HEADER PROTEIN FIBRIL 22-MAY-25 9RBD TITLE CRYO-EM STRUCTURE OF ANP AMYLOIDS FROM LEFT ATRIAL APPENDAGE OF ATRIAL TITLE 2 FIBRILLATION PATIENT - POLYMORPH A COMPND MOL_ID: 1; COMPND 2 MOLECULE: NATRIURETIC PEPTIDES A; COMPND 3 CHAIN: J, L, g, i, A, B, C, D, E, F, G, H, I, K, M, N, O, P, Q, R; COMPND 4 SYNONYM: ATRIAL NATRIURETIC FACTOR PROHORMONE,PROANF,ATRIAL COMPND 5 NATRIURETIC PEPTIDE PROHORMONE,PREPROANP,PROANP,ATRIOPEPTIGEN, COMPND 6 CARDIODILATIN,CDD,PREPROCDD-ANF SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS AMYLOID, CARDIAC AMYLOIDOSIS, IN VIVO, AGGREGATION, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR L.BROGGINI,A.CHAVES-SANJUAN,S.RICAGNO REVDAT 2 12-NOV-25 9RBD 1 JRNL REVDAT 1 27-AUG-25 9RBD 0 JRNL AUTH L.BROGGINI,M.PICCOLI,A.CHAVES-SANJUAN,D.M.V.BONNET, JRNL AUTH 2 F.CIRILLO,C.VISENTIN,F.SONZINI,P.SIGNORELLI,I.LAVOTA, JRNL AUTH 3 M.MILAZZO,S.NONNIS,L.MENICANTI,G.CICONTE,C.PAPPONE, JRNL AUTH 4 L.ANASTASIA,S.RICAGNO JRNL TITL STRUCTURAL CHARACTERIZATION OF ATRIAL NATRIURETIC PEPTIDE JRNL TITL 2 AMYLOID FIBRILS FROM PATIENTS WITH ATRIAL FIBRILLATION. JRNL REF NAT COMMUN V. 16 9556 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 41162370 JRNL DOI 10.1038/S41467-025-64618-1 REMARK 2 REMARK 2 RESOLUTION. 2.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, COOT, 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 : NULL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 73.850 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) : 2.960 REMARK 3 NUMBER OF PARTICLES : 67547 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 9RBD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1292148024. 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 : ATRIAL NATRIURETIC PEPTIDE REMARK 245 AMYLOID FIBRILS POLYMORPH A 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 : 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 GLACIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 4100.00 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: 20-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 20-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: J, L, g, i, A, B, C, D, E, F, REMARK 350 AND CHAINS: G, H, I, K, M, N, O, P, Q, 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-53891 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ANP AMYLOIDS FROM LEFT ATRIAL APPENDAGE OF REMARK 900 ATRIAL FIBRILLATION PATIENT - POLYMORPH A DBREF 9RBD J 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD L 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD g 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD i 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD A 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD B 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD C 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD D 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD E 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD F 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD G 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD H 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD I 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD K 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD M 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD N 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD O 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD P 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD Q 103 126 UNP P01160 ANF_HUMAN 128 151 DBREF 9RBD R 103 126 UNP P01160 ANF_HUMAN 128 151 SEQRES 1 J 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 J 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 L 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 L 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 g 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 g 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 i 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 i 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 A 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 A 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 B 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 B 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 C 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 C 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 D 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 D 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 E 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 E 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 F 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 F 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 G 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 G 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 H 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 H 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 I 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 I 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 K 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 K 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 M 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 M 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 N 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 N 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 O 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 O 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 P 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 P 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 Q 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 Q 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 R 24 SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE GLY ALA SEQRES 2 R 24 GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SHEET 1 AA1 5 CYS J 105 PHE J 106 0 SHEET 2 AA1 5 CYS A 105 PHE A 106 1 O PHE A 106 N CYS J 105 SHEET 3 AA1 5 CYS E 105 PHE E 106 1 O PHE E 106 N CYS A 105 SHEET 4 AA1 5 CYS I 105 PHE I 106 1 O PHE I 106 N CYS E 105 SHEET 5 AA1 5 CYS O 105 PHE O 106 1 O PHE O 106 N CYS I 105 SHEET 1 AA2 5 ARG J 109 MET J 110 0 SHEET 2 AA2 5 ARG A 109 MET A 110 1 O ARG A 109 N MET J 110 SHEET 3 AA2 5 ARG E 109 MET E 110 1 O ARG E 109 N MET A 110 SHEET 4 AA2 5 ARG I 109 MET I 110 1 O ARG I 109 N MET E 110 SHEET 5 AA2 5 ARG O 109 MET O 110 1 O ARG O 109 N MET I 110 SHEET 1 AA3 5 GLY J 114 LEU J 119 0 SHEET 2 AA3 5 GLY A 114 LEU A 119 1 O GLN A 116 N ALA J 115 SHEET 3 AA3 5 GLY E 114 LEU E 119 1 O GLY E 118 N LEU A 119 SHEET 4 AA3 5 GLY I 114 LEU I 119 1 O GLY I 118 N LEU E 119 SHEET 5 AA3 5 GLY O 114 LEU O 119 1 O GLY O 114 N ALA I 115 SHEET 1 AA4 5 CYS L 105 PHE L 106 0 SHEET 2 AA4 5 CYS B 105 PHE B 106 1 O PHE B 106 N CYS L 105 SHEET 3 AA4 5 CYS F 105 PHE F 106 1 O PHE F 106 N CYS B 105 SHEET 4 AA4 5 CYS K 105 PHE K 106 1 O PHE K 106 N CYS F 105 SHEET 5 AA4 5 CYS P 105 PHE P 106 1 O PHE P 106 N CYS K 105 SHEET 1 AA5 5 ARG L 109 LEU L 119 0 SHEET 2 AA5 5 ARG B 109 LEU B 119 1 O ARG B 109 N MET L 110 SHEET 3 AA5 5 ARG F 109 LEU F 119 1 O GLY F 118 N LEU B 119 SHEET 4 AA5 5 ARG K 109 LEU K 119 1 O ARG K 109 N MET F 110 SHEET 5 AA5 5 ARG P 109 LEU P 119 1 O ARG P 109 N MET K 110 SHEET 1 AA6 5 SER g 104 CYS g 105 0 SHEET 2 AA6 5 SER C 104 CYS C 105 1 O SER C 104 N CYS g 105 SHEET 3 AA6 5 SER G 104 CYS G 105 1 O SER G 104 N CYS C 105 SHEET 4 AA6 5 SER M 104 CYS M 105 1 O SER M 104 N CYS G 105 SHEET 5 AA6 5 SER Q 104 CYS Q 105 1 O SER Q 104 N CYS M 105 SHEET 1 AA7 5 MET g 110 LEU g 119 0 SHEET 2 AA7 5 MET C 110 LEU C 119 1 O GLY C 118 N LEU g 119 SHEET 3 AA7 5 MET G 110 LEU G 119 1 O GLN G 116 N ALA C 115 SHEET 4 AA7 5 MET M 110 LEU M 119 1 O ARG M 112 N ILE G 113 SHEET 5 AA7 5 MET Q 110 LEU Q 119 1 O GLN Q 116 N ALA M 115 SHEET 1 AA8 4 ARG i 109 MET i 110 0 SHEET 2 AA8 4 ARG D 109 MET D 110 1 O ARG D 109 N MET i 110 SHEET 3 AA8 4 ARG H 109 MET H 110 1 O ARG H 109 N MET D 110 SHEET 4 AA8 4 ARG N 109 MET N 110 1 O ARG N 109 N MET H 110 SHEET 1 AA9 5 GLY i 114 LEU i 119 0 SHEET 2 AA9 5 GLY D 114 LEU D 119 1 O GLY D 118 N LEU i 119 SHEET 3 AA9 5 GLY H 114 LEU H 119 1 O GLN H 116 N ALA D 115 SHEET 4 AA9 5 GLY N 114 LEU N 119 1 O GLN N 116 N ALA H 115 SHEET 5 AA9 5 GLY R 114 LEU R 119 1 O GLY R 114 N ALA N 115 SSBOND 1 CYS J 105 CYS g 121 1555 1555 2.13 SSBOND 2 CYS L 105 CYS i 121 1555 1555 2.11 SSBOND 3 CYS A 105 CYS C 121 1555 1555 2.15 SSBOND 4 CYS B 105 CYS D 121 1555 1555 1.91 SSBOND 5 CYS E 105 CYS G 121 1555 1555 2.11 SSBOND 6 CYS F 105 CYS H 121 1555 1555 1.94 SSBOND 7 CYS I 105 CYS M 121 1555 1555 1.95 SSBOND 8 CYS K 105 CYS N 121 1555 1555 2.21 SSBOND 9 CYS O 105 CYS Q 121 1555 1555 1.80 SSBOND 10 CYS P 105 CYS R 121 1555 1555 2.00 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 TER 179 TYR J 126 TER 358 TYR L 126 TER 537 TYR g 126 TER 716 TYR i 126 TER 895 TYR A 126 TER 1074 TYR B 126 TER 1253 TYR C 126 TER 1432 TYR D 126 TER 1611 TYR E 126 TER 1790 TYR F 126 TER 1969 TYR G 126 TER 2148 TYR H 126 TER 2327 TYR I 126 TER 2506 TYR K 126 TER 2685 TYR M 126 TER 2864 TYR N 126 TER 3043 TYR O 126 TER 3222 TYR P 126 TER 3401 TYR Q 126 TER 3580 TYR R 126 CONECT 18 487 CONECT 197 666 CONECT 487 18 CONECT 666 197 CONECT 734 1203 CONECT 913 1382 CONECT 1203 734 CONECT 1382 913 CONECT 1450 1919 CONECT 1629 2098 CONECT 1919 1450 CONECT 2098 1629 CONECT 2166 2635 CONECT 2345 2814 CONECT 2635 2166 CONECT 2814 2345 CONECT 2882 3351 CONECT 3061 3530 CONECT 3351 2882 CONECT 3530 3061 MASTER 102 0 0 0 44 0 0 6 3560 20 20 40 END