HEADER PROTEIN FIBRIL 08-JUL-19 6PQA TITLE GAVVGG SEGMENT 119-124 FROM HUMAN PRION COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 119-124; COMPND 5 SYNONYM: PRP, ASCR, PRP27-30, PRP33-35C; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS AMYLOID-LIKE PROTOFIBRIL, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.I.APOSTOL,M.R.SAWAYA,D.EISENBERG REVDAT 4 13-MAR-24 6PQA 1 REMARK REVDAT 3 27-MAY-20 6PQA 1 JRNL REVDAT 2 29-APR-20 6PQA 1 JRNL REVDAT 1 15-APR-20 6PQA 0 JRNL AUTH C.GLYNN,M.R.SAWAYA,P.GE,M.GALLAGHER-JONES,C.W.SHORT, JRNL AUTH 2 R.BOWMAN,M.APOSTOL,Z.H.ZHOU,D.S.EISENBERG,J.A.RODRIGUEZ JRNL TITL CRYO-EM STRUCTURE OF A HUMAN PRION FIBRIL WITH A JRNL TITL 2 HYDROPHOBIC, PROTEASE-RESISTANT CORE. JRNL REF NAT.STRUCT.MOL.BIOL. V. 27 417 2020 JRNL REFN ESSN 1545-9985 JRNL PMID 32284600 JRNL DOI 10.1038/S41594-020-0403-Y REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0061 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.600 REMARK 3 FREE R VALUE TEST SET COUNT : 46 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.46 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.63 REMARK 3 REFLECTION IN BIN (WORKING SET) : 108 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 10 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 32 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : 0.88000 REMARK 3 B33 (A**2) : -0.60000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.28000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.105 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.044 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.099 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.878 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 31 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 16 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 41 ; 1.081 ; 2.039 REMARK 3 BOND ANGLES OTHERS (DEGREES): 40 ; 0.554 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 5 ; 7.501 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 2 ; 5.267 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 5 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 39 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 5 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6PQA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000242876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8-7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9465 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK 1.97.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 455 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : 0.15000 REMARK 200 FOR THE DATA SET : 31.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.31100 REMARK 200 R SYM FOR SHELL (I) : 0.31000 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.3.2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 11.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML PEPTIDE IN 2.4 M SODIUM REMARK 280 MALONATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 6.40500 REMARK 290 SMTRY3 2 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: OCTAMERIC 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 4.78600 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 9.57200 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 14.35800 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 0.86256 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 6.40500 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 -20.75308 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 5.64856 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 6.40500 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 -20.75308 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 10.43456 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 6.40500 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 -20.75308 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 15.22056 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 6.40500 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 -20.75308 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6PQ5 RELATED DB: PDB REMARK 900 AGAAAA SEGMENT 113-118 FROM HUMAN PRION DBREF 6PQA A 1 6 UNP P04156 PRIO_HUMAN 119 124 SEQRES 1 A 6 GLY ALA VAL VAL GLY GLY FORMUL 2 HOH *3(H2 O) CRYST1 4.786 12.810 20.771 90.00 92.38 90.00 P 1 21 1 2 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 0.208943 0.000000 0.008673 0.00000 SCALE2 0.000000 0.078064 0.000000 0.00000 SCALE3 0.000000 0.000000 0.048186 0.00000 ATOM 1 N GLY A 1 0.774 -0.653 0.808 1.00 11.97 N ATOM 2 CA GLY A 1 1.132 -0.206 -0.563 1.00 10.78 C ATOM 3 C GLY A 1 0.132 -0.673 -1.601 1.00 9.55 C ATOM 4 O GLY A 1 -0.396 -1.790 -1.506 1.00 10.46 O ATOM 5 N ALA A 2 -0.121 0.181 -2.592 1.00 8.11 N ATOM 6 CA ALA A 2 -0.966 -0.180 -3.727 1.00 6.19 C ATOM 7 C ALA A 2 -0.278 -1.240 -4.576 1.00 4.89 C ATOM 8 O ALA A 2 0.939 -1.340 -4.573 1.00 5.11 O ATOM 9 CB ALA A 2 -1.289 1.037 -4.580 1.00 6.83 C ATOM 10 N VAL A 3 -1.075 -2.038 -5.280 1.00 3.34 N ATOM 11 CA VAL A 3 -0.561 -3.013 -6.241 1.00 2.77 C ATOM 12 C VAL A 3 -1.204 -2.660 -7.579 1.00 1.72 C ATOM 13 O VAL A 3 -2.425 -2.621 -7.686 1.00 0.88 O ATOM 14 CB VAL A 3 -0.941 -4.442 -5.852 1.00 2.95 C ATOM 15 CG1 VAL A 3 -0.339 -5.406 -6.851 1.00 3.95 C ATOM 16 CG2 VAL A 3 -0.480 -4.754 -4.446 1.00 3.05 C ATOM 17 N VAL A 4 -0.378 -2.357 -8.578 1.00 1.12 N ATOM 18 CA VAL A 4 -0.881 -1.715 -9.796 1.00 1.51 C ATOM 19 C VAL A 4 -0.228 -2.337 -11.019 1.00 1.44 C ATOM 20 O VAL A 4 1.000 -2.463 -11.064 1.00 1.21 O ATOM 21 CB VAL A 4 -0.600 -0.197 -9.802 1.00 1.36 C ATOM 22 CG1 VAL A 4 -1.214 0.434 -11.059 1.00 2.62 C ATOM 23 CG2 VAL A 4 -1.145 0.480 -8.547 1.00 2.27 C ATOM 24 N GLY A 5 -1.047 -2.729 -11.998 1.00 2.03 N ATOM 25 CA GLY A 5 -0.529 -3.281 -13.262 1.00 2.55 C ATOM 26 C GLY A 5 -1.183 -2.602 -14.452 1.00 3.81 C ATOM 27 O GLY A 5 -2.399 -2.406 -14.457 1.00 2.07 O ATOM 28 N GLY A 6 -0.371 -2.231 -15.439 1.00 5.33 N ATOM 29 CA GLY A 6 -0.852 -1.554 -16.645 1.00 7.37 C ATOM 30 C GLY A 6 -0.182 -2.095 -17.889 1.00 9.40 C ATOM 31 O GLY A 6 0.747 -2.913 -17.805 1.00 11.70 O ATOM 32 OXT GLY A 6 -0.547 -1.764 -19.023 1.00 11.72 O TER 33 GLY A 6 HETATM 34 O HOH A 101 1.254 -3.046 0.683 1.00 33.98 O HETATM 35 O HOH A 102 -0.634 0.785 -19.162 1.00 29.96 O HETATM 36 O HOH A 103 -2.633 -3.168 -2.027 1.00 30.43 O MASTER 258 0 0 0 0 0 0 6 35 1 0 1 END