HEADER PROTEIN FIBRIL 14-MAY-25 9R7E TITLE CRYO-EM STRUCTURE OF CATALYTIC AMYLOIDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO; COMPND 3 CHAIN: A, B, C, D, E, F, G, L, M, N, O, P, Q, R, S, T; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ANAERAMOEBA IGNAVA; SOURCE 4 ORGANISM_TAXID: 1746090 KEYWDS ALLOSTERIC AMYLOID COILED-COIL FIBRILS, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR A.SHAHAR,R.ZALK,E.ARAD REVDAT 1 11-JUN-25 9R7E 0 JRNL AUTH S.M.KUNNATH,E.ARAD,R.ZALK,I.KASS,A.SHAHAR,A.BATUSHANSKY, JRNL AUTH 2 H.RAPAPORT,R.JELINEK JRNL TITL ALLOSTERIC AMYLOID CATALYSIS BY COILED COIL FIBRILS. JRNL REF NAT COMMUN V. 16 5071 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40450012 JRNL DOI 10.1038/S41467-025-60379-Z REMARK 2 REMARK 2 RESOLUTION. 5.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 5.000 REMARK 3 NUMBER OF PARTICLES : 507432 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9R7E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1292147872. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : PFK REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS GLACIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: 16-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 16-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, L, M, N, REMARK 350 AND CHAINS: O, P, Q, R, S, T 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: 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 PHE A 3 CG PHE A 3 CD2 0.531 REMARK 500 PHE A 3 CG PHE A 3 CD1 0.509 REMARK 500 PHE A 3 CD1 PHE A 3 CE1 0.628 REMARK 500 PHE A 3 CE1 PHE A 3 CZ 0.922 REMARK 500 PHE A 3 CZ PHE A 3 CE2 0.861 REMARK 500 PHE A 3 CE2 PHE A 3 CD2 0.625 REMARK 500 PHE B 11 CB PHE B 11 CG 0.746 REMARK 500 PHE B 11 CG PHE B 11 CD2 0.123 REMARK 500 PHE B 11 CG PHE B 11 CD1 0.120 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 PHE A 9 N - CA - CB ANGL. DEV. = -11.2 DEGREES REMARK 500 PHE B 11 CA - CB - CG ANGL. DEV. = 34.0 DEGREES REMARK 500 PHE B 11 CB - CG - CD2 ANGL. DEV. = 13.6 DEGREES REMARK 500 PHE B 11 CD1 - CG - CD2 ANGL. DEV. = -29.1 DEGREES REMARK 500 PHE B 11 CB - CG - CD1 ANGL. DEV. = 15.5 DEGREES REMARK 500 PHE B 11 CG - CD1 - CE1 ANGL. DEV. = 16.2 DEGREES REMARK 500 PHE B 11 CG - CD2 - CE2 ANGL. DEV. = 16.4 DEGREES REMARK 500 PHE M 9 N - CA - CB ANGL. DEV. = -11.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-53305 RELATED DB: EMDB DBREF 9R7E A 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E B 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E C 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E D 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E E 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E F 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E G 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E L 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E M 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E N 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E O 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E P 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E Q 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E R 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E S 1 13 PDB 9R7E 9R7E 1 13 DBREF 9R7E T 1 13 PDB 9R7E 9R7E 1 13 SEQRES 1 A 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 B 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 C 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 D 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 E 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 F 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 G 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 L 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 M 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 N 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 O 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 P 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 Q 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 R 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 S 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO SEQRES 1 T 13 PRO LYS PHE LYS PHE LYS PHE LYS PHE LYS PHE LYS PRO HET NEF B 101 36 HET NEF D 101 36 HET NEF R 101 36 HET NEF S 101 36 HETNAM NEF NITROCEFIN - OPEN FORM HETSYN NEF (2R)-5-[(E)-2-(2,4-DINITROPHENYL)ETHENYL]-2-[(1R)-2- HETSYN 2 NEF OXIDANYL-2-OXIDANYLIDENE-1-(2-THIOPHEN-2- HETSYN 3 NEF YLETHANOYLAMINO)ETHYL]-3,6-DIHYDRO-2H-1,3-THIAZINE-4- HETSYN 4 NEF CARBOXYLIC ACID FORMUL 17 NEF 4(C21 H18 N4 O9 S2) SHEET 1 AA1 4 LYS A 2 PHE A 11 0 SHEET 2 AA1 4 PHE B 3 LYS B 12 -1 O LYS B 8 N LYS A 6 SHEET 3 AA1 4 PHE C 3 PHE C 11 1 O LYS C 4 N PHE B 5 SHEET 4 AA1 4 PHE D 3 PHE D 11 -1 O PHE D 9 N PHE C 5 SHEET 1 AA2 4 PHE E 3 PHE E 11 0 SHEET 2 AA2 4 LYS G 2 PHE G 11 -1 O PHE G 5 N PHE E 9 SHEET 3 AA2 4 PHE F 3 LYS F 12 -1 N LYS F 6 O LYS G 8 SHEET 4 AA2 4 LYS L 4 PHE L 11 -1 O PHE L 11 N PHE F 3 SHEET 1 AA3 4 LYS M 2 PHE M 11 0 SHEET 2 AA3 4 PHE N 3 LYS N 12 -1 O LYS N 8 N LYS M 6 SHEET 3 AA3 4 PHE O 3 PHE O 11 1 O LYS O 10 N PHE N 9 SHEET 4 AA3 4 PHE P 3 PHE P 11 -1 O PHE P 9 N PHE O 5 SHEET 1 AA4 4 PHE Q 3 PHE Q 11 0 SHEET 2 AA4 4 PHE S 3 LYS S 12 -1 O PHE S 5 N PHE Q 9 SHEET 3 AA4 4 LYS R 2 PHE R 11 -1 N LYS R 10 O LYS S 4 SHEET 4 AA4 4 PHE T 3 PHE T 11 -1 O PHE T 11 N PHE R 3 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 CONECT 2001 2003 2013 CONECT 2002 2008 2014 2016 CONECT 2003 2001 2004 2010 CONECT 2004 2003 2025 CONECT 2005 2006 2017 CONECT 2006 2005 2019 2021 CONECT 2007 2020 2021 CONECT 2008 2002 2013 2022 CONECT 2009 2012 2025 2029 CONECT 2010 2003 2011 2022 CONECT 2011 2010 2023 2024 CONECT 2012 2009 2026 CONECT 2013 2001 2008 CONECT 2014 2002 2015 2036 CONECT 2015 2014 CONECT 2016 2002 2017 CONECT 2017 2005 2016 2018 CONECT 2018 2017 CONECT 2019 2006 2020 CONECT 2020 2007 2019 CONECT 2021 2006 2007 CONECT 2022 2008 2010 CONECT 2023 2011 CONECT 2024 2011 CONECT 2025 2004 2009 CONECT 2026 2012 2027 CONECT 2027 2026 2028 2031 CONECT 2028 2027 2029 CONECT 2029 2009 2028 2030 CONECT 2030 2029 2032 2033 CONECT 2031 2027 2034 2035 CONECT 2032 2030 CONECT 2033 2030 CONECT 2034 2031 CONECT 2035 2031 CONECT 2036 2014 CONECT 2037 2039 2049 CONECT 2038 2044 2050 2052 CONECT 2039 2037 2040 2046 CONECT 2040 2039 2061 CONECT 2041 2042 2053 CONECT 2042 2041 2055 2057 CONECT 2043 2056 2057 CONECT 2044 2038 2049 2058 CONECT 2045 2048 2061 2065 CONECT 2046 2039 2047 2058 CONECT 2047 2046 2059 2060 CONECT 2048 2045 2062 CONECT 2049 2037 2044 CONECT 2050 2038 2051 2072 CONECT 2051 2050 CONECT 2052 2038 2053 CONECT 2053 2041 2052 2054 CONECT 2054 2053 CONECT 2055 2042 2056 CONECT 2056 2043 2055 CONECT 2057 2042 2043 CONECT 2058 2044 2046 CONECT 2059 2047 CONECT 2060 2047 CONECT 2061 2040 2045 CONECT 2062 2048 2063 CONECT 2063 2062 2064 2067 CONECT 2064 2063 2065 CONECT 2065 2045 2064 2066 CONECT 2066 2065 2068 2069 CONECT 2067 2063 2070 2071 CONECT 2068 2066 CONECT 2069 2066 CONECT 2070 2067 CONECT 2071 2067 CONECT 2072 2050 CONECT 2073 2075 2085 CONECT 2074 2080 2086 2088 CONECT 2075 2073 2076 2082 CONECT 2076 2075 2097 CONECT 2077 2078 2089 CONECT 2078 2077 2091 2093 CONECT 2079 2092 2093 CONECT 2080 2074 2085 2094 CONECT 2081 2084 2097 2101 CONECT 2082 2075 2083 2094 CONECT 2083 2082 2095 2096 CONECT 2084 2081 2098 CONECT 2085 2073 2080 CONECT 2086 2074 2087 2108 CONECT 2087 2086 CONECT 2088 2074 2089 CONECT 2089 2077 2088 2090 CONECT 2090 2089 CONECT 2091 2078 2092 CONECT 2092 2079 2091 CONECT 2093 2078 2079 CONECT 2094 2080 2082 CONECT 2095 2083 CONECT 2096 2083 CONECT 2097 2076 2081 CONECT 2098 2084 2099 CONECT 2099 2098 2100 2103 CONECT 2100 2099 2101 CONECT 2101 2081 2100 2102 CONECT 2102 2101 2104 2105 CONECT 2103 2099 2106 2107 CONECT 2104 2102 CONECT 2105 2102 CONECT 2106 2103 CONECT 2107 2103 CONECT 2108 2086 CONECT 2109 2111 2121 CONECT 2110 2116 2122 2124 CONECT 2111 2109 2112 2118 CONECT 2112 2111 2133 CONECT 2113 2114 2125 CONECT 2114 2113 2127 2129 CONECT 2115 2128 2129 CONECT 2116 2110 2121 2130 CONECT 2117 2120 2133 2137 CONECT 2118 2111 2119 2130 CONECT 2119 2118 2131 2132 CONECT 2120 2117 2134 CONECT 2121 2109 2116 CONECT 2122 2110 2123 2144 CONECT 2123 2122 CONECT 2124 2110 2125 CONECT 2125 2113 2124 2126 CONECT 2126 2125 CONECT 2127 2114 2128 CONECT 2128 2115 2127 CONECT 2129 2114 2115 CONECT 2130 2116 2118 CONECT 2131 2119 CONECT 2132 2119 CONECT 2133 2112 2117 CONECT 2134 2120 2135 CONECT 2135 2134 2136 2139 CONECT 2136 2135 2137 CONECT 2137 2117 2136 2138 CONECT 2138 2137 2140 2141 CONECT 2139 2135 2142 2143 CONECT 2140 2138 CONECT 2141 2138 CONECT 2142 2139 CONECT 2143 2139 CONECT 2144 2122 MASTER 151 0 4 0 16 0 0 6 2128 16 144 16 END