HEADER PROTEIN FIBRIL 25-MAR-21 7M61 TITLE CRYO-EM STRUCTURE OF HUMAN ISLET AMYLOID POLYPEPTIDE (HIAPP, OR TITLE 2 AMYLIN) FIBRILS SEEDED BY PATIENT EXTRACTED FIBRILS, POLYMORPH 1 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 FRAGMENT: C-TERMINAL AMIDATED PEPTIDE (UNP RESIDUES 34-70); COMPND 5 SYNONYM: AMYLIN,DIABETES-ASSOCIATED PEPTIDE,DAP,INSULINOMA AMYLOID COMPND 6 PEPTIDE; COMPND 7 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 HIAPP, TYPE II DIABETES, AMYLOID, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR Q.CAO,D.R.BOYER,M.R.SAWAYA,D.S.EISENBERG REVDAT 2 06-NOV-24 7M61 1 REMARK REVDAT 1 22-SEP-21 7M61 0 JRNL AUTH Q.CAO,D.R.BOYER,M.R.SAWAYA,R.ABSKHARON,L.SAELICES, JRNL AUTH 2 B.A.NGUYEN,J.LU,K.A.MURRAY,F.KANDEEL,D.S.EISENBERG JRNL TITL CRYO-EM STRUCTURES OF HIAPP FIBRILS SEEDED BY JRNL TITL 2 PATIENT-EXTRACTED FIBRILS REVEAL NEW POLYMORPHS AND JRNL TITL 3 CONSERVED FIBRIL CORES JRNL REF NAT.STRUCT.MOL.BIOL. V. 28 724 2021 JRNL REFN ESSN 1545-9985 JRNL DOI 10.1038/S41594-021-00646-X REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EMAN2, SERIALEM, CTFFIND, 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 : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 83.000 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 26608 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 7M61 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000254085. 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 : HIAPP FIBRIL 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 : 7.40 REMARK 245 SAMPLE DETAILS : SYNTHETIC HIAPP SEEDED BY HIAPP REMARK 245 FIBRILS EXTRACTED FROM A PATIENT WITH TYPE II DIABETES 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 K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 4500.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = -2.94 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 4.81 ANGSTROMS 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 GLN A 10 REMARK 465 ARG A 11 REMARK 465 LEU A 12 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 GLN B 10 REMARK 465 ARG B 11 REMARK 465 LEU B 12 REMARK 465 ALA B 13 REMARK 465 ASN B 14 REMARK 465 PHE B 15 REMARK 465 LEU B 16 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 ARG C 11 REMARK 465 LEU C 12 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 GLN D 10 REMARK 465 ARG D 11 REMARK 465 LEU D 12 REMARK 465 ALA D 13 REMARK 465 ASN D 14 REMARK 465 PHE D 15 REMARK 465 LEU D 16 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 ARG E 11 REMARK 465 LEU E 12 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 GLN F 10 REMARK 465 ARG F 11 REMARK 465 LEU F 12 REMARK 465 ALA F 13 REMARK 465 ASN F 14 REMARK 465 PHE F 15 REMARK 465 LEU F 16 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 465 ARG G 11 REMARK 465 LEU G 12 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 GLN H 10 REMARK 465 ARG H 11 REMARK 465 LEU H 12 REMARK 465 ALA H 13 REMARK 465 ASN H 14 REMARK 465 PHE H 15 REMARK 465 LEU H 16 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 GLN I 10 REMARK 465 ARG I 11 REMARK 465 LEU I 12 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 465 GLN J 10 REMARK 465 ARG J 11 REMARK 465 LEU J 12 REMARK 465 ALA J 13 REMARK 465 ASN J 14 REMARK 465 PHE J 15 REMARK 465 LEU J 16 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6VW2 RELATED DB: PDB REMARK 900 RELATED ID: EMD-23686 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-23688 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-23689 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-23687 RELATED DB: EMDB DBREF 7M61 A 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7M61 B 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7M61 C 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7M61 D 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7M61 E 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7M61 F 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7M61 G 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7M61 H 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7M61 I 1 37 UNP P10997 IAPP_HUMAN 34 70 DBREF 7M61 J 1 37 UNP P10997 IAPP_HUMAN 34 70 SEQADV 7M61 NH2 A 38 UNP P10997 AMIDATION SEQADV 7M61 NH2 B 38 UNP P10997 AMIDATION SEQADV 7M61 NH2 C 38 UNP P10997 AMIDATION SEQADV 7M61 NH2 D 38 UNP P10997 AMIDATION SEQADV 7M61 NH2 E 38 UNP P10997 AMIDATION SEQADV 7M61 NH2 F 38 UNP P10997 AMIDATION SEQADV 7M61 NH2 G 38 UNP P10997 AMIDATION SEQADV 7M61 NH2 H 38 UNP P10997 AMIDATION SEQADV 7M61 NH2 I 38 UNP P10997 AMIDATION SEQADV 7M61 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 SER 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 SER 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 SER 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 SER 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 SER 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 SER 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 SER 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 SER 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 SER 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 SER 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) SHEET 1 AA1 5 ASN C 14 PHE C 15 0 SHEET 2 AA1 5 ASN E 14 PHE E 15 1 O ASN E 14 N PHE C 15 SHEET 3 AA1 5 ASN G 14 PHE G 15 1 O ASN G 14 N PHE E 15 SHEET 4 AA1 5 ASN A 14 PHE A 15 1 N ASN A 14 O PHE G 15 SHEET 5 AA1 5 ASN I 14 PHE I 15 1 O ASN I 14 N PHE A 15 SHEET 1 AA2 5 ASN C 35 THR C 36 0 SHEET 2 AA2 5 ASN E 35 THR E 36 1 O ASN E 35 N THR C 36 SHEET 3 AA2 5 ASN G 35 THR G 36 1 O ASN G 35 N THR E 36 SHEET 4 AA2 5 ASN A 35 THR A 36 1 N ASN A 35 O THR G 36 SHEET 5 AA2 5 ASN I 35 THR I 36 1 O ASN I 35 N THR A 36 SHEET 1 AA3 5 PHE D 23 ALA D 25 0 SHEET 2 AA3 5 PHE F 23 ALA F 25 1 O PHE F 23 N GLY D 24 SHEET 3 AA3 5 PHE H 23 ALA H 25 1 O PHE H 23 N GLY F 24 SHEET 4 AA3 5 PHE B 23 ALA B 25 1 N PHE B 23 O GLY H 24 SHEET 5 AA3 5 PHE J 23 ALA J 25 1 O PHE J 23 N GLY B 24 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 1.33 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 1.33 LINK C TYR G 37 N NH2 G 38 1555 1555 1.33 LINK C TYR H 37 N NH2 H 38 1555 1555 1.33 LINK C TYR I 37 N NH2 I 38 1555 1555 1.33 LINK C TYR J 37 N NH2 J 38 1555 1555 1.33 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