HEADER PROTEIN FIBRIL 07-SEP-17 6AXZ TITLE SEGMENT FROM BANK VOLE PRION PROTEIN 168-176 QYNNQNNFV COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 168-176; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: MYODES GLAREOLUS; SOURCE 4 ORGANISM_COMMON: BANK VOLE; SOURCE 5 ORGANISM_TAXID: 447135 KEYWDS POLAR CLASP, AMYLOID FIBRIL, PRION, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR C.GLYNN,J.A.RODRIGUEZ,D.R.BOYER,M.GALLAGHER-JONES REVDAT 4 13-MAR-24 6AXZ 1 REMARK REVDAT 3 21-FEB-18 6AXZ 1 JRNL REVDAT 2 31-JAN-18 6AXZ 1 JRNL REVDAT 1 17-JAN-18 6AXZ 0 JRNL AUTH M.GALLAGHER-JONES,C.GLYNN,D.R.BOYER,M.W.MARTYNOWYCZ, JRNL AUTH 2 E.HERNANDEZ,J.MIAO,C.T.ZEE,I.V.NOVIKOVA,L.GOLDSCHMIDT, JRNL AUTH 3 H.T.MCFARLANE,G.F.HELGUERA,J.E.EVANS,M.R.SAWAYA,D.CASCIO, JRNL AUTH 4 D.S.EISENBERG,T.GONEN,J.A.RODRIGUEZ JRNL TITL SUB-ANGSTROM CRYO-EM STRUCTURE OF A PRION PROTOFIBRIL JRNL TITL 2 REVEALS A POLAR CLASP. JRNL REF NAT. STRUCT. MOL. BIOL. V. 25 131 2018 JRNL REFN ESSN 1545-9985 JRNL PMID 29335561 JRNL DOI 10.1038/S41594-017-0018-0 REMARK 2 REMARK 2 RESOLUTION. 0.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.950 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 7473 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.010 REMARK 3 FREE R VALUE TEST SET COUNT : 673 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 10.3387 - 1.2810 0.97 1355 135 0.1875 0.1851 REMARK 3 2 1.2810 - 1.0171 0.99 1391 137 0.2436 0.2620 REMARK 3 3 1.0171 - 0.8886 0.97 1383 137 0.2859 0.2859 REMARK 3 4 0.8886 - 0.8074 0.97 1313 130 0.3442 0.3662 REMARK 3 5 0.8074 - 0.7495 0.95 1358 134 0.3683 0.3907 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 6.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.014 82 REMARK 3 ANGLE : 1.014 111 REMARK 3 CHIRALITY : 0.104 10 REMARK 3 PLANARITY : 0.005 17 REMARK 3 DIHEDRAL : 18.838 29 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6AXZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000229892. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : 100.0 REMARK 240 PH : 6.00 REMARK 240 NUMBER OF CRYSTALS USED : 1 REMARK 240 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 7474 REMARK 240 RESOLUTION RANGE HIGH (A) : 0.750 REMARK 240 RESOLUTION RANGE LOW (A) : 10.338 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 240 DATA REDUNDANCY : 5.787 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :0.75 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :0.77 REMARK 240 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 240 DATA REDUNDANCY IN SHELL : 4.43 REMARK 240 R MERGE FOR SHELL (I) : 0.63800 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DECAMERIC 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 4.94000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 9.88000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 14.82000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 19.76000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 -2.18510 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 10.10648 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 7 1.000000 0.000000 0.000000 2.75490 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 10.10648 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 7.69490 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 10.10648 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 9 1.000000 0.000000 0.000000 12.63490 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 10.10648 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 10 1.000000 0.000000 0.000000 17.57490 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 10.10648 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-7017 RELATED DB: EMDB REMARK 900 SEGMENT FROM BANK VOLE PRION PROTEIN 168-176 QYNNQNNFV DBREF 6AXZ A 168 176 UNP Q8VHV5 Q8VHV5_MYOGA 168 176 SEQRES 1 A 9 GLN TYR ASN ASN GLN ASN ASN PHE VAL FORMUL 2 HOH *2(H2 O) CRYST1 4.940 10.340 31.150 94.21 92.38 102.20 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 0.202429 0.043782 0.012119 0.00000 SCALE2 0.000000 0.098948 0.008347 0.00000 SCALE3 0.000000 0.000000 0.032244 0.00000