HEADER PROTEIN FIBRIL 27-MAY-25 9RBW TITLE CRYO-EM STRUCTURE OF ANP AMYLOIDS FROM LEFT ATRIAL APPENDAGE OF ATRIAL TITLE 2 FIBRILLATION PATIENT - POLYMORPH B COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATRIAL NATRIURETIC PEPTIDE; COMPND 3 CHAIN: C, D, B, A, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T; COMPND 4 SYNONYM: ANP,ALPHA-ATRIAL NATRIURETIC PEPTIDE,ALPHA-HANP,ATRIAL COMPND 5 NATRIURETIC FACTOR,ANF,CDD-ANF,CDD-ANP (99-126),CARDIONATRIN,PRO COMPND 6 ATRIAL NATRIURETIC FACTOR 99-126,PROANF 99-126 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 9RBW 1 JRNL REVDAT 1 27-AUG-25 9RBW 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. 3.30 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 : 62.890 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 31454 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 9RBW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1292148027. 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: C, D, B, A, E, F, G, H, I, J, REMARK 350 AND CHAINS: K, L, M, N, O, P, Q, R, S, T 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 ARG B 3 REMARK 465 ARG G 3 REMARK 465 ARG K 3 REMARK 465 ARG O 3 REMARK 465 ARG S 3 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS I 23 SG CYS J 23 1.77 REMARK 500 REMARK 500 REMARK: NULL 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 CYS C 7 11.23 -141.55 REMARK 500 ASP C 13 -164.93 -126.14 REMARK 500 CYS B 7 11.27 -141.51 REMARK 500 ASP B 13 -165.00 -126.14 REMARK 500 CYS E 7 11.22 -141.51 REMARK 500 ASP E 13 -164.96 -126.13 REMARK 500 CYS G 7 11.23 -141.51 REMARK 500 ASP G 13 -164.96 -126.16 REMARK 500 CYS I 7 11.14 -141.48 REMARK 500 ASP I 13 -164.98 -126.18 REMARK 500 CYS K 7 11.14 -141.44 REMARK 500 ASP K 13 -165.00 -126.21 REMARK 500 CYS M 7 11.17 -141.47 REMARK 500 ASP M 13 -164.94 -126.15 REMARK 500 CYS O 7 11.21 -141.48 REMARK 500 ASP O 13 -165.00 -126.18 REMARK 500 CYS Q 7 11.20 -141.54 REMARK 500 ASP Q 13 -164.97 -126.23 REMARK 500 CYS S 7 11.09 -141.47 REMARK 500 ASP S 13 -164.95 -126.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9RBD RELATED DB: PDB REMARK 900 POLYMORPH A REMARK 900 RELATED ID: EMD-53910 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ANP AMYLOIDS FROM LEFT ATRIAL APPENDAGE OF REMARK 900 ATRIAL FIBRILLATION PATIENT - POLYMORPH B DBREF 9RBW C 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW D 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW B 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW A 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW E 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW F 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW G 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW H 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW I 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW J 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW K 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW L 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW M 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW N 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW O 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW P 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW Q 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW R 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW S 3 28 UNP P01160 ANF_HUMAN 126 151 DBREF 9RBW T 3 28 UNP P01160 ANF_HUMAN 126 151 SEQRES 1 C 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 C 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 D 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 D 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 B 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 B 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 A 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 A 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 E 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 E 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 F 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 F 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 G 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 G 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 H 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 H 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 I 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 I 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 J 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 J 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 K 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 K 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 L 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 L 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 M 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 M 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 N 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 N 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 O 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 O 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 P 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 P 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 Q 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 Q 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 R 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 R 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 S 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 S 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SEQRES 1 T 26 ARG ARG SER SER CYS PHE GLY GLY ARG MET ASP ARG ILE SEQRES 2 T 26 GLY ALA GLN SER GLY LEU GLY CYS ASN SER PHE ARG TYR SHEET 1 AA1 5 SER E 19 LEU E 21 0 SHEET 2 AA1 5 SER I 19 LEU I 21 1 O GLY I 20 N LEU E 21 SHEET 3 AA1 5 SER C 19 LEU C 21 1 N GLY C 20 O LEU I 21 SHEET 4 AA1 5 SER Q 19 LEU Q 21 1 O GLY Q 20 N LEU C 21 SHEET 5 AA1 5 SER M 19 LEU M 21 1 N SER M 19 O GLY Q 20 SHEET 1 AA2 5 SER G 19 LEU G 21 0 SHEET 2 AA2 5 SER K 19 LEU K 21 1 O SER K 19 N GLY G 20 SHEET 3 AA2 5 SER B 19 LEU B 21 1 N GLY B 20 O LEU K 21 SHEET 4 AA2 5 SER S 19 LEU S 21 1 O GLY S 20 N LEU B 21 SHEET 5 AA2 5 SER O 19 LEU O 21 1 N GLY O 20 O LEU S 21 SHEET 1 AA3 2 MET A 12 ASP A 13 0 SHEET 2 AA3 2 MET L 12 ASP L 13 1 O MET L 12 N ASP A 13 SSBOND 1 CYS C 7 CYS D 7 1555 1555 1.93 SSBOND 2 CYS C 23 CYS D 23 1555 1555 2.04 SSBOND 3 CYS B 7 CYS A 7 1555 1555 2.15 SSBOND 4 CYS B 23 CYS A 23 1555 1555 1.95 SSBOND 5 CYS E 7 CYS F 7 1555 1555 1.97 SSBOND 6 CYS E 23 CYS F 23 1555 1555 2.08 SSBOND 7 CYS G 7 CYS H 7 1555 1555 2.10 SSBOND 8 CYS G 23 CYS H 23 1555 1555 2.05 SSBOND 9 CYS I 7 CYS J 7 1555 1555 2.16 SSBOND 10 CYS K 7 CYS L 7 1555 1555 2.14 SSBOND 11 CYS K 23 CYS L 23 1555 1555 2.15 SSBOND 12 CYS M 7 CYS N 7 1555 1555 2.18 SSBOND 13 CYS M 23 CYS N 23 1555 1555 2.01 SSBOND 14 CYS O 7 CYS P 7 1555 1555 1.92 SSBOND 15 CYS O 23 CYS P 23 1555 1555 1.92 SSBOND 16 CYS Q 7 CYS R 7 1555 1555 1.80 SSBOND 17 CYS Q 23 CYS R 23 1555 1555 2.35 SSBOND 18 CYS S 7 CYS T 7 1555 1555 2.04 SSBOND 19 CYS S 23 CYS T 23 1555 1555 2.05 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 201 TYR C 28 TER 402 TYR D 28 TER 592 TYR B 28 TER 793 TYR A 28 TER 994 TYR E 28 TER 1195 TYR F 28 TER 1385 TYR G 28 TER 1586 TYR H 28 TER 1787 TYR I 28 TER 1988 TYR J 28 TER 2178 TYR K 28 TER 2379 TYR L 28 TER 2580 TYR M 28 TER 2781 TYR N 28 TER 2971 TYR O 28 TER 3172 TYR P 28 TER 3373 TYR Q 28 TER 3574 TYR R 28 TER 3764 TYR S 28 TER 3965 TYR T 28 CONECT 40 241 CONECT 151 352 CONECT 241 40 CONECT 352 151 CONECT 431 632 CONECT 542 743 CONECT 632 431 CONECT 743 542 CONECT 833 1034 CONECT 944 1145 CONECT 1034 833 CONECT 1145 944 CONECT 1224 1425 CONECT 1335 1536 CONECT 1425 1224 CONECT 1536 1335 CONECT 1626 1827 CONECT 1827 1626 CONECT 2017 2218 CONECT 2128 2329 CONECT 2218 2017 CONECT 2329 2128 CONECT 2419 2620 CONECT 2530 2731 CONECT 2620 2419 CONECT 2731 2530 CONECT 2810 3011 CONECT 2921 3122 CONECT 3011 2810 CONECT 3122 2921 CONECT 3212 3413 CONECT 3323 3524 CONECT 3413 3212 CONECT 3524 3323 CONECT 3603 3804 CONECT 3714 3915 CONECT 3804 3603 CONECT 3915 3714 MASTER 163 0 0 0 12 0 0 6 3945 20 38 40 END