HEADER PROTEIN FIBRIL 19-JAN-22 7QV6 TITLE AMYLOID FIBRIL FROM THE ANTIMICROBIAL PEPTIDE AUREIN 3.3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUREIN-3.3; COMPND 3 CHAIN: B, A, E, D, C, F, H, G, K, J, I, L, N, M, Q, P, O, R; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: RANOIDEA RANIFORMIS; SOURCE 4 ORGANISM_COMMON: BLUE-THIGHED TREEFROG; SOURCE 5 ORGANISM_TAXID: 116057 KEYWDS ANTIMICROBIAL PEPTIDE, AMYLOID, FILAMENT, CROSS-BETA, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR R.BUECKER,C.SEURING,C.CAZEY,K.VEITH,M.GARCIA-ALAI,K.GRUENEWALD, AUTHOR 2 M.LANDAU REVDAT 2 10-AUG-22 7QV6 1 JRNL REVDAT 1 29-JUN-22 7QV6 0 JRNL AUTH R.BUCKER,C.SEURING,C.CAZEY,K.VEITH,M.GARCIA-ALAI, JRNL AUTH 2 K.GRUNEWALD,M.LANDAU JRNL TITL THE CRYO-EM STRUCTURES OF TWO AMPHIBIAN ANTIMICROBIAL JRNL TITL 2 CROSS-BETA AMYLOID FIBRILS. JRNL REF NAT COMMUN V. 13 4356 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35896552 JRNL DOI 10.1038/S41467-022-32039-Z REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, DIGITALMICROGRAPH, RELION, UCSF REMARK 3 CHIMERAX, COOT, CRYOSPARC, RELION, REMARK 3 RELION, RELION, RELION, PHENIX, ISOLDE 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 : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CC REMARK 3 OVERALL ANISOTROPIC B VALUE : 78.370 REMARK 3 REMARK 3 FITTING PROCEDURE : - INITIAL MODEL BUILDING OF A SINGLE HELICAL REMARK 3 LAYER USING CHIMERAX AND COOT - EXPANSION TO THREE LAYERS, REMARK 3 REFINEMENT IN ISOLDE - TRUNCATION OF OUTER LAYERS, RE-EXPANSION REMARK 3 TO THREE LAYERS, REFINEMENT USING PHENIX.REAL_SPACE_REFINE 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 35289 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 7QV6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1292120105. 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 : AUREIN 3.3 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 5.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : WAIT TIME 15S AFTER REMARK 245 APPLICATION, BLOT TIME 4S REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 5514 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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 : 105000 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: OCTADECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, E, D, C, F, H, G, K, J, REMARK 350 AND CHAINS: I, L, N, M, Q, P, O, R 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-14168 RELATED DB: EMDB REMARK 900 AMYLOID FIBRIL FROM THE ANTIMICROBIAL PEPTIDE AUREIN 3.3 DBREF 7QV6 B 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 A 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 E 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 D 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 C 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 F 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 H 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 G 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 K 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 J 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 I 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 L 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 N 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 M 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 Q 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 P 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 O 1 17 UNP P82396 AUR33_RANRN 1 17 DBREF 7QV6 R 1 17 UNP P82396 AUR33_RANRN 1 17 SEQRES 1 B 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 B 17 VAL SER SER ILE SEQRES 1 A 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 A 17 VAL SER SER ILE SEQRES 1 E 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 E 17 VAL SER SER ILE SEQRES 1 D 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 D 17 VAL SER SER ILE SEQRES 1 C 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 C 17 VAL SER SER ILE SEQRES 1 F 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 F 17 VAL SER SER ILE SEQRES 1 H 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 H 17 VAL SER SER ILE SEQRES 1 G 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 G 17 VAL SER SER ILE SEQRES 1 K 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 K 17 VAL SER SER ILE SEQRES 1 J 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 J 17 VAL SER SER ILE SEQRES 1 I 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 I 17 VAL SER SER ILE SEQRES 1 L 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 L 17 VAL SER SER ILE SEQRES 1 N 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 N 17 VAL SER SER ILE SEQRES 1 M 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 M 17 VAL SER SER ILE SEQRES 1 Q 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 Q 17 VAL SER SER ILE SEQRES 1 P 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 P 17 VAL SER SER ILE SEQRES 1 O 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 O 17 VAL SER SER ILE SEQRES 1 R 17 GLY LEU PHE ASP ILE VAL LYS LYS ILE ALA GLY HIS ILE SEQRES 2 R 17 VAL SER SER ILE SHEET 1 AA1 3 LEU B 2 ALA B 10 0 SHEET 2 AA1 3 LEU H 2 ALA H 10 1 O PHE H 3 N ASP B 4 SHEET 3 AA1 3 LEU N 2 ALA N 10 1 O PHE N 3 N ASP H 4 SHEET 1 AA2 3 ILE B 13 SER B 16 0 SHEET 2 AA2 3 ILE H 13 SER H 16 1 O SER H 16 N SER B 15 SHEET 3 AA2 3 ILE N 13 SER N 16 1 O SER N 16 N SER H 15 SHEET 1 AA3 3 LEU A 2 LYS A 8 0 SHEET 2 AA3 3 LEU G 2 LYS G 8 1 O VAL G 6 N ILE A 5 SHEET 3 AA3 3 LEU M 2 LYS M 8 1 O VAL M 6 N ILE G 5 SHEET 1 AA4 3 ILE A 13 VAL A 14 0 SHEET 2 AA4 3 ILE G 13 VAL G 14 1 O ILE G 13 N VAL A 14 SHEET 3 AA4 3 ILE M 13 VAL M 14 1 O ILE M 13 N VAL G 14 SHEET 1 AA5 3 ILE E 5 LYS E 7 0 SHEET 2 AA5 3 ILE K 5 LYS K 7 1 O ILE K 5 N VAL E 6 SHEET 3 AA5 3 ILE Q 5 LYS Q 7 1 O ILE Q 5 N VAL K 6 SHEET 1 AA6 3 ALA E 10 HIS E 12 0 SHEET 2 AA6 3 ALA K 10 HIS K 12 1 O GLY K 11 N ALA E 10 SHEET 3 AA6 3 ALA Q 10 HIS Q 12 1 O GLY Q 11 N ALA K 10 SHEET 1 AA7 3 LEU D 2 SER D 16 0 SHEET 2 AA7 3 LEU J 2 SER J 16 1 O SER J 16 N SER D 15 SHEET 3 AA7 3 LEU P 2 SER P 16 1 O SER P 16 N SER J 15 SHEET 1 AA8 3 PHE C 3 SER C 15 0 SHEET 2 AA8 3 PHE I 3 SER I 15 1 O ASP I 4 N PHE C 3 SHEET 3 AA8 3 PHE O 3 SER O 15 1 O ASP O 4 N PHE I 3 SHEET 1 AA9 3 PHE F 3 SER F 15 0 SHEET 2 AA9 3 PHE L 3 SER L 15 1 O ILE L 5 N VAL F 6 SHEET 3 AA9 3 PHE R 3 SER R 15 1 O ILE R 5 N VAL L 6 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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