HEADER PROTEIN FIBRIL 25-JUL-22 7YKW TITLE STRUCTURE OF HIAPP FIBRIL AT 3.6 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISLET AMYLOID POLYPEPTIDE; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 SYNONYM: AMYLIN,DIABETES-ASSOCIATED PEPTIDE,DAP,INSULINOMA AMYLOID COMPND 5 PEPTIDE; COMPND 6 ENGINEERED: YES 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 AMYLIN, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR D.LI,X.ZHANG,Y.WANG,P.ZHU REVDAT 2 08-MAY-24 7YKW 1 JRNL REVDAT 1 18-JAN-23 7YKW 0 JRNL AUTH D.LI,X.ZHANG,Y.WANG,H.ZHANG,K.SONG,K.BAO,P.ZHU JRNL TITL A NEW POLYMORPHISM OF HUMAN AMYLIN FIBRILS WITH SIMILAR JRNL TITL 2 PROTOFILAMENTS AND A CONSERVED CORE. JRNL REF ISCIENCE V. 25 05705 2022 JRNL REFN ESSN 2589-0042 JRNL PMID 36567711 JRNL DOI 10.1016/J.ISCI.2022.105705 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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 : 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) : 3.600 REMARK 3 NUMBER OF PARTICLES : 58039 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 7YKW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300031131. 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 : ISLET AMYLOID POLYPEPTIDE 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 : 7.00 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) : 1000.00 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 : 2.80 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 GLN A 10 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 GLN C 10 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 GLN E 10 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 GLN G 10 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33897 RELATED DB: EMDB REMARK 900 HIAPP-SF DBREF 7YKW A 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7YKW B 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7YKW C 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7YKW D 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7YKW E 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7YKW F 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7YKW G 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7YKW H 1 37 UNP P10997 IAPP_HUMAN 34 70 SEQRES 1 A 37 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 A 37 ASN PHE LEU VAL HIS SER SER ASN ASN PHE GLY ALA ILE SEQRES 3 A 37 LEU SER SER THR ASN VAL GLY SER ASN THR TYC SEQRES 1 B 37 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 B 37 ASN PHE LEU VAL HIS SER SER ASN ASN PHE GLY ALA ILE SEQRES 3 B 37 LEU SER SER THR ASN VAL GLY SER ASN THR TYC SEQRES 1 C 37 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 C 37 ASN PHE LEU VAL HIS SER SER ASN ASN PHE GLY ALA ILE SEQRES 3 C 37 LEU SER SER THR ASN VAL GLY SER ASN THR TYC SEQRES 1 D 37 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 D 37 ASN PHE LEU VAL HIS SER SER ASN ASN PHE GLY ALA ILE SEQRES 3 D 37 LEU SER SER THR ASN VAL GLY SER ASN THR TYC SEQRES 1 E 37 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 E 37 ASN PHE LEU VAL HIS SER SER ASN ASN PHE GLY ALA ILE SEQRES 3 E 37 LEU SER SER THR ASN VAL GLY SER ASN THR TYC SEQRES 1 F 37 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 F 37 ASN PHE LEU VAL HIS SER SER ASN ASN PHE GLY ALA ILE SEQRES 3 F 37 LEU SER SER THR ASN VAL GLY SER ASN THR TYC SEQRES 1 G 37 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 G 37 ASN PHE LEU VAL HIS SER SER ASN ASN PHE GLY ALA ILE SEQRES 3 G 37 LEU SER SER THR ASN VAL GLY SER ASN THR TYC SEQRES 1 H 37 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 H 37 ASN PHE LEU VAL HIS SER SER ASN ASN PHE GLY ALA ILE SEQRES 3 H 37 LEU SER SER THR ASN VAL GLY SER ASN THR TYC MODRES 7YKW TYC A 37 TYR MODIFIED RESIDUE MODRES 7YKW TYC B 37 TYR MODIFIED RESIDUE MODRES 7YKW TYC C 37 TYR MODIFIED RESIDUE MODRES 7YKW TYC D 37 TYR MODIFIED RESIDUE MODRES 7YKW TYC E 37 TYR MODIFIED RESIDUE MODRES 7YKW TYC F 37 TYR MODIFIED RESIDUE MODRES 7YKW TYC G 37 TYR MODIFIED RESIDUE MODRES 7YKW TYC H 37 TYR MODIFIED RESIDUE HET TYC A 37 13 HET TYC B 37 13 HET TYC C 37 13 HET TYC D 37 13 HET TYC E 37 13 HET TYC F 37 13 HET TYC G 37 13 HET TYC H 37 13 HETNAM TYC L-TYROSINAMIDE FORMUL 1 TYC 8(C9 H12 N2 O2) SHEET 1 AA1 4 ALA A 13 ASN A 22 0 SHEET 2 AA1 4 ALA C 13 ASN C 22 1 O VAL C 17 N HIS A 18 SHEET 3 AA1 4 ALA E 13 ASN E 22 1 O VAL E 17 N HIS C 18 SHEET 4 AA1 4 ALA G 13 ASN G 22 1 O VAL G 17 N HIS E 18 SHEET 1 AA2 4 ILE A 26 VAL A 32 0 SHEET 2 AA2 4 ILE C 26 VAL C 32 1 O ASN C 31 N VAL A 32 SHEET 3 AA2 4 ILE E 26 VAL E 32 1 O ASN E 31 N VAL C 32 SHEET 4 AA2 4 ILE G 26 VAL G 32 1 O ASN G 31 N VAL E 32 SHEET 1 AA3 4 ASN A 35 THR A 36 0 SHEET 2 AA3 4 ASN C 35 THR C 36 1 O THR C 36 N ASN A 35 SHEET 3 AA3 4 ASN E 35 THR E 36 1 O THR E 36 N ASN C 35 SHEET 4 AA3 4 ASN G 35 THR G 36 1 O THR G 36 N ASN E 35 SHEET 1 AA4 4 THR B 6 ASN B 22 0 SHEET 2 AA4 4 THR D 6 ASN D 22 1 O PHE D 15 N ASN B 14 SHEET 3 AA4 4 THR F 6 ASN F 22 1 O PHE F 15 N LEU D 16 SHEET 4 AA4 4 THR H 6 ASN H 22 1 O PHE H 15 N ASN F 14 SHEET 1 AA5 4 ALA B 25 VAL B 32 0 SHEET 2 AA5 4 ALA D 25 VAL D 32 1 O ASN D 31 N THR B 30 SHEET 3 AA5 4 ALA F 25 VAL F 32 1 O ASN F 31 N THR D 30 SHEET 4 AA5 4 ALA H 25 VAL H 32 1 O ASN H 31 N THR F 30 SHEET 1 AA6 4 ASN B 35 THR B 36 0 SHEET 2 AA6 4 ASN D 35 THR D 36 1 O THR D 36 N ASN B 35 SHEET 3 AA6 4 ASN F 35 THR F 36 1 O THR F 36 N ASN D 35 SHEET 4 AA6 4 ASN H 35 THR H 36 1 O THR H 36 N ASN F 35 SSBOND 1 CYS B 2 CYS B 7 1555 1555 2.03 SSBOND 2 CYS D 2 CYS D 7 1555 1555 2.03 SSBOND 3 CYS F 2 CYS F 7 1555 1555 2.03 SSBOND 4 CYS H 2 CYS H 7 1555 1555 2.03 LINK C THR A 36 N TYC A 37 1555 1555 1.37 LINK C THR B 36 N TYC B 37 1555 1555 1.26 LINK C THR C 36 N TYC C 37 1555 1555 1.37 LINK C THR D 36 N TYC D 37 1555 1555 1.26 LINK C THR E 36 N TYC E 37 1555 1555 1.37 LINK C THR F 36 N TYC F 37 1555 1555 1.26 LINK C THR G 36 N TYC G 37 1555 1555 1.37 LINK C THR H 36 N TYC H 37 1555 1555 1.26 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 187 192 CONECT 192 187 193 CONECT 193 192 194 196 CONECT 194 193 195 204 CONECT 195 194 CONECT 196 193 197 CONECT 197 196 198 199 CONECT 198 197 200 CONECT 199 197 201 CONECT 200 198 203 CONECT 201 199 203 CONECT 202 203 CONECT 203 200 201 202 CONECT 204 194 CONECT 220 253 CONECT 253 220 CONECT 461 466 CONECT 466 461 467 CONECT 467 466 468 470 CONECT 468 467 469 478 CONECT 469 468 CONECT 470 467 471 CONECT 471 470 472 473 CONECT 472 471 474 CONECT 473 471 475 CONECT 474 472 477 CONECT 475 473 477 CONECT 476 477 CONECT 477 474 475 476 CONECT 478 468 CONECT 666 671 CONECT 671 666 672 CONECT 672 671 673 675 CONECT 673 672 674 683 CONECT 674 673 CONECT 675 672 676 CONECT 676 675 677 678 CONECT 677 676 679 CONECT 678 676 680 CONECT 679 677 682 CONECT 680 678 682 CONECT 681 682 CONECT 682 679 680 681 CONECT 683 673 CONECT 699 732 CONECT 732 699 CONECT 940 945 CONECT 945 940 946 CONECT 946 945 947 949 CONECT 947 946 948 957 CONECT 948 947 CONECT 949 946 950 CONECT 950 949 951 952 CONECT 951 950 953 CONECT 952 950 954 CONECT 953 951 956 CONECT 954 952 956 CONECT 955 956 CONECT 956 953 954 955 CONECT 957 947 CONECT 1145 1150 CONECT 1150 1145 1151 CONECT 1151 1150 1152 1154 CONECT 1152 1151 1153 1162 CONECT 1153 1152 CONECT 1154 1151 1155 CONECT 1155 1154 1156 1157 CONECT 1156 1155 1158 CONECT 1157 1155 1159 CONECT 1158 1156 1161 CONECT 1159 1157 1161 CONECT 1160 1161 CONECT 1161 1158 1159 1160 CONECT 1162 1152 CONECT 1178 1211 CONECT 1211 1178 CONECT 1419 1424 CONECT 1424 1419 1425 CONECT 1425 1424 1426 1428 CONECT 1426 1425 1427 1436 CONECT 1427 1426 CONECT 1428 1425 1429 CONECT 1429 1428 1430 1431 CONECT 1430 1429 1432 CONECT 1431 1429 1433 CONECT 1432 1430 1435 CONECT 1433 1431 1435 CONECT 1434 1435 CONECT 1435 1432 1433 1434 CONECT 1436 1426 CONECT 1624 1629 CONECT 1629 1624 1630 CONECT 1630 1629 1631 1633 CONECT 1631 1630 1632 1641 CONECT 1632 1631 CONECT 1633 1630 1634 CONECT 1634 1633 1635 1636 CONECT 1635 1634 1637 CONECT 1636 1634 1638 CONECT 1637 1635 1640 CONECT 1638 1636 1640 CONECT 1639 1640 CONECT 1640 1637 1638 1639 CONECT 1641 1631 CONECT 1657 1690 CONECT 1690 1657 CONECT 1898 1903 CONECT 1903 1898 1904 CONECT 1904 1903 1905 1907 CONECT 1905 1904 1906 1915 CONECT 1906 1905 CONECT 1907 1904 1908 CONECT 1908 1907 1909 1910 CONECT 1909 1908 1911 CONECT 1910 1908 1912 CONECT 1911 1909 1914 CONECT 1912 1910 1914 CONECT 1913 1914 CONECT 1914 1911 1912 1913 CONECT 1915 1905 MASTER 143 0 8 0 24 0 0 6 1908 8 120 24 END