HEADER TRANSPORT PROTEIN 31-MAY-16 5L6R TITLE PRP226* - SOLUTION-STATE NMR STRUCTURE OF TRUNCATED HUMAN PRION TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 90-226; COMPND 5 SYNONYM: PRP,ASCR,PRP27-30,PRP33-35C; COMPND 6 ENGINEERED: 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, ALTPRP, PRIP, PRP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRUNCATED FORM OF HUMAN PRION PROTEIN, BINDS TO MAB V5B2, STRUCTURE KEYWDS 2 FROM CYANA 3.0, TRANSPORT PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR V.KOVAC,B.ZUPANCIC,G.ILC,V.CURIN SERBEC,J.PLAVEC REVDAT 5 14-JUN-23 5L6R 1 REMARK REVDAT 4 08-MAY-19 5L6R 1 REMARK REVDAT 3 15-FEB-17 5L6R 1 JRNL REVDAT 2 01-FEB-17 5L6R 1 JRNL REVDAT 1 05-OCT-16 5L6R 0 JRNL AUTH V.KOVAC,B.ZUPANCIC,G.ILC,J.PLAVEC,V.CURIN SERBEC JRNL TITL TRUNCATED PRION PROTEIN PRP226* - A STRUCTURAL VIEW ON ITS JRNL TITL 2 ROLE IN AMYLOID DISEASE. JRNL REF BIOCHEM. BIOPHYS. RES. V. 484 45 2017 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 28109886 JRNL DOI 10.1016/J.BBRC.2017.01.078 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : YASARA REMARK 3 AUTHORS : PROF. DR. GREGOR HOEGENAUER, PROF. DR. GUENTHER REMARK 3 KORAIMANN, PROF. DR. ANDREAS KUNGL, PROF. DR. GERT REMARK 3 VRIEND REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5L6R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1200000206. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.9 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.9 MM (13C, 15N)-DOUBLY LABELED REMARK 210 PRP226*, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-15N HSQC REMARK 210 NH2 ONLY; 3D HNCACB; 3D HBHA(CO) REMARK 210 NH; 3D 1H-15N NOESY; 3D CBCA(CO) REMARK 210 NH; 3D HNCO; 3D HN(CO)CA; 2D 1H- REMARK 210 13C HSQC ALIPHATIC; 2D 1H-13C REMARK 210 HSQC AROMATIC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D CCH-TOCSY; 3D HCCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : VNMRS REMARK 210 SPECTROMETER MANUFACTURER : AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, SPARKY, CYANA, TALOS, REMARK 210 VNMR, NMRPIPE, UCSF CHIMERA REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 1 VAL A 161 CA VAL A 161 CB 0.155 REMARK 500 1 VAL A 161 CB VAL A 161 CG1 0.141 REMARK 500 2 VAL A 161 CA VAL A 161 CB 0.161 REMARK 500 2 VAL A 161 CB VAL A 161 CG1 0.138 REMARK 500 3 VAL A 161 CA VAL A 161 CB 0.150 REMARK 500 3 VAL A 161 CB VAL A 161 CG1 0.147 REMARK 500 4 VAL A 161 CA VAL A 161 CB 0.154 REMARK 500 4 VAL A 161 CB VAL A 161 CG1 0.142 REMARK 500 5 VAL A 161 CA VAL A 161 CB 0.149 REMARK 500 5 VAL A 161 CB VAL A 161 CG1 0.151 REMARK 500 6 VAL A 161 CA VAL A 161 CB 0.156 REMARK 500 6 VAL A 161 CB VAL A 161 CG1 0.157 REMARK 500 7 VAL A 161 CA VAL A 161 CB 0.152 REMARK 500 7 VAL A 161 CB VAL A 161 CG1 0.151 REMARK 500 8 VAL A 161 CA VAL A 161 CB 0.155 REMARK 500 8 VAL A 161 CB VAL A 161 CG1 0.145 REMARK 500 9 VAL A 161 CA VAL A 161 CB 0.150 REMARK 500 9 VAL A 161 CB VAL A 161 CG1 0.156 REMARK 500 10 VAL A 161 CA VAL A 161 CB 0.151 REMARK 500 10 VAL A 161 CB VAL A 161 CG1 0.142 REMARK 500 11 VAL A 161 CA VAL A 161 CB 0.151 REMARK 500 11 VAL A 161 CB VAL A 161 CG1 0.148 REMARK 500 12 VAL A 161 CA VAL A 161 CB 0.158 REMARK 500 12 VAL A 161 CB VAL A 161 CG1 0.140 REMARK 500 13 VAL A 161 CA VAL A 161 CB 0.147 REMARK 500 13 VAL A 161 CB VAL A 161 CG1 0.136 REMARK 500 14 VAL A 161 CA VAL A 161 CB 0.148 REMARK 500 14 VAL A 161 CB VAL A 161 CG1 0.139 REMARK 500 15 VAL A 161 CA VAL A 161 CB 0.160 REMARK 500 15 VAL A 161 CB VAL A 161 CG1 0.151 REMARK 500 16 VAL A 161 CA VAL A 161 CB 0.148 REMARK 500 16 VAL A 161 CB VAL A 161 CG1 0.140 REMARK 500 17 VAL A 161 CA VAL A 161 CB 0.149 REMARK 500 17 VAL A 161 CB VAL A 161 CG1 0.130 REMARK 500 18 VAL A 161 CA VAL A 161 CB 0.139 REMARK 500 18 VAL A 161 CB VAL A 161 CG1 0.145 REMARK 500 19 VAL A 161 CA VAL A 161 CB 0.158 REMARK 500 19 VAL A 161 CB VAL A 161 CG1 0.161 REMARK 500 20 VAL A 161 CA VAL A 161 CB 0.153 REMARK 500 20 VAL A 161 CB VAL A 161 CG1 0.149 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 220 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 151 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 136 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 151 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 ARG A 151 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 136 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 164 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 136 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 136 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG A 136 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 151 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 164 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 156 NE - CZ - NH1 ANGL. DEV. = 3.0 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 ASN A 100 -33.09 -172.65 REMARK 500 1 ASN A 108 6.95 59.47 REMARK 500 1 PHE A 141 -84.42 -92.35 REMARK 500 1 PRO A 165 20.53 -76.72 REMARK 500 1 GLN A 172 54.98 -69.08 REMARK 500 1 VAL A 176 -74.09 72.41 REMARK 500 1 ARG A 220 -71.32 -117.31 REMARK 500 1 HIS A 229 96.38 -62.89 REMARK 500 2 HIS A 96 -83.37 -60.57 REMARK 500 2 ASN A 100 -84.83 -158.76 REMARK 500 2 PHE A 141 -84.65 -100.97 REMARK 500 2 ASP A 144 0.41 -67.32 REMARK 500 2 PRO A 165 -148.40 -85.30 REMARK 500 2 MET A 166 49.29 -71.71 REMARK 500 2 HIS A 177 -66.63 -140.09 REMARK 500 2 HIS A 230 69.31 26.95 REMARK 500 3 ASN A 100 -82.65 -158.11 REMARK 500 3 PHE A 141 -85.19 -107.39 REMARK 500 3 PRO A 165 48.98 -81.46 REMARK 500 3 MET A 166 -113.96 -145.65 REMARK 500 3 GLN A 172 -52.85 -162.47 REMARK 500 3 VAL A 176 -63.69 80.40 REMARK 500 3 ARG A 220 -75.47 -115.96 REMARK 500 3 HIS A 229 45.49 -73.16 REMARK 500 3 HIS A 233 44.18 -150.24 REMARK 500 4 ASN A 100 -39.32 -166.00 REMARK 500 4 PHE A 141 -86.32 -102.37 REMARK 500 4 GLN A 172 -41.57 -157.83 REMARK 500 4 VAL A 176 -72.04 74.55 REMARK 500 4 ASN A 197 61.96 62.38 REMARK 500 4 ARG A 220 -76.49 -120.85 REMARK 500 5 ASN A 100 -28.49 168.25 REMARK 500 5 LYS A 110 65.37 -107.32 REMARK 500 5 ALA A 115 27.01 -142.25 REMARK 500 5 PHE A 141 -86.56 -98.03 REMARK 500 5 TYR A 169 12.80 45.43 REMARK 500 5 ASN A 171 -84.42 -144.45 REMARK 500 5 VAL A 176 -59.75 79.46 REMARK 500 6 ASN A 100 -31.80 172.38 REMARK 500 6 SER A 103 178.90 64.80 REMARK 500 6 PHE A 141 -86.27 -103.72 REMARK 500 6 PRO A 165 51.42 -94.06 REMARK 500 6 ASN A 171 92.71 -12.92 REMARK 500 6 VAL A 176 -13.69 80.39 REMARK 500 6 HIS A 177 -65.24 -101.75 REMARK 500 6 ASN A 197 68.69 60.64 REMARK 500 6 ARG A 220 -71.25 -120.17 REMARK 500 6 HIS A 229 92.87 -67.01 REMARK 500 7 ASN A 100 -37.18 145.35 REMARK 500 7 ALA A 113 37.83 -88.24 REMARK 500 REMARK 500 THIS ENTRY HAS 168 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34003 RELATED DB: BMRB DBREF 5L6R A 90 226 UNP P04156 PRIO_HUMAN 90 226 SEQADV 5L6R GLY A 227 UNP P04156 EXPRESSION TAG SEQADV 5L6R GLY A 228 UNP P04156 EXPRESSION TAG SEQADV 5L6R HIS A 229 UNP P04156 EXPRESSION TAG SEQADV 5L6R HIS A 230 UNP P04156 EXPRESSION TAG SEQADV 5L6R HIS A 231 UNP P04156 EXPRESSION TAG SEQADV 5L6R HIS A 232 UNP P04156 EXPRESSION TAG SEQADV 5L6R HIS A 233 UNP P04156 EXPRESSION TAG SEQADV 5L6R HIS A 234 UNP P04156 EXPRESSION TAG SEQRES 1 A 145 GLY GLN GLY GLY GLY THR HIS SER GLN TRP ASN LYS PRO SEQRES 2 A 145 SER LYS PRO LYS THR ASN MET LYS HIS MET ALA GLY ALA SEQRES 3 A 145 ALA ALA ALA GLY ALA VAL VAL GLY GLY LEU GLY GLY TYR SEQRES 4 A 145 MET LEU GLY SER ALA MET SER ARG PRO ILE ILE HIS PHE SEQRES 5 A 145 GLY SER ASP TYR GLU ASP ARG TYR TYR ARG GLU ASN MET SEQRES 6 A 145 HIS ARG TYR PRO ASN GLN VAL TYR TYR ARG PRO MET ASP SEQRES 7 A 145 GLU TYR SER ASN GLN ASN ASN PHE VAL HIS ASP CYS VAL SEQRES 8 A 145 ASN ILE THR ILE LYS GLN HIS THR VAL THR THR THR THR SEQRES 9 A 145 LYS GLY GLU ASN PHE THR GLU THR ASP VAL LYS MET MET SEQRES 10 A 145 GLU ARG VAL VAL GLU GLN MET CYS ILE THR GLN TYR GLU SEQRES 11 A 145 ARG GLU SER GLN ALA TYR TYR GLY GLY HIS HIS HIS HIS SEQRES 12 A 145 HIS HIS HELIX 1 AA1 SER A 143 ASN A 153 1 11 HELIX 2 AA2 MET A 154 ARG A 156 5 3 HELIX 3 AA3 ASP A 178 LYS A 194 1 17 HELIX 4 AA4 THR A 199 GLU A 219 1 21 HELIX 5 AA5 ARG A 220 TYR A 226 1 7 SHEET 1 AA1 2 MET A 129 LEU A 130 0 SHEET 2 AA1 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 MODEL 1