HEADER ANTIMICROBIAL PROTEIN 05-JUN-25 9RFV TITLE CRYO-EM STRUCTURE OF AMYLOIDOGENIC ANTIMICROBIAL PEPTIDE AUREIN 1.2 TITLE 2 POLYMORPH 2 IN AQUEOUS SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUREIN-1.2; COMPND 3 CHAIN: A, C, D, E, G, H, I, K, L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: AUREIN-1.2; COMPND 7 CHAIN: B, F, J; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RANOIDEA AUREA; SOURCE 3 ORGANISM_COMMON: GREEN AND GOLDEN BELL FROG; SOURCE 4 ORGANISM_TAXID: 8371; SOURCE 5 EXPRESSION_SYSTEM: RANOIDEA AUREA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 8371; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: RANOIDEA AUREA; SOURCE 9 ORGANISM_COMMON: GREEN AND GOLDEN BELL FROG; SOURCE 10 ORGANISM_TAXID: 8371; SOURCE 11 EXPRESSION_SYSTEM: RANOIDEA AUREA; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 8371 KEYWDS AMYLOID, ANTIMICROBIAL, ANTIMICROBIAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR P.RAGONIS-BACHAR,F.STRATI,E.GUSTAVSSON,A.KHOKHLOV,E.BARNEA,B.RAYAN, AUTHOR 2 A.UPCHR,M.LANDAU,S.BANERJEE REVDAT 1 26-AUG-26 9RFV 0 JRNL AUTH P.RAGONIS-BACHAR,F.STRATI,E.GUSTAVSSON,A.KHOKHLOV,E.BARNEA, JRNL AUTH 2 B.RAYAN,A.UPCHR,M.LANDAU,S.BANERJEE JRNL TITL AMYLOIDOGENIC NATURE AND STRUCTURAL POLYMORPHISM OF JRNL TITL 2 ANTIMICROBIAL, VIRULENT AND DEFENSE PEPTIDES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, EPU, CTFFIND, COOT, SERVALCAT, REMARK 3 RELION, RELION, RELION, 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 : NULL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT 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) : 3.780 REMARK 3 NUMBER OF PARTICLES : 90810 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 9RFV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1292148156. 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 1.2 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 : 5.50 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 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) : 3500.00 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) : 5000.00 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K, L 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: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 8 -74.81 -135.41 REMARK 500 GLU B 11 43.84 -151.01 REMARK 500 LYS E 8 -46.10 -143.45 REMARK 500 LYS F 8 45.78 -85.69 REMARK 500 GLU F 11 32.24 -156.12 REMARK 500 LYS I 8 -53.89 -133.17 REMARK 500 LYS J 8 34.47 -88.38 REMARK 500 GLU J 11 29.44 -149.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-53942 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF AMYLOIDOGENIC ANTIMICROBIAL PEPTIDE AUREIN 1.2 REMARK 900 POLYMORPH 2 IN AQUEOUS SOLUTION DBREF 9RFV A 4 13 UNP P82387 AUR12_RANRN 4 13 DBREF 9RFV B 3 13 UNP P82387 AUR12_RANRN 3 13 DBREF 9RFV C 4 13 UNP P82387 AUR12_RANRN 4 13 DBREF 9RFV D 4 13 UNP P82387 AUR12_RANRN 4 13 DBREF 9RFV E 4 13 UNP P82387 AUR12_RANRN 4 13 DBREF 9RFV F 3 13 UNP P82387 AUR12_RANRN 3 13 DBREF 9RFV G 4 13 UNP P82387 AUR12_RANRN 4 13 DBREF 9RFV H 4 13 UNP P82387 AUR12_RANRN 4 13 DBREF 9RFV I 4 13 UNP P82387 AUR12_RANRN 4 13 DBREF 9RFV J 3 13 UNP P82387 AUR12_RANRN 3 13 DBREF 9RFV K 4 13 UNP P82387 AUR12_RANRN 4 13 DBREF 9RFV L 4 13 UNP P82387 AUR12_RANRN 4 13 SEQADV 9RFV NH2 A 14 UNP P82387 AMIDATION SEQADV 9RFV NH2 B 14 UNP P82387 AMIDATION SEQADV 9RFV NH2 C 14 UNP P82387 AMIDATION SEQADV 9RFV NH2 D 14 UNP P82387 AMIDATION SEQADV 9RFV NH2 E 14 UNP P82387 AMIDATION SEQADV 9RFV NH2 F 14 UNP P82387 AMIDATION SEQADV 9RFV NH2 G 14 UNP P82387 AMIDATION SEQADV 9RFV NH2 H 14 UNP P82387 AMIDATION SEQADV 9RFV NH2 I 14 UNP P82387 AMIDATION SEQADV 9RFV NH2 J 14 UNP P82387 AMIDATION SEQADV 9RFV NH2 K 14 UNP P82387 AMIDATION SEQADV 9RFV NH2 L 14 UNP P82387 AMIDATION SEQRES 1 A 11 ASP ILE ILE LYS LYS ILE ALA GLU SER PHE NH2 SEQRES 1 B 12 PHE ASP ILE ILE LYS LYS ILE ALA GLU SER PHE NH2 SEQRES 1 C 11 ASP ILE ILE LYS LYS ILE ALA GLU SER PHE NH2 SEQRES 1 D 11 ASP ILE ILE LYS LYS ILE ALA GLU SER PHE NH2 SEQRES 1 E 11 ASP ILE ILE LYS LYS ILE ALA GLU SER PHE NH2 SEQRES 1 F 12 PHE ASP ILE ILE LYS LYS ILE ALA GLU SER PHE NH2 SEQRES 1 G 11 ASP ILE ILE LYS LYS ILE ALA GLU SER PHE NH2 SEQRES 1 H 11 ASP ILE ILE LYS LYS ILE ALA GLU SER PHE NH2 SEQRES 1 I 11 ASP ILE ILE LYS LYS ILE ALA GLU SER PHE NH2 SEQRES 1 J 12 PHE ASP ILE ILE LYS LYS ILE ALA GLU SER PHE NH2 SEQRES 1 K 11 ASP ILE ILE LYS LYS ILE ALA GLU SER PHE NH2 SEQRES 1 L 11 ASP ILE ILE LYS LYS ILE ALA GLU SER PHE NH2 HET NH2 A 14 3 HET NH2 B 14 3 HET NH2 C 14 3 HET NH2 D 14 3 HET NH2 E 14 3 HET NH2 F 14 3 HET NH2 G 14 3 HET NH2 H 14 3 HET NH2 I 14 3 HET NH2 J 14 3 HET NH2 K 14 3 HET NH2 L 14 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 12(H2 N) SHEET 1 AA1 3 ASP F 4 LYS F 7 0 SHEET 2 AA1 3 ASP B 4 LYS B 7 1 N ILE B 5 O ILE F 6 SHEET 3 AA1 3 ASP J 4 LYS J 7 1 O ILE J 5 N ILE B 6 SHEET 1 AA2 3 ILE G 5 ALA G 10 0 SHEET 2 AA2 3 ILE C 5 ALA C 10 1 N ILE C 9 O LYS G 8 SHEET 3 AA2 3 ILE K 5 LYS K 8 1 O LYS K 7 N LYS C 8 SHEET 1 AA3 3 ILE H 5 ILE H 9 0 SHEET 2 AA3 3 ILE D 5 ILE D 9 1 N ILE D 9 O LYS H 8 SHEET 3 AA3 3 ILE L 5 ILE L 9 1 O LYS L 7 N LYS D 8 LINK C PHE A 13 N NH2 A 14 1555 1555 1.32 LINK C PHE B 13 N NH2 B 14 1555 1555 1.32 LINK C PHE C 13 N NH2 C 14 1555 1555 1.32 LINK C PHE D 13 N NH2 D 14 1555 1555 1.32 LINK C PHE E 13 N NH2 E 14 1555 1555 1.32 LINK C PHE F 13 N NH2 F 14 1555 1555 1.32 LINK C PHE G 13 N NH2 G 14 1555 1555 1.32 LINK C PHE H 13 N NH2 H 14 1555 1555 1.33 LINK C PHE I 13 N NH2 I 14 1555 1555 1.32 LINK C PHE J 13 N NH2 J 14 1555 1555 1.32 LINK C PHE K 13 N NH2 K 14 1555 1555 1.33 LINK C PHE L 13 N NH2 L 14 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 CONECT 152 170 CONECT 170 152 171 172 CONECT 171 170 CONECT 172 170 CONECT 347 365 CONECT 365 347 366 367 CONECT 366 365 CONECT 367 365 CONECT 520 538 CONECT 538 520 539 540 CONECT 539 538 CONECT 540 538 CONECT 693 711 CONECT 711 693 712 713 CONECT 712 711 CONECT 713 711 CONECT 866 884 CONECT 884 866 885 886 CONECT 885 884 CONECT 886 884 CONECT 1061 1079 CONECT 1079 1061 1080 1081 CONECT 1080 1079 CONECT 1081 1079 CONECT 1234 1252 CONECT 1252 1234 1253 1254 CONECT 1253 1252 CONECT 1254 1252 CONECT 1407 1425 CONECT 1425 1407 1426 1427 CONECT 1426 1425 CONECT 1427 1425 CONECT 1580 1598 CONECT 1598 1580 1599 1600 CONECT 1599 1598 CONECT 1600 1598 CONECT 1775 1793 CONECT 1793 1775 1794 1795 CONECT 1794 1793 CONECT 1795 1793 CONECT 1948 1966 CONECT 1966 1948 1967 1968 CONECT 1967 1966 CONECT 1968 1966 CONECT 2121 2139 CONECT 2139 2121 2140 2141 CONECT 2140 2139 CONECT 2141 2139 MASTER 128 0 12 0 9 0 0 6 1017 12 48 12 END