HEADER PRION PROTEIN 20-SEP-99 1QM3 TITLE HUMAN PRION PROTEIN FRAGMENT 121-230 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 121-230; COMPND 5 SYNONYM: PRP, MAJOR PRION PROTEIN, PRP27-30, PRP33-35C, COMPND 6 (ASCR).PRP; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: BRAIN; SOURCE 6 CELLULAR_LOCATION: EXTRACELLULAR; SOURCE 7 GENE: PRNP; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PRSET A KEYWDS PRION PROTEIN, PRION, BRAIN, GLYCOPROTEIN, GPI-ANCHOR, KEYWDS 2 REPEAT, POLYMORPHISM, DISEASE MUTATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.ZAHN,A.LIU,T.LUHRS,K.WUTHRICH REVDAT 3 24-FEB-09 1QM3 1 VERSN REVDAT 2 28-FEB-02 1QM3 1 JRNL REMARK REVDAT 1 16-DEC-99 1QM3 0 JRNL AUTH R.ZAHN,A.LIU,T.LUHRS,R.RIEK,C.VON SCHROETTER, JRNL AUTH 2 F.L.GARCIA,M.BILLETER,L.CALZOLAI,G.WIDER,K.WUTHRICH JRNL TITL NMR SOLUTION STRUCTURE OF THE HUMAN PRION PROTEIN JRNL REF PROC.NATL.ACAD.SCI.USA V. 97 145 2000 JRNL REFN ISSN 0027-8424 JRNL PMID 10618385 JRNL DOI 10.1073/PNAS.97.1.145 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPALP REMARK 3 AUTHORS : KORADI, BILLETER, GUNTERT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QM3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-SEP-99. REMARK 100 THE PDBE ID CODE IS EBI-4132. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 0.01 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 90% WATER / 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 REMARK 210 SPECTROMETER MODEL : DRX750 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA 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 : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 12 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE REMARK 210 SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 119 REMARK 465 SER A 120 REMARK 465 VAL A 121 REMARK 465 VAL A 122 REMARK 465 GLY A 123 REMARK 465 GLY A 124 REMARK 465 GLY A 229 REMARK 465 SER A 230 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 3 VAL A 210 CG1 - CB - CG2 ANGL. DEV. = -10.1 DEGREES REMARK 500 4 VAL A 210 CG1 - CB - CG2 ANGL. DEV. = -11.3 DEGREES REMARK 500 5 ARG A 148 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 11 TYR A 150 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 16 ARG A 156 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 17 ARG A 220 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 CYS A 179 CA - CB - SG ANGL. DEV. = 12.5 DEGREES REMARK 500 18 CYS A 179 CA - CB - SG ANGL. DEV. = 12.7 DEGREES REMARK 500 18 CYS A 214 CA - CB - SG ANGL. DEV. = -8.3 DEGREES REMARK 500 20 CYS A 179 CA - CB - SG ANGL. DEV. = 13.4 DEGREES REMARK 500 20 CYS A 179 CA - CB - SG ANGL. DEV. = 13.6 DEGREES REMARK 500 20 ARG A 208 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 208 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 20 VAL A 210 CG1 - CB - CG2 ANGL. DEV. = -9.7 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 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 ARG A 136 104.84 -43.64 REMARK 500 1 MET A 166 -9.21 59.61 REMARK 500 1 ASP A 167 -160.05 51.74 REMARK 500 2 MET A 166 45.10 -87.05 REMARK 500 2 GLU A 168 11.18 -149.20 REMARK 500 2 SER A 170 90.80 170.50 REMARK 500 2 GLN A 172 -92.81 -90.38 REMARK 500 2 VAL A 189 -75.35 -73.24 REMARK 500 3 SER A 132 179.15 -54.74 REMARK 500 3 MET A 166 35.34 -69.93 REMARK 500 3 GLN A 172 -86.69 -92.29 REMARK 500 3 GLU A 196 107.22 51.21 REMARK 500 3 ALA A 224 2.94 -69.77 REMARK 500 4 ARG A 156 -95.72 -112.84 REMARK 500 4 TYR A 157 175.70 47.95 REMARK 500 4 TYR A 163 -166.81 -163.43 REMARK 500 4 PRO A 165 -178.27 -62.27 REMARK 500 4 MET A 166 41.09 -73.91 REMARK 500 4 GLU A 168 2.57 -167.29 REMARK 500 4 GLN A 172 -96.16 -100.57 REMARK 500 4 GLU A 196 101.93 34.54 REMARK 500 5 ARG A 136 78.50 39.47 REMARK 500 5 HIS A 140 109.87 -57.24 REMARK 500 5 ASP A 167 -65.83 -144.57 REMARK 500 5 SER A 170 93.51 -160.72 REMARK 500 5 GLN A 172 -71.61 -73.77 REMARK 500 5 HIS A 187 23.20 -76.35 REMARK 500 5 GLN A 227 15.96 -146.26 REMARK 500 6 SER A 132 172.98 -58.92 REMARK 500 6 MET A 166 43.54 -70.72 REMARK 500 6 GLU A 168 1.38 -155.34 REMARK 500 6 TYR A 169 -77.93 -83.66 REMARK 500 6 GLN A 227 11.36 -149.57 REMARK 500 7 MET A 166 -82.43 -35.38 REMARK 500 7 ASP A 167 -93.61 63.92 REMARK 500 7 GLU A 168 44.39 -149.68 REMARK 500 7 ASN A 171 -158.41 177.32 REMARK 500 7 GLN A 172 -101.03 -72.25 REMARK 500 7 GLN A 227 17.24 -143.12 REMARK 500 8 ARG A 136 84.00 36.06 REMARK 500 8 MET A 166 32.79 -71.49 REMARK 500 8 GLU A 168 -33.58 177.30 REMARK 500 8 GLN A 172 -99.34 -91.34 REMARK 500 9 MET A 166 87.54 -65.03 REMARK 500 9 ASP A 167 -68.44 -134.14 REMARK 500 9 GLU A 168 -158.17 -85.48 REMARK 500 9 ASN A 171 174.81 63.93 REMARK 500 9 GLN A 172 -86.28 -87.52 REMARK 500 9 VAL A 189 -75.31 -78.53 REMARK 500 9 ASN A 197 97.85 -67.34 REMARK 500 9 GLN A 227 17.28 -140.04 REMARK 500 10 SER A 132 -165.76 -72.43 REMARK 500 10 ARG A 136 107.52 -43.32 REMARK 500 10 GLN A 172 -101.17 -87.29 REMARK 500 10 VAL A 189 -71.87 -68.05 REMARK 500 10 GLN A 227 24.99 -141.72 REMARK 500 11 SER A 132 -171.16 -64.49 REMARK 500 11 ARG A 136 104.22 -43.81 REMARK 500 11 ASP A 167 -97.65 34.23 REMARK 500 11 GLN A 172 -89.34 -119.38 REMARK 500 11 GLU A 196 128.85 53.74 REMARK 500 11 GLN A 227 28.66 -141.94 REMARK 500 12 MET A 166 55.84 -62.28 REMARK 500 12 GLU A 168 -51.04 -147.51 REMARK 500 12 TYR A 169 24.57 -78.12 REMARK 500 12 GLN A 172 -95.00 -98.54 REMARK 500 13 TYR A 169 62.08 34.22 REMARK 500 13 GLN A 172 -99.82 -77.46 REMARK 500 13 ASN A 197 96.96 -64.31 REMARK 500 13 GLN A 227 35.43 -148.34 REMARK 500 14 SER A 132 -169.74 -71.57 REMARK 500 14 GLU A 168 -54.09 -141.41 REMARK 500 14 SER A 170 48.77 -146.49 REMARK 500 14 GLN A 172 -87.71 -79.35 REMARK 500 14 VAL A 189 -71.76 -70.74 REMARK 500 15 ARG A 136 105.20 -45.48 REMARK 500 15 GLU A 168 -50.00 74.40 REMARK 500 15 GLN A 172 -82.69 -85.65 REMARK 500 15 GLN A 227 21.82 -145.53 REMARK 500 16 MET A 166 -18.70 -49.32 REMARK 500 16 GLU A 168 177.00 54.89 REMARK 500 16 TYR A 169 -71.04 65.53 REMARK 500 16 GLN A 172 -72.54 -116.55 REMARK 500 16 ASN A 197 103.58 -56.24 REMARK 500 17 TYR A 128 -179.58 -65.38 REMARK 500 17 PRO A 165 -178.00 -64.41 REMARK 500 17 MET A 166 -81.72 -40.72 REMARK 500 17 ASP A 167 -81.24 56.18 REMARK 500 17 GLU A 168 51.61 -156.38 REMARK 500 17 GLN A 172 -81.40 -63.58 REMARK 500 17 ASN A 174 2.11 -68.87 REMARK 500 18 SER A 132 174.46 -59.50 REMARK 500 18 GLU A 168 -155.46 50.75 REMARK 500 18 SER A 170 -80.46 -81.77 REMARK 500 18 ASN A 171 -158.45 50.71 REMARK 500 18 ASP A 178 -64.68 -91.99 REMARK 500 18 GLN A 186 3.07 -68.15 REMARK 500 18 GLN A 227 29.95 -145.86 REMARK 500 19 GLN A 172 -102.73 -105.33 REMARK 500 19 ASP A 178 -60.70 -100.32 REMARK 500 19 GLN A 227 24.11 -147.33 REMARK 500 20 MET A 166 35.07 -81.34 REMARK 500 20 GLU A 168 -63.19 -152.44 REMARK 500 20 GLN A 172 -99.90 -87.14 REMARK 500 20 HIS A 187 11.58 -67.52 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 ASN A 153 MET A 154 10 -136.29 REMARK 500 LEU A 125 GLY A 126 16 -142.41 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 151 0.09 SIDE CHAIN REMARK 500 2 TYR A 162 0.08 SIDE CHAIN REMARK 500 3 ARG A 156 0.08 SIDE CHAIN REMARK 500 3 TYR A 157 0.10 SIDE CHAIN REMARK 500 3 ARG A 228 0.09 SIDE CHAIN REMARK 500 6 ARG A 151 0.08 SIDE CHAIN REMARK 500 6 ARG A 156 0.11 SIDE CHAIN REMARK 500 6 TYR A 225 0.09 SIDE CHAIN REMARK 500 8 TYR A 169 0.08 SIDE CHAIN REMARK 500 9 ARG A 156 0.08 SIDE CHAIN REMARK 500 9 ARG A 208 0.11 SIDE CHAIN REMARK 500 10 TYR A 163 0.08 SIDE CHAIN REMARK 500 10 TYR A 226 0.10 SIDE CHAIN REMARK 500 11 TYR A 163 0.07 SIDE CHAIN REMARK 500 11 TYR A 218 0.10 SIDE CHAIN REMARK 500 12 ARG A 148 0.08 SIDE CHAIN REMARK 500 12 ARG A 151 0.14 SIDE CHAIN REMARK 500 12 ARG A 228 0.09 SIDE CHAIN REMARK 500 13 TYR A 128 0.08 SIDE CHAIN REMARK 500 13 ARG A 148 0.10 SIDE CHAIN REMARK 500 13 TYR A 163 0.09 SIDE CHAIN REMARK 500 13 ARG A 208 0.10 SIDE CHAIN REMARK 500 14 ARG A 148 0.10 SIDE CHAIN REMARK 500 14 TYR A 157 0.07 SIDE CHAIN REMARK 500 15 TYR A 157 0.09 SIDE CHAIN REMARK 500 15 ARG A 208 0.08 SIDE CHAIN REMARK 500 16 TYR A 157 0.07 SIDE CHAIN REMARK 500 17 ARG A 156 0.14 SIDE CHAIN REMARK 500 18 ARG A 151 0.10 SIDE CHAIN REMARK 500 18 TYR A 226 0.07 SIDE CHAIN REMARK 500 19 ARG A 136 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AG2 RELATED DB: PDB REMARK 900 PRION PROTEIN DOMAIN PRP(121-231) FROM MOUSE, NMR, REMARK 900 MINIMIZED AVERAGE STRUCTURE REMARK 900 RELATED ID: 1QLZ RELATED DB: PDB REMARK 900 HUMAN PRION PROTEIN NMR, 20 STRUCTURES, RESIDUES 23-230 REMARK 900 RELATED ID: 1QLX RELATED DB: PDB REMARK 900 HUMAN PRION PROTEIN, NMR, REPRESENTATIVE STRUCTURE REMARK 900 RESIDUES 23-230 REMARK 900 RELATED ID: 1QM0 RELATED DB: PDB REMARK 900 HUMAN PRION PROTEIN FRAGMENT 90-230, NMR, REPRESENTATIVE REMARK 900 STRUCTURE REMARK 900 RELATED ID: 1QM1 RELATED DB: PDB REMARK 900 HUMAN PRION PROTEIN FRAGMENT 90-230, NMR, 20 STRUCTURES REMARK 900 RELATED ID: 1QM2 RELATED DB: PDB REMARK 900 HUMAN PRION PROTEIN FRAGMENT 121-230, NMR, REPRESENTATIVE REMARK 900 STRUCTURE REMARK 999 REMARK 999 SEQUENCE REMARK 999 2 RESIDUES (GLY SER) INSERTED AT THE N-TERMINUS DBREF 1QM3 A 121 230 UNP P04156 PRIO_HUMAN 121 230 SEQADV 1QM3 GLY A 119 UNP P04156 CLONING ARTIFACT SEQADV 1QM3 SER A 120 UNP P04156 CLONING ARTIFACT SEQRES 1 A 112 GLY SER VAL VAL GLY GLY LEU GLY GLY TYR MET LEU GLY SEQRES 2 A 112 SER ALA MET SER ARG PRO ILE ILE HIS PHE GLY SER ASP SEQRES 3 A 112 TYR GLU ASP ARG TYR TYR ARG GLU ASN MET HIS ARG TYR SEQRES 4 A 112 PRO ASN GLN VAL TYR TYR ARG PRO MET ASP GLU TYR SER SEQRES 5 A 112 ASN GLN ASN ASN PHE VAL HIS ASP CYS VAL ASN ILE THR SEQRES 6 A 112 ILE LYS GLN HIS THR VAL THR THR THR THR LYS GLY GLU SEQRES 7 A 112 ASN PHE THR GLU THR ASP VAL LYS MET MET GLU ARG VAL SEQRES 8 A 112 VAL GLU GLN MET CYS ILE THR GLN TYR GLU ARG GLU SER SEQRES 9 A 112 GLN ALA TYR TYR GLN ARG GLY SER HELIX 1 H1 ASP A 144 MET A 154 1 11 HELIX 2 H2 ASN A 173 LYS A 194 1 22 HELIX 3 H3 GLU A 200 ARG A 228 1 29 SHEET 1 S1 2 TYR A 128 GLY A 131 0 SHEET 2 S1 2 VAL A 161 ARG A 164 -1 N TYR A 128 O VAL A 161 SSBOND 1 CYS A 179 CYS A 214 1555 1555 2.05 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