PDB Short entry for 2L40 HEADER MEMBRANE PROTEIN 28-SEP-10 2L40 TITLE MOUSE PRION PROTEIN (121-231) CONTAINING THE SUBSTITUTION Y169A COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 120-231; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PRNP, RP23-401J24.1-001; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PRSETA KEYWDS PRION, MUTATION, MEMBRANE PROTEIN, PRP EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.CHRISTEN,F.F.DAMBERGER,D.R.PEREZ,S.HORNEMANN,K.WUTHRICH REVDAT 4 14-JUN-23 2L40 1 REMARK REVDAT 3 26-FEB-20 2L40 1 REMARK SEQADV REVDAT 2 09-NOV-11 2L40 1 JRNL REVDAT 1 10-AUG-11 2L40 0 JRNL AUTH F.F.DAMBERGER,B.CHRISTEN,D.R.PEREZ,S.HORNEMANN,K.WUTHRICH JRNL TITL CELLULAR PRION PROTEIN CONFORMATION AND FUNCTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 17308 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21987789 JRNL DOI 10.1073/PNAS.1106325108 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, OPALP REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), LUGINBUHL, GUNTERT, REMARK 3 BILLETER AND WUTHRICH (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L40 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000101928. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.2 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 0.01 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.4 MM [U-99% 13C; U-99% 15N] REMARK 210 ENTITY-1, 10 MM [U-2H] SODIUM REMARK 210 ACETATE-2, 0.02 % SODIUM AZIDE-3, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 900 MHZ; 750 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, CARA, ATNOS/CANDID 1.2, REMARK 210 DYANA 1.0.3, MOLMOL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 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: TWO 13C-RESOLVED [1H,1H]-NOESY SPECTRA WERE OBTAINED WITH REMARK 210 THE 13C CARRIER AND SPECTRAL WIDTH OPTIMIZED FOR ALIPHATIC AND REMARK 210 AROMATIC 13C RESONANCES RESPECTIVELY. 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 HG1 THR A 199 OD1 ASP A 202 1.59 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 ARG A 151 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 CYS A 179 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 4 THR A 199 CA - CB - CG2 ANGL. DEV. = -8.8 DEGREES REMARK 500 7 TYR A 149 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 7 ARG A 208 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 10 TYR A 157 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 12 VAL A 176 CA - CB - CG2 ANGL. DEV. = 9.7 DEGREES REMARK 500 14 CYS A 179 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 16 ARG A 230 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 164 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 18 TYR A 157 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 18 VAL A 209 CA - CB - CG2 ANGL. DEV. = 15.7 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 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 SER A 132 170.42 -58.47 REMARK 500 1 MET A 134 -160.22 -103.70 REMARK 500 1 GLN A 168 -52.36 45.50 REMARK 500 1 ALA A 169 -79.53 -138.05 REMARK 500 1 SER A 170 24.80 45.76 REMARK 500 1 THR A 191 -42.55 -153.52 REMARK 500 1 ASN A 197 56.58 -169.08 REMARK 500 2 VAL A 121 16.33 57.52 REMARK 500 2 VAL A 122 -61.56 -24.01 REMARK 500 2 ALA A 169 -108.87 -125.38 REMARK 500 2 SER A 170 27.53 40.82 REMARK 500 2 GLN A 186 -90.22 -78.05 REMARK 500 2 THR A 191 -42.88 -150.89 REMARK 500 2 LYS A 194 33.93 -94.35 REMARK 500 2 ASN A 197 41.46 -172.71 REMARK 500 2 PHE A 198 123.43 -39.50 REMARK 500 2 SER A 231 38.44 -151.49 REMARK 500 3 ALA A 169 -98.72 -94.05 REMARK 500 3 SER A 170 25.51 40.41 REMARK 500 3 HIS A 187 -41.81 -136.11 REMARK 500 3 THR A 191 -39.76 -155.51 REMARK 500 3 ASN A 197 64.96 -170.01 REMARK 500 3 ASP A 227 3.09 -69.44 REMARK 500 4 VAL A 121 66.02 61.67 REMARK 500 4 SER A 170 21.28 -143.35 REMARK 500 4 HIS A 187 -35.06 -136.69 REMARK 500 4 THR A 191 -34.77 -150.60 REMARK 500 4 LYS A 194 59.11 -117.53 REMARK 500 4 ASN A 197 52.35 -167.62 REMARK 500 4 SER A 231 76.96 -164.46 REMARK 500 5 SER A 120 176.23 65.59 REMARK 500 5 VAL A 121 27.39 -147.80 REMARK 500 5 VAL A 122 -38.26 -37.30 REMARK 500 5 PRO A 165 47.31 -84.27 REMARK 500 5 VAL A 166 127.90 44.22 REMARK 500 5 GLN A 168 -29.21 -39.67 REMARK 500 5 SER A 170 42.30 -81.62 REMARK 500 5 ASN A 171 160.17 -42.19 REMARK 500 5 HIS A 187 -36.52 -155.24 REMARK 500 5 THR A 191 -30.40 -151.44 REMARK 500 5 ASN A 197 60.46 -174.16 REMARK 500 5 SER A 231 12.29 -147.51 REMARK 500 6 PHE A 141 -14.60 49.44 REMARK 500 6 MET A 154 -3.02 -58.02 REMARK 500 6 ALA A 169 22.43 -147.37 REMARK 500 6 SER A 170 38.14 -89.51 REMARK 500 6 ASN A 171 159.89 -43.45 REMARK 500 6 HIS A 187 -37.02 -143.63 REMARK 500 6 THR A 191 -30.27 -144.89 REMARK 500 6 LYS A 194 52.07 -96.68 REMARK 500 REMARK 500 THIS ENTRY HAS 177 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 GLY A 124 LEU A 125 3 -148.99 REMARK 500 GLY A 142 ASN A 143 4 142.68 REMARK 500 GLN A 186 HIS A 187 4 149.76 REMARK 500 GLY A 124 LEU A 125 7 -145.23 REMARK 500 GLY A 124 LEU A 125 8 -137.82 REMARK 500 SER A 231 SER A 232 8 -143.84 REMARK 500 GLY A 124 LEU A 125 9 -141.60 REMARK 500 ASN A 171 GLN A 172 10 -134.38 REMARK 500 THR A 190 THR A 191 11 -146.86 REMARK 500 GLN A 186 HIS A 187 13 147.82 REMARK 500 GLY A 124 LEU A 125 20 -149.31 REMARK 500 ASN A 171 GLN A 172 20 -132.19 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 218 0.07 SIDE CHAIN REMARK 500 2 ARG A 136 0.12 SIDE CHAIN REMARK 500 2 ARG A 151 0.11 SIDE CHAIN REMARK 500 2 ARG A 164 0.08 SIDE CHAIN REMARK 500 2 TYR A 226 0.13 SIDE CHAIN REMARK 500 3 TYR A 128 0.08 SIDE CHAIN REMARK 500 4 TYR A 128 0.10 SIDE CHAIN REMARK 500 4 TYR A 162 0.09 SIDE CHAIN REMARK 500 5 TYR A 218 0.10 SIDE CHAIN REMARK 500 6 TYR A 149 0.07 SIDE CHAIN REMARK 500 6 TYR A 218 0.09 SIDE CHAIN REMARK 500 6 ARG A 230 0.12 SIDE CHAIN REMARK 500 7 ARG A 148 0.10 SIDE CHAIN REMARK 500 7 TYR A 149 0.09 SIDE CHAIN REMARK 500 7 TYR A 162 0.08 SIDE CHAIN REMARK 500 7 TYR A 163 0.07 SIDE CHAIN REMARK 500 7 ARG A 164 0.08 SIDE CHAIN REMARK 500 8 HIS A 140 0.10 SIDE CHAIN REMARK 500 8 ARG A 156 0.09 SIDE CHAIN REMARK 500 8 TYR A 163 0.07 SIDE CHAIN REMARK 500 9 HIS A 140 0.09 SIDE CHAIN REMARK 500 9 ARG A 148 0.09 SIDE CHAIN REMARK 500 10 ARG A 164 0.14 SIDE CHAIN REMARK 500 10 TYR A 226 0.13 SIDE CHAIN REMARK 500 11 ARG A 151 0.08 SIDE CHAIN REMARK 500 11 ARG A 208 0.10 SIDE CHAIN REMARK 500 12 HIS A 140 0.10 SIDE CHAIN REMARK 500 13 ARG A 136 0.09 SIDE CHAIN REMARK 500 13 ARG A 208 0.09 SIDE CHAIN REMARK 500 13 TYR A 226 0.10 SIDE CHAIN REMARK 500 14 ARG A 136 0.10 SIDE CHAIN REMARK 500 14 TYR A 150 0.08 SIDE CHAIN REMARK 500 14 TYR A 226 0.07 SIDE CHAIN REMARK 500 15 TYR A 128 0.06 SIDE CHAIN REMARK 500 15 ARG A 136 0.10 SIDE CHAIN REMARK 500 15 ARG A 148 0.12 SIDE CHAIN REMARK 500 15 ARG A 230 0.10 SIDE CHAIN REMARK 500 17 PHE A 141 0.08 SIDE CHAIN REMARK 500 17 TYR A 225 0.10 SIDE CHAIN REMARK 500 18 TYR A 157 0.08 SIDE CHAIN REMARK 500 18 ARG A 164 0.09 SIDE CHAIN REMARK 500 20 ARG A 136 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2L1D RELATED DB: PDB REMARK 900 MOUSE PRION PROTEIN (121-231) WITH THE MUTATION Y169G REMARK 900 RELATED ID: 2L1H RELATED DB: PDB REMARK 900 MOUSE PRION PROTEIN (121-231) AT 20 C DEGREES REMARK 900 RELATED ID: 2L39 RELATED DB: PDB REMARK 900 MOUSE PRION PROTEIN (121-231) AT 37 C DEGREES REMARK 900 RELATED ID: 2L1K RELATED DB: PDB REMARK 900 MOUSE PRION PROTEIN (121-231) WITH THE MUTATIONS Y169A, Y225A, AND REMARK 900 Y226A REMARK 900 RELATED ID: 2L1E RELATED DB: PDB REMARK 900 MOUSE PRION PROTEIN (121-231) WITH THE MUTATION F175A REMARK 900 RELATED ID: 17213 RELATED DB: BMRB DBREF 2L40 A 121 232 UNP Q4FJQ7 Q4FJQ7_MOUSE 120 231 SEQADV 2L40 GLY A 119 UNP Q4FJQ7 EXPRESSION TAG SEQADV 2L40 SER A 120 UNP Q4FJQ7 EXPRESSION TAG SEQADV 2L40 ALA A 169 UNP Q4FJQ7 TYR 168 ENGINEERED MUTATION SEQRES 1 A 114 GLY SER VAL VAL GLY GLY LEU GLY GLY TYR MET LEU GLY SEQRES 2 A 114 SER ALA MET SER ARG PRO MET ILE HIS PHE GLY ASN ASP SEQRES 3 A 114 TRP GLU ASP ARG TYR TYR ARG GLU ASN MET TYR ARG TYR SEQRES 4 A 114 PRO ASN GLN VAL TYR TYR ARG PRO VAL ASP GLN ALA SER SEQRES 5 A 114 ASN GLN ASN ASN PHE VAL HIS ASP CYS VAL ASN ILE THR SEQRES 6 A 114 ILE LYS GLN HIS THR VAL THR THR THR THR LYS GLY GLU SEQRES 7 A 114 ASN PHE THR GLU THR ASP VAL LYS MET MET GLU ARG VAL SEQRES 8 A 114 VAL GLU GLN MET CYS VAL THR GLN TYR GLN LYS GLU SER SEQRES 9 A 114 GLN ALA TYR TYR ASP GLY ARG ARG SER SER HELIX 1 1 TRP A 145 MET A 154 1 10 HELIX 2 2 TYR A 155 TYR A 157 5 3 HELIX 3 3 ASN A 171 GLN A 186 1 16 HELIX 4 4 THR A 199 ASP A 227 1 29 SHEET 1 A 2 MET A 129 LEU A 130 0 SHEET 2 A 2 TYR A 162 TYR A 163 -1 O TYR A 163 N MET A 129 SSBOND 1 CYS A 179 CYS A 214 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