HEADER PROTEIN FIBRIL 18-MAY-16 5K2F TITLE STRUCTURE OF NNQQNY FROM YEAST PRION SUP35 WITH CADMIUM ACETATE TITLE 2 DETERMINED BY MICROED COMPND MOL_ID: 1; COMPND 2 MOLECULE: EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING COMPND 3 SUBUNIT; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 8-13; COMPND 6 SYNONYM: SUP35, ERF-3, ERF3, ERF2, G1 TO S PHASE TRANSITION PROTEIN COMPND 7 1, OMNIPOTENT SUPPRESSOR PROTEIN 2, PSI NO MORE PROTEIN 2, COMPND 8 POLYPEPTIDE RELEASE FACTOR 3, TRANSLATION RELEASE FACTOR 3; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 4932 KEYWDS AMYLOID, YEAST PRION, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR J.A.RODRIGUEZ,M.R.SAWAYA,D.CASCIO,D.S.EISENBERG REVDAT 9 30-JUN-21 5K2F 1 REMARK LINK REVDAT 8 20-NOV-19 5K2F 1 REMARK REVDAT 7 25-APR-18 5K2F 1 REMARK REVDAT 6 13-SEP-17 5K2F 1 REMARK REVDAT 5 30-NOV-16 5K2F 1 REMARK REVDAT 4 19-OCT-16 5K2F 1 JRNL REVDAT 3 05-OCT-16 5K2F 1 JRNL REVDAT 2 21-SEP-16 5K2F 1 JRNL REVDAT 1 14-SEP-16 5K2F 0 JRNL AUTH M.R.SAWAYA,J.RODRIGUEZ,D.CASCIO,M.J.COLLAZO,D.SHI,F.E.REYES, JRNL AUTH 2 J.HATTNE,T.GONEN,D.S.EISENBERG JRNL TITL AB INITIO STRUCTURE DETERMINATION FROM PRION NANOCRYSTALS AT JRNL TITL 2 ATOMIC RESOLUTION BY MICROED. JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 11232 2016 JRNL REFN ESSN 1091-6490 JRNL PMID 27647903 JRNL DOI 10.1073/PNAS.1606287113 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.0 REMARK 3 NUMBER OF REFLECTIONS : 2308 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 253 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 55 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 7 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 6.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : -0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.36000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.047 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.045 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.367 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5K2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000221621. 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 : 03-FEB-16 REMARK 240 TEMPERATURE (KELVIN) : 100.0 REMARK 240 PH : 7.00 REMARK 240 NUMBER OF CRYSTALS USED : NULL 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 : 2564 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 240 RESOLUTION RANGE LOW (A) : 90.000 REMARK 240 DATA SCALING SOFTWARE : SCALEPACK REMARK 240 COMPLETENESS FOR RANGE (%) : 84.5 REMARK 240 DATA REDUNDANCY : 4.600 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.00 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.08 REMARK 240 COMPLETENESS FOR SHELL (%) : 66.0 REMARK 240 DATA REDUNDANCY IN SHELL : 3.30 REMARK 240 R MERGE FOR SHELL (I) : 0.28200 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 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 2.46600 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 300 REMARK: THE BIOLOGICAL UNIT IS AN EXTENDED PAIR OF BETA SHEETS REMARK 300 COMPRISING PEPTIDES AT POSITIONS X,Y,Z AND -X,Y+1/2,-Z EXTENDED AD REMARK 300 INFINITUM ALONG THE B CRYSTAL AXIS. 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: OCTADECAMERIC 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -19.72800 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 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -14.79600 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 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 -9.86400 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 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 -4.93200 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 0.00000 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 4.93200 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 0.00000 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 9.86400 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 0.00000 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 14.79600 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 0.00000 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 19.72800 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 0.00000 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 -17.26200 REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 11 0.000000 1.000000 0.000000 -12.33000 REMARK 350 BIOMT3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 12 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 12 0.000000 1.000000 0.000000 -7.39800 REMARK 350 BIOMT3 12 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 13 0.000000 1.000000 0.000000 -2.46600 REMARK 350 BIOMT3 13 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 14 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 14 0.000000 1.000000 0.000000 2.46600 REMARK 350 BIOMT3 14 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 15 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 15 0.000000 1.000000 0.000000 7.39800 REMARK 350 BIOMT3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 16 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 16 0.000000 1.000000 0.000000 12.33000 REMARK 350 BIOMT3 16 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 17 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 17 0.000000 1.000000 0.000000 17.26200 REMARK 350 BIOMT3 17 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 18 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 18 0.000000 1.000000 0.000000 22.19400 REMARK 350 BIOMT3 18 0.000000 0.000000 -1.000000 0.00000 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 101 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 1 N REMARK 620 2 TYR A 6 O 78.5 REMARK 620 3 TYR A 6 OXT 84.0 5.8 REMARK 620 4 ACT A 102 OXT 81.5 3.0 3.2 REMARK 620 5 ACT A 102 O 80.7 8.2 6.9 8.1 REMARK 620 6 HOH A 201 O 76.5 8.0 9.5 9.3 4.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-8197 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8196 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8198 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8199 RELATED DB: EMDB REMARK 900 RELATED ID: 5K2E RELATED DB: PDB REMARK 900 NNQQNY FROM YEAST PRION SUP35 WITH ZINC REMARK 900 RELATED ID: 5K2G RELATED DB: PDB REMARK 900 GNNQQNY FROM YEAST PRION SUP35 IN SPACE GROUP P21 REMARK 900 RELATED ID: 5K2H RELATED DB: PDB REMARK 900 GNNQQNY FROM YEAST PRION SUP35 IN SPACE GROUP P212121 DBREF 5K2F A 1 6 UNP P05453 ERF3_YEAST 8 13 SEQRES 1 A 6 ASN ASN GLN GLN ASN TYR HET CD A 101 1 HET ACT A 102 7 HETNAM CD CADMIUM ION HETNAM ACT ACETATE ION FORMUL 2 CD CD 2+ FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *7(H2 O) LINK N ASN A 1 CD CD A 101 1555 1455 2.36 LINK O TYR A 6 CD CD A 101 1555 1555 2.47 LINK OXT TYR A 6 CD CD A 101 1555 1555 2.48 LINK CD CD A 101 OXT ACT A 102 1555 1555 2.23 LINK CD CD A 101 O ACT A 102 1555 1565 2.12 LINK CD CD A 101 O HOH A 201 1555 1555 2.63 SITE 1 AC1 3 TYR A 6 ACT A 102 HOH A 201 SITE 1 AC2 2 TYR A 6 CD A 101 CRYST1 22.074 4.932 23.510 90.00 104.29 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 0.045302 0.000000 0.011537 0.00000 SCALE2 0.000000 0.202757 0.000000 0.00000 SCALE3 0.000000 0.000000 0.043893 0.00000 MASTER 260 0 2 0 0 0 2 6 0 0 0 1 END