HEADER PROTEIN FIBRIL 20-MAY-09 2KJ3 TITLE HIGH-RESOLUTION STRUCTURE OF THE HET-S(218-289) PRION IN ITS AMYLOID TITLE 2 FORM OBTAINED BY SOLID-STATE NMR COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMALL S PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: C-TERMINAL PRION FORMING DOMAIN OF HET-S, RESIDUES 218-289; COMPND 5 SYNONYM: HET-S; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PODOSPORA ANSERINA; SOURCE 3 ORGANISM_TAXID: 5145; SOURCE 4 GENE: SMALL S; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-24A KEYWDS HET-S(218-289), BETA-SOLENOID, PRION, AMYLOID FIBRIL, PARALLEL BETA- KEYWDS 2 SHEETS, HYDROPHOBIC CORE, SALT BRIDGES, ASPARAGINE LADDERS, BETA- KEYWDS 3 HELIX, PROTEIN FIBRIL EXPDTA SOLID-STATE NMR NUMMDL 20 AUTHOR H.VAN MELCKEBEKE,C.WASMER,A.LANGE,E.AB,A.LOQUET,B.H.MEIER REVDAT 5 01-MAY-24 2KJ3 1 REMARK SEQADV REVDAT 4 13-OCT-10 2KJ3 1 JRNL REVDAT 3 29-SEP-10 2KJ3 1 JRNL REVDAT 2 11-AUG-10 2KJ3 1 REMARK REVDAT 1 02-JUN-10 2KJ3 0 JRNL AUTH H.VAN MELCKEBEKE,C.WASMER,A.LANGE,E.AB,A.LOQUET,A.BOCKMANN, JRNL AUTH 2 B.H.MEIER JRNL TITL ATOMIC-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF JRNL TITL 2 HET-S(218-289) AMYLOID FIBRILS BY SOLID-STATE NMR JRNL TITL 3 SPECTROSCOPY JRNL REF J.AM.CHEM.SOC. V. 132 13765 2010 JRNL REFN ISSN 0002-7863 JRNL PMID 20828131 JRNL DOI 10.1021/JA104213J REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.WASMER,A.LANGE,H.VAN MELCKEBEKE,A.B.SIEMER,R.RIEK, REMARK 1 AUTH 2 B.H.MEIER REMARK 1 TITL AMYLOID FIBRILS OF THE HET-S(218-289) PRION FORM A BETA REMARK 1 TITL 2 SOLENOID WITH A TRIANGULAR HYDROPHOBIC CORE REMARK 1 REF SCIENCE V. 319 1523 2008 REMARK 1 REFN ISSN 0036-8075 REMARK 1 PMID 18339938 REMARK 1 DOI 10.1126/SCIENCE.1151839 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.LANGE,Z.GATTIN,H.VAN MELCKEBEKE,C.WASMER,A.SORAGNI, REMARK 1 AUTH 2 W.F.VAN GUNSTEREN,B.H.MEIER REMARK 1 TITL A COMBINED SOLID-STATE NMR AND MD CHARACTERIZATION OF THE REMARK 1 TITL 2 STABILITY AND DYNAMICS OF THE HET-S(218-289) PRION IN ITS REMARK 1 TITL 3 AMYLOID CONFORMATION REMARK 1 REF CHEMBIOCHEM V. 10 1657 2009 REMARK 1 REFN ISSN 1439-4227 REMARK 1 PMID 19504509 REMARK 1 DOI 10.1002/CBIC.200900019 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, CNS REMARK 3 AUTHORS : GUNTERT, MUMENTHALER (CYANA), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CNS WATER REFINEMENT REMARK 4 REMARK 4 2KJ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000101182. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 100% [U-100% 13C; U-100% 15N] REMARK 210 HET-S(218-289)-1, 100% H2O; 100% REMARK 210 [U-100% 2-13C; U-100% 15N] HET- REMARK 210 S(218-289)-2, 100% H2O; 40% [U- REMARK 210 100% 2-13C; U-100% 15N] HET- REMARK 210 S(218-289)-3, 60% UNLABELLED HET- REMARK 210 S(218-289)-4, 100% H2O; 40% [U- REMARK 210 100% 1,3-13C; U-100% 15N] HET- REMARK 210 S(218-289)-5, 60% UNLABELLED HET- REMARK 210 S(218-289)-6, 100% H2O; 50% [U- REMARK 210 100% 15N] HET-S(218-289)-7, 50% REMARK 210 [U-100% 13C] HET-S(218-289)-8, REMARK 210 100% H2O; 40% [U-100% 13C; U-100% REMARK 210 15N] HET-S(218-289)-9, 60% REMARK 210 UNLABELLED HET-S(218-289)-10, REMARK 210 100% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : PDSD; PAR; CHHC; NHHC; PAIN REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, MOLMOL, PROCHECKNMR, REMARK 210 CARA, XWINNMR REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS 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: THE STUDY HAS BEEN PERFORMED BY SOLID-STATE NMR. REMARK 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 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 300 REMARK: THE RIGID PARTS (I222-A249, T260-W287) OF MOLECULES B AND C REMARK 300 CAN BE OBTAINED BY TRANSLATION AND TWIST OF THE RIGID PART OF REMARK 300 MOLECULE A. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8133 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: 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 LYS A 229 -60.01 -97.71 REMARK 500 1 GLU A 235 88.88 62.34 REMARK 500 1 HIS A 251 -63.53 -93.81 REMARK 500 1 ILE A 254 82.78 70.85 REMARK 500 1 ARG A 255 179.06 63.92 REMARK 500 1 GLN A 259 39.33 -155.19 REMARK 500 1 GLU A 265 -79.11 -87.14 REMARK 500 1 HIS A 290 -168.61 -120.01 REMARK 500 1 HIS A 294 133.67 77.47 REMARK 500 1 LYS B 218 87.15 81.53 REMARK 500 1 ALA B 221 -159.93 -98.53 REMARK 500 1 GLU B 235 97.93 64.37 REMARK 500 1 SER B 257 21.39 -141.79 REMARK 500 1 GLU B 265 -86.42 -92.80 REMARK 500 1 HIS B 290 112.71 -161.25 REMARK 500 1 HIS B 291 -168.91 -129.69 REMARK 500 1 ALA C 221 132.29 78.84 REMARK 500 1 GLU C 235 93.43 63.13 REMARK 500 1 HIS C 251 -69.24 -108.93 REMARK 500 1 ARG C 255 108.91 154.94 REMARK 500 1 GLU C 265 -88.49 -91.11 REMARK 500 1 LYS C 284 -7.30 -146.88 REMARK 500 2 GLU A 235 -87.23 67.07 REMARK 500 2 LEU A 250 114.53 81.04 REMARK 500 2 ARG A 255 -83.92 -105.53 REMARK 500 2 GLN A 259 -49.79 72.19 REMARK 500 2 GLU A 265 -72.18 -78.58 REMARK 500 2 ASP A 288 132.18 70.73 REMARK 500 2 ILE B 219 -65.63 -123.19 REMARK 500 2 ALA B 221 -169.99 -175.32 REMARK 500 2 LYS B 229 -64.10 -100.69 REMARK 500 2 GLU B 235 -74.16 75.87 REMARK 500 2 ARG B 236 24.72 -140.26 REMARK 500 2 LEU B 250 -79.97 65.53 REMARK 500 2 ILE B 254 -156.05 -168.93 REMARK 500 2 ILE B 256 -56.54 -127.01 REMARK 500 2 SER B 257 -61.28 -169.06 REMARK 500 2 GLU B 265 -76.21 -86.01 REMARK 500 2 ASP B 288 101.00 56.18 REMARK 500 2 HIS B 290 30.35 -153.59 REMARK 500 2 ILE C 219 97.87 89.75 REMARK 500 2 ALA C 221 -45.90 -162.85 REMARK 500 2 LYS C 229 -64.22 -93.38 REMARK 500 2 GLU C 235 -73.05 74.42 REMARK 500 2 HIS C 251 -51.41 -144.18 REMARK 500 2 ARG C 255 174.87 67.74 REMARK 500 2 SER C 257 -32.69 172.42 REMARK 500 2 ASP C 258 106.67 -34.86 REMARK 500 2 TRP C 287 32.36 -79.04 REMARK 500 2 ASN C 289 -34.49 177.16 REMARK 500 REMARK 500 THIS ENTRY HAS 538 RAMACHANDRAN OUTLIERS. 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 ARG C 236 0.10 SIDE CHAIN REMARK 500 3 ARG C 238 0.08 SIDE CHAIN REMARK 500 7 ARG A 238 0.08 SIDE CHAIN REMARK 500 7 ARG B 238 0.09 SIDE CHAIN REMARK 500 7 ARG C 255 0.07 SIDE CHAIN REMARK 500 8 ARG B 274 0.07 SIDE CHAIN REMARK 500 8 ARG C 225 0.08 SIDE CHAIN REMARK 500 9 ARG B 274 0.09 SIDE CHAIN REMARK 500 9 ARG C 236 0.11 SIDE CHAIN REMARK 500 9 ARG C 238 0.07 SIDE CHAIN REMARK 500 10 ARG B 232 0.09 SIDE CHAIN REMARK 500 10 ARG B 274 0.08 SIDE CHAIN REMARK 500 11 ARG A 225 0.08 SIDE CHAIN REMARK 500 11 ARG A 238 0.09 SIDE CHAIN REMARK 500 11 ARG A 274 0.12 SIDE CHAIN REMARK 500 11 ARG C 236 0.11 SIDE CHAIN REMARK 500 14 ARG B 238 0.08 SIDE CHAIN REMARK 500 15 ARG A 238 0.07 SIDE CHAIN REMARK 500 15 ARG C 236 0.08 SIDE CHAIN REMARK 500 17 ARG A 236 0.09 SIDE CHAIN REMARK 500 17 ARG A 238 0.07 SIDE CHAIN REMARK 500 18 ARG A 274 0.09 SIDE CHAIN REMARK 500 18 ARG C 232 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11064 RELATED DB: BMRB REMARK 900 COMPLETED CHEMICAL SHIFT ASSIGNMENT OF HET-S(218-289) REMARK 900 RELATED ID: 2RNM RELATED DB: PDB REMARK 900 FIRST HET-S(218-289) STRUCTURE REMARK 900 RELATED ID: 11028 RELATED DB: BMRB REMARK 900 FIRST CHEMICAL SHIFT ASSIGNMENT OF HET-S(218-289) DBREF 2KJ3 A 218 289 UNP Q03689 Q03689_PODAN 218 289 DBREF 2KJ3 B 218 289 UNP Q03689 Q03689_PODAN 218 289 DBREF 2KJ3 C 218 289 UNP Q03689 Q03689_PODAN 218 289 SEQADV 2KJ3 MET A 217 UNP Q03689 INITIATING METHIONINE SEQADV 2KJ3 HIS A 290 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS A 291 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS A 292 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS A 293 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS A 294 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS A 295 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 MET B 217 UNP Q03689 INITIATING METHIONINE SEQADV 2KJ3 HIS B 290 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS B 291 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS B 292 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS B 293 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS B 294 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS B 295 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 MET C 217 UNP Q03689 INITIATING METHIONINE SEQADV 2KJ3 HIS C 290 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS C 291 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS C 292 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS C 293 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS C 294 UNP Q03689 EXPRESSION TAG SEQADV 2KJ3 HIS C 295 UNP Q03689 EXPRESSION TAG SEQRES 1 A 79 MET LYS ILE ASP ALA ILE VAL GLY ARG ASN SER ALA LYS SEQRES 2 A 79 ASP ILE ARG THR GLU GLU ARG ALA ARG VAL GLN LEU GLY SEQRES 3 A 79 ASN VAL VAL THR ALA ALA ALA LEU HIS GLY GLY ILE ARG SEQRES 4 A 79 ILE SER ASP GLN THR THR ASN SER VAL GLU THR VAL VAL SEQRES 5 A 79 GLY LYS GLY GLU SER ARG VAL LEU ILE GLY ASN GLU TYR SEQRES 6 A 79 GLY GLY LYS GLY PHE TRP ASP ASN HIS HIS HIS HIS HIS SEQRES 7 A 79 HIS SEQRES 1 B 79 MET LYS ILE ASP ALA ILE VAL GLY ARG ASN SER ALA LYS SEQRES 2 B 79 ASP ILE ARG THR GLU GLU ARG ALA ARG VAL GLN LEU GLY SEQRES 3 B 79 ASN VAL VAL THR ALA ALA ALA LEU HIS GLY GLY ILE ARG SEQRES 4 B 79 ILE SER ASP GLN THR THR ASN SER VAL GLU THR VAL VAL SEQRES 5 B 79 GLY LYS GLY GLU SER ARG VAL LEU ILE GLY ASN GLU TYR SEQRES 6 B 79 GLY GLY LYS GLY PHE TRP ASP ASN HIS HIS HIS HIS HIS SEQRES 7 B 79 HIS SEQRES 1 C 79 MET LYS ILE ASP ALA ILE VAL GLY ARG ASN SER ALA LYS SEQRES 2 C 79 ASP ILE ARG THR GLU GLU ARG ALA ARG VAL GLN LEU GLY SEQRES 3 C 79 ASN VAL VAL THR ALA ALA ALA LEU HIS GLY GLY ILE ARG SEQRES 4 C 79 ILE SER ASP GLN THR THR ASN SER VAL GLU THR VAL VAL SEQRES 5 C 79 GLY LYS GLY GLU SER ARG VAL LEU ILE GLY ASN GLU TYR SEQRES 6 C 79 GLY GLY LYS GLY PHE TRP ASP ASN HIS HIS HIS HIS HIS SEQRES 7 C 79 HIS SHEET 1 A 6 ASN A 226 GLU A 234 0 SHEET 2 A 6 THR A 261 LYS A 270 1 O GLU A 265 N ASP A 230 SHEET 3 A 6 ARG B 225 GLU B 234 1 O ALA B 228 N SER A 263 SHEET 4 A 6 THR B 261 LYS B 270 1 O GLU B 265 N ASP B 230 SHEET 5 A 6 ARG C 225 GLU C 234 1 O THR C 233 N VAL B 268 SHEET 6 A 6 ASN C 262 LYS C 270 1 O GLU C 265 N ASP C 230 SHEET 1 B 6 ARG A 238 VAL A 245 0 SHEET 2 B 6 ARG A 274 TYR A 281 1 O ILE A 277 N GLN A 240 SHEET 3 B 6 ARG B 238 VAL B 245 1 O LEU B 241 N GLY A 278 SHEET 4 B 6 ARG B 274 TYR B 281 1 O ILE B 277 N GLN B 240 SHEET 5 B 6 ARG C 238 VAL C 245 1 O LEU C 241 N GLY B 278 SHEET 6 B 6 ARG C 274 TYR C 281 1 O ILE C 277 N GLN C 240 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