HEADER PROTEIN FIBRIL 05-SEP-22 8AZ4 TITLE IAPP S20G PLATEAU-PHASE FIBRIL POLYMORPH 2PF-L COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISLET AMYLOID POLYPEPTIDE; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J; COMPND 4 SYNONYM: AMYLIN,DIABETES-ASSOCIATED PEPTIDE,DAP,INSULINOMA AMYLOID COMPND 5 PEPTIDE; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: SYNTHESISED WITH C-TERMINAL AMIDATION SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS AMYLOID, FIBRIL, HELICAL, CROSS-BETA, AMYLIN, POLYMORPH, ISLET, KEYWDS 2 PROTEIN FIBRIL, DIABETES EXPDTA ELECTRON MICROSCOPY AUTHOR M.WILKINSON,Y.XU,R.GALLARDO,S.E.RADFORD,N.A.RANSON REVDAT 2 23-OCT-24 8AZ4 1 REMARK REVDAT 1 10-JAN-24 8AZ4 0 JRNL AUTH M.WILKINSON,Y.XU,D.THACKER,A.I.P.TAYLOR,D.G.FISHER, JRNL AUTH 2 R.U.GALLARDO,S.E.RADFORD,N.A.RANSON JRNL TITL STRUCTURAL EVOLUTION OF FIBRIL POLYMORPHS DURING AMYLOID JRNL TITL 2 ASSEMBLY. JRNL REF CELL V. 186 5798 2023 JRNL REFN ISSN 1097-4172 JRNL PMID 38134875 JRNL DOI 10.1016/J.CELL.2023.11.025 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CTFFIND, COOT, RELION, RELION, REMARK 3 RELION, RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 8AZ0 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : 47.000 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) : 2.200 REMARK 3 NUMBER OF PARTICLES : 643005 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 8AZ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292125452. 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 : IAPP S20G PLATEAU-PHASE FIBRIL REMARK 245 POLYMORPH 2PF-L REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.12 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : 6S BLOT REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.80 REMARK 245 SAMPLE DETAILS : IN VITRO FIBRIL GROWTH FOR 22 REMARK 245 WEEKS AT ROOM TEMPERATURE REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 2186 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 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) : 3900.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 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: DECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 1 REMARK 465 CYS A 2 REMARK 465 ASN A 3 REMARK 465 THR A 4 REMARK 465 ALA A 5 REMARK 465 THR A 6 REMARK 465 CYS A 7 REMARK 465 ALA A 8 REMARK 465 THR A 9 REMARK 465 LYS B 1 REMARK 465 CYS B 2 REMARK 465 ASN B 3 REMARK 465 THR B 4 REMARK 465 ALA B 5 REMARK 465 THR B 6 REMARK 465 CYS B 7 REMARK 465 ALA B 8 REMARK 465 THR B 9 REMARK 465 LYS C 1 REMARK 465 CYS C 2 REMARK 465 ASN C 3 REMARK 465 THR C 4 REMARK 465 ALA C 5 REMARK 465 THR C 6 REMARK 465 CYS C 7 REMARK 465 ALA C 8 REMARK 465 THR C 9 REMARK 465 LYS D 1 REMARK 465 CYS D 2 REMARK 465 ASN D 3 REMARK 465 THR D 4 REMARK 465 ALA D 5 REMARK 465 THR D 6 REMARK 465 CYS D 7 REMARK 465 ALA D 8 REMARK 465 THR D 9 REMARK 465 LYS E 1 REMARK 465 CYS E 2 REMARK 465 ASN E 3 REMARK 465 THR E 4 REMARK 465 ALA E 5 REMARK 465 THR E 6 REMARK 465 CYS E 7 REMARK 465 ALA E 8 REMARK 465 THR E 9 REMARK 465 LYS F 1 REMARK 465 CYS F 2 REMARK 465 ASN F 3 REMARK 465 THR F 4 REMARK 465 ALA F 5 REMARK 465 THR F 6 REMARK 465 CYS F 7 REMARK 465 ALA F 8 REMARK 465 THR F 9 REMARK 465 LYS G 1 REMARK 465 CYS G 2 REMARK 465 ASN G 3 REMARK 465 THR G 4 REMARK 465 ALA G 5 REMARK 465 THR G 6 REMARK 465 CYS G 7 REMARK 465 ALA G 8 REMARK 465 THR G 9 REMARK 465 LYS H 1 REMARK 465 CYS H 2 REMARK 465 ASN H 3 REMARK 465 THR H 4 REMARK 465 ALA H 5 REMARK 465 THR H 6 REMARK 465 CYS H 7 REMARK 465 ALA H 8 REMARK 465 THR H 9 REMARK 465 LYS I 1 REMARK 465 CYS I 2 REMARK 465 ASN I 3 REMARK 465 THR I 4 REMARK 465 ALA I 5 REMARK 465 THR I 6 REMARK 465 CYS I 7 REMARK 465 ALA I 8 REMARK 465 THR I 9 REMARK 465 LYS J 1 REMARK 465 CYS J 2 REMARK 465 ASN J 3 REMARK 465 THR J 4 REMARK 465 ALA J 5 REMARK 465 THR J 6 REMARK 465 CYS J 7 REMARK 465 ALA J 8 REMARK 465 THR J 9 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-15754 RELATED DB: EMDB REMARK 900 CRYOEM MAP OF THE FIBRIL POLYMORPH 4PF-CU FROM THE SAME DATASET REMARK 900 RELATED ID: EMD-15755 RELATED DB: EMDB REMARK 900 CRYOEM MAP OF THE FIBRIL POLYMORPH 4PF-LU FROM THE SAME DATASET REMARK 900 RELATED ID: EMD-15756 RELATED DB: EMDB REMARK 900 CRYOEM MAP OF THE FIBRIL POLYMORPH 4PF-LJ FROM THE SAME DATASET REMARK 900 RELATED ID: EMD-15728 RELATED DB: EMDB REMARK 900 CRYOEM MAP OF THE SAME FIBRIL FORM FROM A DIFFERENT SAMPLE WITHIN REMARK 900 THE STUDY (GROWTH-PHASE 2PF-L) REMARK 900 RELATED ID: 8AZ0 RELATED DB: PDB REMARK 900 CRYOEM MODEL OF THE SAME FIBRIL FORM FROM A DIFFERENT SAMPLE WITHIN REMARK 900 THE STUDY (GROWTH-PHASE 2PF-L) REMARK 900 RELATED ID: EMD-15753 RELATED DB: EMDB REMARK 900 IAPP S20G PLATEAU-PHASE FIBRIL POLYMORPH 2PF-L DBREF 8AZ4 A 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 8AZ4 B 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 8AZ4 C 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 8AZ4 D 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 8AZ4 E 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 8AZ4 F 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 8AZ4 G 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 8AZ4 H 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 8AZ4 I 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 8AZ4 J 1 37 UNP P10997 IAPP_HUMAN 34 70 SEQADV 8AZ4 GLY A 20 UNP P10997 SER 53 VARIANT SEQADV 8AZ4 NH2 A 38 UNP P10997 AMIDATION SEQADV 8AZ4 GLY B 20 UNP P10997 SER 53 VARIANT SEQADV 8AZ4 NH2 B 38 UNP P10997 AMIDATION SEQADV 8AZ4 GLY C 20 UNP P10997 SER 53 VARIANT SEQADV 8AZ4 NH2 C 38 UNP P10997 AMIDATION SEQADV 8AZ4 GLY D 20 UNP P10997 SER 53 VARIANT SEQADV 8AZ4 NH2 D 38 UNP P10997 AMIDATION SEQADV 8AZ4 GLY E 20 UNP P10997 SER 53 VARIANT SEQADV 8AZ4 NH2 E 38 UNP P10997 AMIDATION SEQADV 8AZ4 GLY F 20 UNP P10997 SER 53 VARIANT SEQADV 8AZ4 NH2 F 38 UNP P10997 AMIDATION SEQADV 8AZ4 GLY G 20 UNP P10997 SER 53 VARIANT SEQADV 8AZ4 NH2 G 38 UNP P10997 AMIDATION SEQADV 8AZ4 GLY H 20 UNP P10997 SER 53 VARIANT SEQADV 8AZ4 NH2 H 38 UNP P10997 AMIDATION SEQADV 8AZ4 GLY I 20 UNP P10997 SER 53 VARIANT SEQADV 8AZ4 NH2 I 38 UNP P10997 AMIDATION SEQADV 8AZ4 GLY J 20 UNP P10997 SER 53 VARIANT SEQADV 8AZ4 NH2 J 38 UNP P10997 AMIDATION SEQRES 1 A 38 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 A 38 ASN PHE LEU VAL HIS SER GLY ASN ASN PHE GLY ALA ILE SEQRES 3 A 38 LEU SER SER THR ASN VAL GLY SER ASN THR TYR NH2 SEQRES 1 B 38 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 B 38 ASN PHE LEU VAL HIS SER GLY ASN ASN PHE GLY ALA ILE SEQRES 3 B 38 LEU SER SER THR ASN VAL GLY SER ASN THR TYR NH2 SEQRES 1 C 38 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 C 38 ASN PHE LEU VAL HIS SER GLY ASN ASN PHE GLY ALA ILE SEQRES 3 C 38 LEU SER SER THR ASN VAL GLY SER ASN THR TYR NH2 SEQRES 1 D 38 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 D 38 ASN PHE LEU VAL HIS SER GLY ASN ASN PHE GLY ALA ILE SEQRES 3 D 38 LEU SER SER THR ASN VAL GLY SER ASN THR TYR NH2 SEQRES 1 E 38 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 E 38 ASN PHE LEU VAL HIS SER GLY ASN ASN PHE GLY ALA ILE SEQRES 3 E 38 LEU SER SER THR ASN VAL GLY SER ASN THR TYR NH2 SEQRES 1 F 38 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 F 38 ASN PHE LEU VAL HIS SER GLY ASN ASN PHE GLY ALA ILE SEQRES 3 F 38 LEU SER SER THR ASN VAL GLY SER ASN THR TYR NH2 SEQRES 1 G 38 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 G 38 ASN PHE LEU VAL HIS SER GLY ASN ASN PHE GLY ALA ILE SEQRES 3 G 38 LEU SER SER THR ASN VAL GLY SER ASN THR TYR NH2 SEQRES 1 H 38 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 H 38 ASN PHE LEU VAL HIS SER GLY ASN ASN PHE GLY ALA ILE SEQRES 3 H 38 LEU SER SER THR ASN VAL GLY SER ASN THR TYR NH2 SEQRES 1 I 38 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 I 38 ASN PHE LEU VAL HIS SER GLY ASN ASN PHE GLY ALA ILE SEQRES 3 I 38 LEU SER SER THR ASN VAL GLY SER ASN THR TYR NH2 SEQRES 1 J 38 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 J 38 ASN PHE LEU VAL HIS SER GLY ASN ASN PHE GLY ALA ILE SEQRES 3 J 38 LEU SER SER THR ASN VAL GLY SER ASN THR TYR NH2 HET NH2 A 38 1 HET NH2 B 38 1 HET NH2 C 38 1 HET NH2 D 38 1 HET NH2 E 38 1 HET NH2 F 38 1 HET NH2 G 38 1 HET NH2 H 38 1 HET NH2 I 38 1 HET NH2 J 38 1 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 10(H2 N) FORMUL 11 HOH *100(H2 O) SHEET 1 AA1 5 ARG A 11 ASN A 22 0 SHEET 2 AA1 5 ARG C 11 ASN C 22 1 O HIS C 18 N SER A 19 SHEET 3 AA1 5 ARG E 11 ASN E 22 1 O HIS E 18 N SER C 19 SHEET 4 AA1 5 ARG G 11 ASN G 22 1 O HIS G 18 N SER E 19 SHEET 5 AA1 5 ARG I 11 ASN I 22 1 O HIS I 18 N SER G 19 SHEET 1 AA2 5 ALA A 25 ILE A 26 0 SHEET 2 AA2 5 ALA C 25 ILE C 26 1 O ALA C 25 N ILE A 26 SHEET 3 AA2 5 ALA E 25 ILE E 26 1 O ALA E 25 N ILE C 26 SHEET 4 AA2 5 ALA G 25 ILE G 26 1 O ALA G 25 N ILE E 26 SHEET 5 AA2 5 ALA I 25 ILE I 26 1 O ALA I 25 N ILE G 26 SHEET 1 AA3 5 SER A 29 VAL A 32 0 SHEET 2 AA3 5 SER C 29 VAL C 32 1 O THR C 30 N ASN A 31 SHEET 3 AA3 5 SER E 29 VAL E 32 1 O THR E 30 N ASN C 31 SHEET 4 AA3 5 SER G 29 VAL G 32 1 O THR G 30 N ASN E 31 SHEET 5 AA3 5 SER I 29 VAL I 32 1 O THR I 30 N ASN G 31 SHEET 1 AA4 5 ARG B 11 ASN B 22 0 SHEET 2 AA4 5 ARG D 11 ASN D 22 1 O HIS D 18 N SER B 19 SHEET 3 AA4 5 ARG F 11 ASN F 22 1 O HIS F 18 N SER D 19 SHEET 4 AA4 5 ARG H 11 ASN H 22 1 O HIS H 18 N SER F 19 SHEET 5 AA4 5 ARG J 11 ASN J 22 1 O HIS J 18 N SER H 19 SHEET 1 AA5 5 ALA B 25 ILE B 26 0 SHEET 2 AA5 5 ALA D 25 ILE D 26 1 O ALA D 25 N ILE B 26 SHEET 3 AA5 5 ALA F 25 ILE F 26 1 O ALA F 25 N ILE D 26 SHEET 4 AA5 5 ALA H 25 ILE H 26 1 O ALA H 25 N ILE F 26 SHEET 5 AA5 5 ALA J 25 ILE J 26 1 O ALA J 25 N ILE H 26 SHEET 1 AA6 5 SER B 29 VAL B 32 0 SHEET 2 AA6 5 SER D 29 VAL D 32 1 O VAL D 32 N ASN B 31 SHEET 3 AA6 5 SER F 29 VAL F 32 1 O THR F 30 N ASN D 31 SHEET 4 AA6 5 SER H 29 VAL H 32 1 O THR H 30 N ASN F 31 SHEET 5 AA6 5 SER J 29 VAL J 32 1 O THR J 30 N ASN H 31 LINK C TYR A 37 N NH2 A 38 1555 1555 1.33 LINK C TYR B 37 N NH2 B 38 1555 1555 1.33 LINK C TYR C 37 N NH2 C 38 1555 1555 1.32 LINK C TYR D 37 N NH2 D 38 1555 1555 1.33 LINK C TYR E 37 N NH2 E 38 1555 1555 1.33 LINK C TYR F 37 N NH2 F 38 1555 1555 1.32 LINK C TYR G 37 N NH2 G 38 1555 1555 1.33 LINK C TYR H 37 N NH2 H 38 1555 1555 1.32 LINK C TYR I 37 N NH2 I 38 1555 1555 1.32 LINK C TYR J 37 N NH2 J 38 1555 1555 1.32 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