HEADER MEMBRANE PROTEIN 23-FEB-10 2KUN TITLE THREE DIMENSIONAL STRUCTURE OF HUPRP(90-231 M129 Q212P) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 90-231; COMPND 5 SYNONYM: PRP, PRP27-30, PRP33-35C, ASCR; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PRNP, PRIP, PRP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-11A KEYWDS HUMAN PRION MUTANT, AMYLOID, CELL MEMBRANE, DISEASE MUTATION, KEYWDS 2 DISULFIDE BOND, GLYCOPROTEIN, GOLGI APPARATUS, GPI-ANCHOR, KEYWDS 3 LIPOPROTEIN, MEMBRANE, PRION, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.ILC,G.GIACHIN,M.JAREMKO,L.JAREMKO,I.ZHUKOV,J.PLAVEC,G.LEGNAME, AUTHOR 2 F.BENETTI REVDAT 5 06-NOV-24 2KUN 1 REMARK REVDAT 4 14-JUN-23 2KUN 1 REMARK REVDAT 3 10-NOV-21 2KUN 1 SEQADV REVDAT 2 26-FEB-20 2KUN 1 REMARK SEQADV REVDAT 1 25-AUG-10 2KUN 0 JRNL AUTH G.ILC,G.GIACHIN,M.JAREMKO,L.JAREMKO,F.BENETTI,J.PLAVEC, JRNL AUTH 2 I.ZHUKOV,G.LEGNAME JRNL TITL NMR STRUCTURE OF THE HUMAN PRION PROTEIN WITH THE JRNL TITL 2 PATHOLOGICAL Q212P MUTATION REVEALS UNIQUE STRUCTURAL JRNL TITL 3 FEATURES. JRNL REF PLOS ONE V. 5 11715 2010 JRNL REFN ESSN 1932-6203 JRNL PMID 20661422 JRNL DOI 10.1371/JOURNAL.PONE.0011715 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, CNS REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KUN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000101593. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 5.5; NULL REMARK 210 IONIC STRENGTH : 150 NACL; 150 NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-98% 13C; U-98% 15N] REMARK 210 PRP(Q212P)-1, 90% H2O/10% D2O; REMARK 210 1.0 MM [U-98% 13C; U-98% 15N] REMARK 210 PRP(Q212P)-2, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D CBCA(CO)NH; 3D HNCACB; REMARK 210 3D HN(CO)CA; 3D 1H-15N NOESY; 3D REMARK 210 HBHA(CO)NH; 3D 1H-13C NOESY; 3D REMARK 210 CCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : UNIFORM NMR SYSTEM REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, CYANA, CNS, CARA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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 CYS A 179 CA - CB - SG ANGL. DEV. = 7.2 DEGREES REMARK 500 2 CYS A 179 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 3 CYS A 179 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 4 ARG A 148 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 CYS A 179 CA - CB - SG ANGL. DEV. = 7.6 DEGREES REMARK 500 5 ARG A 164 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 CYS A 179 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 6 CYS A 179 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 7 CYS A 179 CA - CB - SG ANGL. DEV. = 7.4 DEGREES REMARK 500 9 CYS A 179 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 10 CYS A 179 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 11 CYS A 179 CA - CB - SG ANGL. DEV. = 6.6 DEGREES REMARK 500 12 ARG A 151 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 13 CYS A 179 CA - CB - SG ANGL. DEV. = 7.4 DEGREES REMARK 500 14 CYS A 179 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 15 CYS A 179 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 16 CYS A 179 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 17 CYS A 179 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 19 CYS A 179 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 20 ARG A 148 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 20 CYS A 179 CA - CB - SG ANGL. DEV. = 6.7 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 THR A 107 -151.75 50.87 REMARK 500 1 ALA A 115 -173.82 65.89 REMARK 500 1 ALA A 116 -160.62 57.88 REMARK 500 1 ALA A 120 36.81 -82.70 REMARK 500 1 VAL A 121 56.29 -92.09 REMARK 500 1 ARG A 136 117.97 -25.74 REMARK 500 1 TYR A 169 -159.14 54.01 REMARK 500 2 ALA A 117 82.28 -151.19 REMARK 500 2 LEU A 125 22.14 48.31 REMARK 500 2 ARG A 136 117.29 -30.71 REMARK 500 2 SER A 230 -72.72 -41.97 REMARK 500 3 THR A 95 158.77 66.72 REMARK 500 3 LYS A 106 -59.62 -149.50 REMARK 500 3 ALA A 115 -158.88 62.10 REMARK 500 3 SER A 135 101.03 -55.18 REMARK 500 3 ARG A 136 118.00 -28.80 REMARK 500 3 TYR A 169 -141.09 55.49 REMARK 500 3 ASN A 171 167.10 77.48 REMARK 500 4 GLN A 91 172.81 58.02 REMARK 500 4 THR A 95 -47.22 68.95 REMARK 500 4 LYS A 104 75.61 56.25 REMARK 500 4 ASN A 108 160.09 70.89 REMARK 500 4 MET A 109 37.22 -152.74 REMARK 500 4 LYS A 110 -147.35 50.76 REMARK 500 4 ALA A 116 -47.71 -147.78 REMARK 500 4 ALA A 118 117.74 59.36 REMARK 500 4 ARG A 136 107.27 -27.20 REMARK 500 4 HIS A 140 79.25 -119.86 REMARK 500 4 TYR A 169 -146.04 55.38 REMARK 500 4 ASN A 171 158.67 70.37 REMARK 500 4 GLU A 221 -61.23 -105.74 REMARK 500 5 HIS A 96 -1.55 66.96 REMARK 500 5 SER A 97 31.13 -148.51 REMARK 500 5 HIS A 111 -175.74 62.23 REMARK 500 5 ALA A 115 -164.84 61.43 REMARK 500 5 ALA A 116 -9.14 -140.93 REMARK 500 5 ARG A 136 117.82 -29.92 REMARK 500 5 MET A 166 0.50 -67.37 REMARK 500 5 TYR A 169 141.31 72.28 REMARK 500 5 GLU A 221 -65.42 -107.15 REMARK 500 5 SER A 222 6.09 48.32 REMARK 500 5 SER A 231 -152.40 48.58 REMARK 500 5 HIS A 233 12.49 -64.15 REMARK 500 5 HIS A 234 -155.89 53.41 REMARK 500 6 TRP A 99 -155.57 54.86 REMARK 500 6 SER A 103 -179.37 61.49 REMARK 500 6 MET A 109 148.59 -174.13 REMARK 500 6 ALA A 116 28.01 -79.34 REMARK 500 6 SER A 135 101.51 -59.89 REMARK 500 6 ARG A 136 116.57 -29.82 REMARK 500 REMARK 500 THIS ENTRY HAS 173 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16743 RELATED DB: BMRB DBREF 2KUN A 90 231 UNP P04156 PRIO_HUMAN 90 231 SEQADV 2KUN PRO A 212 UNP P04156 GLN 212 ENGINEERED MUTATION SEQADV 2KUN HIS A 232 UNP P04156 EXPRESSION TAG SEQADV 2KUN HIS A 233 UNP P04156 EXPRESSION TAG SEQADV 2KUN HIS A 234 UNP P04156 EXPRESSION TAG SEQADV 2KUN HIS A 235 UNP P04156 EXPRESSION TAG SEQADV 2KUN HIS A 236 UNP P04156 EXPRESSION TAG SEQADV 2KUN HIS A 237 UNP P04156 EXPRESSION TAG SEQRES 1 A 148 GLY GLN GLY GLY GLY THR HIS SER GLN TRP ASN LYS PRO SEQRES 2 A 148 SER LYS PRO LYS THR ASN MET LYS HIS MET ALA GLY ALA SEQRES 3 A 148 ALA ALA ALA GLY ALA VAL VAL GLY GLY LEU GLY GLY TYR SEQRES 4 A 148 MET LEU GLY SER ALA MET SER ARG PRO ILE ILE HIS PHE SEQRES 5 A 148 GLY SER ASP TYR GLU ASP ARG TYR TYR ARG GLU ASN MET SEQRES 6 A 148 HIS ARG TYR PRO ASN GLN VAL TYR TYR ARG PRO MET ASP SEQRES 7 A 148 GLU TYR SER ASN GLN ASN ASN PHE VAL HIS ASP CYS VAL SEQRES 8 A 148 ASN ILE THR ILE LYS GLN HIS THR VAL THR THR THR THR SEQRES 9 A 148 LYS GLY GLU ASN PHE THR GLU THR ASP VAL LYS MET MET SEQRES 10 A 148 GLU ARG VAL VAL GLU PRO MET CYS ILE THR GLN TYR GLU SEQRES 11 A 148 ARG GLU SER GLN ALA TYR TYR GLN ARG GLY SER SER HIS SEQRES 12 A 148 HIS HIS HIS HIS HIS HELIX 1 1 SER A 143 ASN A 153 1 11 HELIX 2 2 MET A 154 TYR A 157 5 4 HELIX 3 3 ASN A 173 THR A 190 1 18 HELIX 4 4 THR A 191 GLY A 195 5 5 HELIX 5 5 THR A 199 GLU A 221 1 23 HELIX 6 6 GLU A 221 SER A 231 1 11 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 2.04 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