAL A 134 -66.61 -90.38 REMARK 500 4 ARG A 136 67.18 23.00 REMARK 500 4 PHE A 141 176.25 62.11 REMARK 500 4 ILE A 190 -56.11 -132.52 REMARK 500 4 GLU A 201 -33.77 121.43 REMARK 500 4 GLN A 212 -70.07 -58.99 REMARK 500 5 LEU A 130 137.72 69.71 REMARK 500 5 ASN A 132 176.92 50.37 REMARK 500 5 VAL A 134 -70.85 -129.83 REMARK 500 REMARK 500 THIS ENTRY HAS 208 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 ARG A 163 PRO A 164 8 148.12 REMARK 500 TYR A 139 GLN A 140 20 141.54 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 1 TYR A 139 0.07 SIDE CHAIN REMARK 500 1 ARG A 148 0.08 SIDE CHAIN REMARK 500 1 ARG A 160 0.07 SIDE CHAIN REMARK 500 3 ARG A 148 0.11 SIDE CHAIN REMARK 500 3 ARG A 215 0.08 SIDE CHAIN REMARK 500 3 ARG A 223 0.12 SIDE CHAIN REMARK 500 4 TYR A 139 0.13 SIDE CHAIN REMARK 500 4 TYR A 154 0.07 SIDE CHAIN REMARK 500 4 ARG A 163 0.09 SIDE CHAIN REMARK 500 4 ARG A 167 0.08 SIDE CHAIN REMARK 500 5 TYR A 139 0.06 SIDE CHAIN REMARK 500 5 ARG A 215 0.09 SIDE CHAIN REMARK 500 5 ARG A 223 0.08 SIDE CHAIN REMARK 500 6 TYR A 149 0.12 SIDE CHAIN REMARK 500 6 TYR A 171 0.09 SIDE CHAIN REMARK 500 7 TYR A 128 0.10 SIDE CHAIN REMARK 500 7 TYR A 150 0.09 SIDE CHAIN REMARK 500 7 TYR A 162 0.08 SIDE CHAIN REMARK 500 7 ARG A 215 0.08 SIDE CHAIN REMARK 500 8 TYR A 149 0.08 SIDE CHAIN REMARK 500 8 ARG A 167 0.07 SIDE CHAIN REMARK 500 8 TYR A 189 0.06 SIDE CHAIN REMARK 500 8 ARG A 215 0.09 SIDE CHAIN REMARK 500 9 ARG A 160 0.09 SIDE CHAIN REMARK 500 9 TYR A 162 0.07 SIDE CHAIN REMARK 500 9 ARG A 167 0.08 SIDE CHAIN REMARK 500 9 ARG A 223 0.08 SIDE CHAIN REMARK 500 10 ARG A 163 0.11 SIDE CHAIN REMARK 500 10 TYR A 189 0.07 SIDE CHAIN REMARK 500 11 TYR A 139 0.14 SIDE CHAIN REMARK 500 11 TYR A 222 0.09 SIDE CHAIN REMARK 500 12 TYR A 139 0.08 SIDE CHAIN REMARK 500 12 ARG A 163 0.10 SIDE CHAIN REMARK 500 12 TYR A 166 0.11 SIDE CHAIN REMARK 500 13 ARG A 136 0.09 SIDE CHAIN REMARK 500 13 ARG A 148 0.09 SIDE CHAIN REMARK 500 13 ARG A 160 0.10 SIDE CHAIN REMARK 500 13 TYR A 162 0.09 SIDE CHAIN REMARK 500 13 ARG A 176 0.08 SIDE CHAIN REMARK 500 14 TYR A 171 0.08 SIDE CHAIN REMARK 500 15 TYR A 139 0.08 SIDE CHAIN REMARK 500 15 TYR A 149 0.07 SIDE CHAIN REMARK 500 15 TYR A 153 0.10 SIDE CHAIN REMARK 500 15 TYR A 162 0.07 SIDE CHAIN REMARK 500 15 TYR A 222 0.12 SIDE CHAIN REMARK 500 16 TYR A 139 0.09 SIDE CHAIN REMARK 500 16 TYR A 149 0.09 SIDE CHAIN REMARK 500 16 ARG A 176 0.11 SIDE CHAIN REMARK 500 16 TYR A 189 0.09 SIDE CHAIN REMARK 500 16 ARG A 224 0.10 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 61 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U3M RELATED DB: PDB REMARK 900 PRION PROTEIN FROM CHICKEN REMARK 900 RELATED ID: 1U5L RELATED DB: PDB REMARK 900 PRION PROTEIN FROM TURTLE DBREF 1XU0 A 98 226 UNP Q5S1W7 Q5S1W7_XENLA 43 171 SEQADV 1XU0 GLY A 97 UNP Q5S1W7 CLONING ARTIFACT SEQRES 1 A 130 GLY SER GLY TYR ASN LYS GLN TRP LYS PRO PRO LYS SER SEQRES 2 A 130 LYS THR ASN MET LYS SER VAL ALA ILE GLY ALA ALA ALA SEQRES 3 A 130 GLY ALA ILE GLY GLY TYR MET LEU GLY ASN ALA VAL GLY SEQRES 4 A 130 ARG MET SER TYR GLN PHE ASN ASN PRO MET GLU SER ARG SEQRES 5 A 130 TYR TYR ASN ASP TYR TYR ASN GLN MET PRO ASN ARG VAL SEQRES 6 A 130 TYR ARG PRO MET TYR ARG GLY GLU GLU TYR VAL SER GLU SEQRES 7 A 130 ASP ARG PHE VAL ARG ASP CYS TYR ASN MET SER VAL THR SEQRES 8 A 130 GLU TYR ILE ILE LYS PRO ALA GLU GLY LYS ASN ASN SER SEQRES 9 A 130 GLU LEU ASN GLN LEU ASP THR THR VAL LYS SER GLN ILE SEQRES 10 A 130 ILE ARG GLU MET CYS ILE THR GLU TYR ARG ARG GLY SER HELIX 1 1 ASN A 143 TYR A 153 1 11 HELIX 2 2 TYR A 154 GLN A 156 5 3 HELIX 3 3 SER A 173 TYR A 189 1 17 HELIX 4 4 ILE A 190 GLY A 196 5 7 HELIX 5 5 LEU A 202 GLY A 225 1 24 SHEET 1 A 2 GLY A 127 ALA A 133 0 SHEET 2 A 2 ARG A 160 MET A 165 -1 O ARG A 163 N MET A 129 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