HEADER PROTEIN FIBRIL 16-SEP-22 8B3A TITLE CATALYTIC AMYLOID FIBRIL FORMED BY AC-LHLHLRL-AMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, COMPND 4 V, W, X, Y, Z, a, b, c, d; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS CATALYTIC AMYLOID FIBRIL, PROTEIN FIBRIL, ZINC BINDING, PRION EXPDTA ELECTRON MICROSCOPY AUTHOR T.HEERDE,M.SCHMIDT,M.FAENDRICH REVDAT 1 05-APR-23 8B3A 0 JRNL AUTH T.HEERDE,A.BANSAL,M.SCHMIDT,M.FANDRICH JRNL TITL CRYO-EM STRUCTURE OF A CATALYTIC AMYLOID FIBRIL. JRNL REF SCI REP V. 13 4070 2023 JRNL REFN ESSN 2045-2322 JRNL PMID 36906667 JRNL DOI 10.1038/S41598-023-30711-Y REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, GCTF, COOT, PHENIX, RELION, REMARK 3 RELION REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : BACKBONE TRACE REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 38413 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8B3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292122562. 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 : HELICAL ARRAY REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : CATALYTIC AMYLOID REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.05 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 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) : 300 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: 30-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K, L, M, N, O, P, Q, R, S, REMARK 350 AND CHAINS: T, U, V, W, X, Y, Z, a, b, c, REMARK 350 AND CHAINS: d 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-15824 RELATED DB: EMDB REMARK 900 CATALYTIC AMYLOID FIBRIL FORMED BY AC-LHLHLRL-AMIDE DBREF 8B3A A 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A B 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A C 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A D 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A E 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A F 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A G 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A H 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A I 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A J 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A K 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A L 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A M 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A N 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A O 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A P 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A Q 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A R 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A S 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A T 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A U 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A V 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A W 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A X 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A Y 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A Z 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A a 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A b 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A c 0 8 PDB 8B3A 8B3A 0 8 DBREF 8B3A d 0 8 PDB 8B3A 8B3A 0 8 SEQRES 1 A 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 B 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 C 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 D 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 E 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 F 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 G 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 H 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 I 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 J 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 K 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 L 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 M 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 N 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 O 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 P 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 Q 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 R 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 S 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 T 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 U 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 V 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 W 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 X 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 Y 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 Z 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 a 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 b 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 c 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 SEQRES 1 d 9 ACE LEU HIS LEU HIS LEU ARG LEU NH2 HET ACE A 0 3 HET NH2 A 8 1 HET ACE B 0 3 HET NH2 B 8 1 HET ACE C 0 3 HET NH2 C 8 1 HET ACE D 0 3 HET NH2 D 8 1 HET ACE E 0 3 HET NH2 E 8 1 HET ACE F 0 3 HET NH2 F 8 1 HET ACE G 0 3 HET NH2 G 8 1 HET ACE H 0 3 HET NH2 H 8 1 HET ACE I 0 3 HET NH2 I 8 1 HET ACE J 0 3 HET NH2 J 8 1 HET ACE K 0 3 HET NH2 K 8 1 HET ACE L 0 3 HET NH2 L 8 1 HET ACE M 0 3 HET NH2 M 8 1 HET ACE N 0 3 HET NH2 N 8 1 HET ACE O 0 3 HET NH2 O 8 1 HET ACE P 0 3 HET NH2 P 8 1 HET ACE Q 0 3 HET NH2 Q 8 1 HET ACE R 0 3 HET NH2 R 8 1 HET ACE S 0 3 HET NH2 S 8 1 HET ACE T 0 3 HET NH2 T 8 1 HET ACE U 0 3 HET NH2 U 8 1 HET ACE V 0 3 HET NH2 V 8 1 HET ACE W 0 3 HET NH2 W 8 1 HET ACE X 0 3 HET NH2 X 8 1 HET ACE Y 0 3 HET NH2 Y 8 1 HET ACE Z 0 3 HET NH2 Z 8 1 HET ACE a 0 3 HET NH2 a 8 1 HET ACE b 0 3 HET NH2 b 8 1 HET ACE c 0 3 HET NH2 c 8 1 HET ACE d 0 3 HET NH2 d 8 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 1 ACE 30(C2 H4 O) FORMUL 1 NH2 30(H2 N) SHEET 1 AA1 5 HIS A 2 HIS A 4 0 SHEET 2 AA1 5 HIS G 2 HIS G 4 1 O HIS G 4 N LEU A 3 SHEET 3 AA1 5 HIS M 2 HIS M 4 1 O HIS M 4 N LEU G 3 SHEET 4 AA1 5 HIS S 2 HIS S 4 1 O HIS S 4 N LEU M 3 SHEET 5 AA1 5 HIS Y 2 HIS Y 4 1 O HIS Y 4 N LEU S 3 SHEET 1 AA2 5 HIS B 2 HIS B 4 0 SHEET 2 AA2 5 HIS H 2 HIS H 4 1 O HIS H 4 N LEU B 3 SHEET 3 AA2 5 HIS N 2 HIS N 4 1 O HIS N 4 N LEU H 3 SHEET 4 AA2 5 HIS T 2 HIS T 4 1 O HIS T 4 N LEU N 3 SHEET 5 AA2 5 HIS Z 2 HIS Z 4 1 O HIS Z 4 N LEU T 3 SHEET 1 AA3 5 HIS C 2 ARG C 6 0 SHEET 2 AA3 5 HIS I 2 ARG I 6 1 O HIS I 4 N LEU C 3 SHEET 3 AA3 5 HIS O 2 ARG O 6 1 O HIS O 4 N LEU I 3 SHEET 4 AA3 5 HIS U 2 ARG U 6 1 O HIS U 4 N LEU O 3 SHEET 5 AA3 5 HIS a 2 ARG a 6 1 O HIS a 4 N LEU U 3 SHEET 1 AA4 5 HIS D 2 ARG D 6 0 SHEET 2 AA4 5 HIS J 2 ARG J 6 1 O HIS J 4 N LEU D 3 SHEET 3 AA4 5 HIS P 2 ARG P 6 1 O HIS P 4 N LEU J 3 SHEET 4 AA4 5 HIS V 2 ARG V 6 1 O HIS V 4 N LEU P 3 SHEET 5 AA4 5 HIS b 2 ARG b 6 1 O HIS b 4 N LEU V 3 SHEET 1 AA5 5 HIS E 2 ARG E 6 0 SHEET 2 AA5 5 HIS K 2 ARG K 6 1 O HIS K 4 N LEU E 3 SHEET 3 AA5 5 HIS Q 2 ARG Q 6 1 O HIS Q 4 N LEU K 3 SHEET 4 AA5 5 HIS W 2 ARG W 6 1 O HIS W 4 N LEU Q 3 SHEET 5 AA5 5 HIS c 2 ARG c 6 1 O HIS c 4 N LEU W 3 SHEET 1 AA6 5 HIS F 2 ARG F 6 0 SHEET 2 AA6 5 HIS L 2 ARG L 6 1 O HIS L 4 N LEU F 3 SHEET 3 AA6 5 HIS R 2 ARG R 6 1 O HIS R 4 N LEU L 3 SHEET 4 AA6 5 HIS X 2 ARG X 6 1 O HIS X 4 N LEU R 3 SHEET 5 AA6 5 HIS d 2 ARG d 6 1 O HIS d 4 N LEU X 3 LINK C ACE A 0 N LEU A 1 1555 1555 1.33 LINK C LEU A 7 N NH2 A 8 1555 1555 1.33 LINK C ACE B 0 N LEU B 1 1555 1555 1.33 LINK C LEU B 7 N NH2 B 8 1555 1555 1.33 LINK C ACE C 0 N LEU C 1 1555 1555 1.34 LINK C LEU C 7 N NH2 C 8 1555 1555 1.33 LINK C ACE D 0 N LEU D 1 1555 1555 1.33 LINK C LEU D 7 N NH2 D 8 1555 1555 1.33 LINK C ACE E 0 N LEU E 1 1555 1555 1.33 LINK C LEU E 7 N NH2 E 8 1555 1555 1.33 LINK C ACE F 0 N LEU F 1 1555 1555 1.34 LINK C LEU F 7 N NH2 F 8 1555 1555 1.33 LINK C ACE G 0 N LEU G 1 1555 1555 1.33 LINK C LEU G 7 N NH2 G 8 1555 1555 1.33 LINK C ACE H 0 N LEU H 1 1555 1555 1.33 LINK C LEU H 7 N NH2 H 8 1555 1555 1.33 LINK C ACE I 0 N LEU I 1 1555 1555 1.33 LINK C LEU I 7 N NH2 I 8 1555 1555 1.33 LINK C ACE J 0 N LEU J 1 1555 1555 1.33 LINK C LEU J 7 N NH2 J 8 1555 1555 1.33 LINK C ACE K 0 N LEU K 1 1555 1555 1.33 LINK C LEU K 7 N NH2 K 8 1555 1555 1.33 LINK C ACE L 0 N LEU L 1 1555 1555 1.33 LINK C LEU L 7 N NH2 L 8 1555 1555 1.33 LINK C ACE M 0 N LEU M 1 1555 1555 1.33 LINK C LEU M 7 N NH2 M 8 1555 1555 1.33 LINK C ACE N 0 N LEU N 1 1555 1555 1.33 LINK C LEU N 7 N NH2 N 8 1555 1555 1.33 LINK C ACE O 0 N LEU O 1 1555 1555 1.33 LINK C LEU O 7 N NH2 O 8 1555 1555 1.33 LINK C ACE P 0 N LEU P 1 1555 1555 1.33 LINK C LEU P 7 N NH2 P 8 1555 1555 1.33 LINK C ACE Q 0 N LEU Q 1 1555 1555 1.33 LINK C LEU Q 7 N NH2 Q 8 1555 1555 1.33 LINK C ACE R 0 N LEU R 1 1555 1555 1.33 LINK C LEU R 7 N NH2 R 8 1555 1555 1.33 LINK C ACE S 0 N LEU S 1 1555 1555 1.33 LINK C LEU S 7 N NH2 S 8 1555 1555 1.33 LINK C ACE T 0 N LEU T 1 1555 1555 1.33 LINK C LEU T 7 N NH2 T 8 1555 1555 1.33 LINK C ACE U 0 N LEU U 1 1555 1555 1.33 LINK C LEU U 7 N NH2 U 8 1555 1555 1.33 LINK C ACE V 0 N LEU V 1 1555 1555 1.33 LINK C LEU V 7 N NH2 V 8 1555 1555 1.33 LINK C ACE W 0 N LEU W 1 1555 1555 1.34 LINK C LEU W 7 N NH2 W 8 1555 1555 1.33 LINK C ACE X 0 N LEU X 1 1555 1555 1.33 LINK C LEU X 7 N NH2 X 8 1555 1555 1.33 LINK C ACE Y 0 N LEU Y 1 1555 1555 1.33 LINK C LEU Y 7 N NH2 Y 8 1555 1555 1.33 LINK C ACE Z 0 N LEU Z 1 1555 1555 1.33 LINK C LEU Z 7 N NH2 Z 8 1555 1555 1.33 LINK C ACE a 0 N LEU a 1 1555 1555 1.33 LINK C LEU a 7 N NH2 a 8 1555 1555 1.33 LINK C ACE b 0 N LEU b 1 1555 1555 1.33 LINK C LEU b 7 N NH2 b 8 1555 1555 1.33 LINK C ACE c 0 N LEU c 1 1555 1555 1.33 LINK C LEU c 7 N NH2 c 8 1555 1555 1.33 LINK C ACE d 0 N LEU d 1 1555 1555 1.33 LINK C LEU d 7 N NH2 d 8 1555 1555 1.33 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 HETATM 1 C ACE A 0 91.751 96.572 94.902 1.00 0.00 C HETATM 2 O ACE A 0 91.446 95.406 95.063 1.00 0.00 O HETATM 3 CH3 ACE A 0 90.963 97.596 94.123 1.00 0.00 C