HEADER MEMBRANE PROTEIN 31-DEC-05 2FJ3 TITLE NMR SOLUTION OF RABBIT PRION PROTEIN (91-228) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 91-228; COMPND 5 SYNONYM: PROTEIN(PRION PROTEIN), PRP, PRP27-30, PRP33-35C; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: THE REGION OF RESIDUES 91-123 IS LOOP AND THE COMPND 8 STRUCTURE DOMAIN IS RESIDUES 124-228. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30(+)A KEYWDS PRION PROTEIN, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR J.LI,D.H.LIN REVDAT 4 13-OCT-10 2FJ3 1 JRNL REVDAT 3 01-SEP-10 2FJ3 1 COMPND JRNL REMARK REVDAT 2 24-FEB-09 2FJ3 1 VERSN REVDAT 1 31-DEC-06 2FJ3 0 JRNL AUTH Y.WEN,J.LI,W.YAO,M.XIONG,J.HONG,Y.PENG,G.XIAO,D.H.LIN JRNL TITL UNIQUE STRUCTURAL CHARACTERISTICS OF THE RABBIT PRION JRNL TITL 2 PROTEIN JRNL REF J.BIOL.CHEM. V. 285 31682 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20639199 JRNL DOI 10.1074/JBC.M110.118844 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2 REMARK 3 AUTHORS : NIGLES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FJ3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JAN-06. REMARK 100 THE RCSB ID CODE IS RCSB035935. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1ATM REMARK 210 SAMPLE CONTENTS : 1MM PRP U-15N,13C; 20MM ACETATE REMARK 210 BUFFER (PH 4.5); 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCA-J; 3D_13C-SEPARATED_NOESY; REMARK 210 3D_15N-SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, ARIA 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERG REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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 1-15 REMARK 465 RES C SSSEQI REMARK 465 GLN A 91 REMARK 465 GLY A 92 REMARK 465 GLY A 93 REMARK 465 THR A 94 REMARK 465 HIS A 95 REMARK 465 ASN A 96 REMARK 465 GLN A 97 REMARK 465 TRP A 98 REMARK 465 GLY A 99 REMARK 465 LYS A 100 REMARK 465 PRO A 101 REMARK 465 SER A 102 REMARK 465 LYS A 103 REMARK 465 PRO A 104 REMARK 465 LYS A 105 REMARK 465 THR A 106 REMARK 465 SER A 107 REMARK 465 MET A 108 REMARK 465 LYS A 109 REMARK 465 HIS A 110 REMARK 465 VAL A 111 REMARK 465 ALA A 112 REMARK 465 GLY A 113 REMARK 465 ALA A 114 REMARK 465 ALA A 115 REMARK 465 ALA A 116 REMARK 465 ALA A 117 REMARK 465 GLY A 118 REMARK 465 ALA A 119 REMARK 465 VAL A 120 REMARK 465 VAL A 121 REMARK 465 GLY A 122 REMARK 465 GLY A 123 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-15 REMARK 470 RES CSSEQI ATOMS REMARK 470 ALA A 228 O 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 HE2 MET A 133 HG2 MET A 212 1.13 REMARK 500 HG13 ILE A 138 HG23 VAL A 208 1.25 REMARK 500 HA ASP A 201 HD11 ILE A 204 1.27 REMARK 500 HG11 VAL A 175 HG13 ILE A 214 1.29 REMARK 500 HG12 VAL A 175 HB3 CYS A 213 1.30 REMARK 500 HA VAL A 160 HG1 THR A 182 1.37 REMARK 500 HZ PHE A 140 HD3 ARG A 207 1.39 REMARK 500 HA TYR A 149 HD21 ASN A 152 1.40 REMARK 500 HB3 TYR A 162 HB2 CYS A 178 1.41 REMARK 500 HB2 ASN A 152 HD2 TYR A 156 1.50 REMARK 500 HG23 VAL A 175 HA ILE A 214 1.51 REMARK 500 HH11 ARG A 135 HD1 TYR A 149 1.56 REMARK 500 HA HIS A 186 HB THR A 190 1.57 REMARK 500 HA ARG A 147 HG2 ARG A 150 1.58 REMARK 500 HD2 TYR A 161 HA THR A 182 1.58 REMARK 500 HA ASN A 180 HE3 LYS A 184 1.58 REMARK 500 H GLY A 130 O VAL A 160 1.60 REMARK 500 REMARK 500 REMARK: NULL 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 3 TYR A 148 CE1 TYR A 148 CZ 0.129 REMARK 500 3 TYR A 148 CZ TYR A 148 CE2 -0.137 REMARK 500 4 TYR A 162 CE1 TYR A 162 CZ -0.080 REMARK 500 5 TYR A 148 CE1 TYR A 148 CZ 0.126 REMARK 500 5 TYR A 148 CZ TYR A 148 CE2 -0.114 REMARK 500 6 TYR A 148 CE1 TYR A 148 CZ 0.113 REMARK 500 6 TYR A 148 CZ TYR A 148 CE2 -0.123 REMARK 500 7 PHE A 197 CE1 PHE A 197 CZ 0.118 REMARK 500 10 TYR A 162 CE1 TYR A 162 CZ 0.086 REMARK 500 12 TYR A 162 CZ TYR A 162 CE2 -0.081 REMARK 500 14 TYR A 148 CE1 TYR A 148 CZ 0.134 REMARK 500 14 TYR A 148 CZ TYR A 148 CE2 -0.085 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 TYR A 127 -177.47 55.70 REMARK 500 1 SER A 131 -166.40 59.37 REMARK 500 1 SER A 134 18.01 59.88 REMARK 500 1 ARG A 135 115.88 72.26 REMARK 500 1 LEU A 137 107.73 60.78 REMARK 500 1 HIS A 139 112.22 38.23 REMARK 500 1 ASP A 143 -61.59 -98.13 REMARK 500 1 TYR A 154 -60.17 -108.08 REMARK 500 1 ASP A 166 50.95 -176.96 REMARK 500 1 GLN A 167 19.28 -147.88 REMARK 500 1 GLN A 171 -63.75 -93.92 REMARK 500 1 THR A 189 -46.11 -159.68 REMARK 500 1 GLU A 199 -35.11 -39.60 REMARK 500 2 TYR A 127 178.10 64.09 REMARK 500 2 SER A 131 -160.83 58.33 REMARK 500 2 ALA A 132 75.05 -151.35 REMARK 500 2 ARG A 135 123.13 74.25 REMARK 500 2 LEU A 137 88.35 64.56 REMARK 500 2 HIS A 139 -74.73 33.71 REMARK 500 2 PHE A 140 -34.92 78.55 REMARK 500 2 ASP A 143 -68.59 -98.58 REMARK 500 2 ASP A 166 -37.59 -176.30 REMARK 500 2 SER A 169 -66.39 73.75 REMARK 500 2 LYS A 184 -68.91 -95.69 REMARK 500 2 HIS A 186 -70.35 -89.44 REMARK 500 2 THR A 187 30.41 -55.03 REMARK 500 2 THR A 189 -46.00 -174.68 REMARK 500 2 THR A 192 31.76 -91.08 REMARK 500 3 TYR A 127 169.21 59.83 REMARK 500 3 SER A 131 114.77 66.14 REMARK 500 3 SER A 134 43.67 -89.99 REMARK 500 3 ARG A 135 129.31 73.06 REMARK 500 3 LEU A 137 77.10 54.30 REMARK 500 3 HIS A 139 176.79 38.83 REMARK 500 3 PHE A 140 -10.60 -143.25 REMARK 500 3 ASP A 143 -67.96 -98.81 REMARK 500 3 ASP A 166 -20.41 166.45 REMARK 500 3 HIS A 176 -37.25 -34.57 REMARK 500 3 THR A 189 -46.95 -156.53 REMARK 500 4 SER A 131 118.79 67.21 REMARK 500 4 ARG A 135 126.73 78.86 REMARK 500 4 PRO A 136 46.61 -97.87 REMARK 500 4 LEU A 137 79.31 34.34 REMARK 500 4 HIS A 139 -78.19 49.06 REMARK 500 4 PHE A 140 -25.76 72.58 REMARK 500 4 ASP A 143 -61.17 -100.40 REMARK 500 4 ASN A 152 0.30 -61.00 REMARK 500 4 ASN A 158 56.09 -111.10 REMARK 500 4 ASP A 166 -48.82 -174.65 REMARK 500 4 SER A 169 -66.59 71.64 REMARK 500 REMARK 500 THIS ENTRY HAS 190 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 TYR A 156 PRO A 157 7 -149.09 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 3 TYR A 217 0.06 SIDE CHAIN REMARK 500 5 TYR A 148 0.08 SIDE CHAIN REMARK 500 6 TYR A 149 0.06 SIDE CHAIN REMARK 500 7 TYR A 161 0.06 SIDE CHAIN REMARK 500 8 TYR A 156 0.08 SIDE CHAIN REMARK 500 9 TYR A 156 0.06 SIDE CHAIN REMARK 500 10 TYR A 156 0.06 SIDE CHAIN REMARK 500 10 TYR A 162 0.12 SIDE CHAIN REMARK 500 14 TYR A 148 0.11 SIDE CHAIN REMARK 500 15 TYR A 156 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7142 RELATED DB: BMRB DBREF 2FJ3 A 91 228 UNP Q95211 PRIO_RABIT 91 228 SEQRES 1 A 138 GLN GLY GLY THR HIS ASN GLN TRP GLY LYS PRO SER LYS SEQRES 2 A 138 PRO LYS THR SER MET LYS HIS VAL ALA GLY ALA ALA ALA SEQRES 3 A 138 ALA GLY ALA VAL VAL GLY GLY LEU GLY GLY TYR MET LEU SEQRES 4 A 138 GLY SER ALA MET SER ARG PRO LEU ILE HIS PHE GLY ASN SEQRES 5 A 138 ASP TYR GLU ASP ARG TYR TYR ARG GLU ASN MET TYR ARG SEQRES 6 A 138 TYR PRO ASN GLN VAL TYR TYR ARG PRO VAL ASP GLN TYR SEQRES 7 A 138 SER ASN GLN ASN SER PHE VAL HIS ASP CYS VAL ASN ILE SEQRES 8 A 138 THR VAL LYS GLN HIS THR VAL THR THR THR THR LYS GLY SEQRES 9 A 138 GLU ASN PHE THR GLU THR ASP ILE LYS ILE MET GLU ARG SEQRES 10 A 138 VAL VAL GLU GLN MET CYS ILE THR GLN TYR GLN GLN GLU SEQRES 11 A 138 SER GLN ALA ALA TYR GLN ARG ALA HELIX 1 1 ASP A 143 ASN A 152 1 10 HELIX 2 2 ASN A 170 VAL A 188 1 19 HELIX 3 3 THR A 198 ARG A 227 1 30 SHEET 1 A 2 MET A 128 GLY A 130 0 SHEET 2 A 2 VAL A 160 TYR A 162 -1 O VAL A 160 N GLY A 130 SSBOND 1 CYS A 178 CYS A 213 1555 1555 2.03 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