HEADER PROTEIN FIBRIL 14-JAN-25 9LJ0 TITLE THE CRYO-EM STRUCTURE OF AMYLOID FIBRILS FROM ABDOMINAL FAT OF AN AL TITLE 2 AMYLOIDOSIS PATIENT (CASE 3). COMPND MOL_ID: 1; COMPND 2 MOLECULE: MONOCLONAL IMMUNOGLOBULIN LIGHT CHAINS (LC); COMPND 3 CHAIN: C, A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606 KEYWDS AMYLOID, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR Y.X.YAO,Q.Y.ZHAO,C.LIU,D.LI REVDAT 1 21-JAN-26 9LJ0 0 JRNL AUTH Y.YAO,Q.ZHAO,S.YAO,Y.XU,K.LIU,T.CAO,B.SUN,J.ZHOU,C.LIU,D.LI JRNL TITL BIOPSY-RESOLVED CRYO-EM STRUCTURES OF AMYLOID FIBRILS JRNL TITL 2 PROVIDE MOLECULAR INSIGHTS INTO AL AMYLOIDOSIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 123 54123 2026 JRNL REFN ESSN 1091-6490 JRNL PMID 41493812 JRNL DOI 10.1073/PNAS.2515454123 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 10827 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 9LJ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 19-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1300055663. 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 : AMYLOID LIGHT CHAIN 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5500.00 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, A, B 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 GLN C 1 REMARK 465 SER C 2 REMARK 465 VAL C 3 REMARK 465 LEU C 4 REMARK 465 THR C 5 REMARK 465 GLN C 6 REMARK 465 PRO C 7 REMARK 465 PRO C 8 REMARK 465 SER C 9 REMARK 465 ALA C 10 REMARK 465 SER C 11 REMARK 465 GLY C 12 REMARK 465 THR C 13 REMARK 465 PRO C 14 REMARK 465 GLY C 15 REMARK 465 GLN C 16 REMARK 465 LEU C 111 REMARK 465 SER C 112 REMARK 465 GLN C 113 REMARK 465 PRO C 114 REMARK 465 LYS C 115 REMARK 465 ALA C 116 REMARK 465 ASN C 117 REMARK 465 PRO C 118 REMARK 465 THR C 119 REMARK 465 VAL C 120 REMARK 465 THR C 121 REMARK 465 LEU C 122 REMARK 465 PHE C 123 REMARK 465 PRO C 124 REMARK 465 PRO C 125 REMARK 465 SER C 126 REMARK 465 SER C 127 REMARK 465 GLU C 128 REMARK 465 GLU C 129 REMARK 465 GLN A 1 REMARK 465 SER A 2 REMARK 465 VAL A 3 REMARK 465 LEU A 4 REMARK 465 THR A 5 REMARK 465 GLN A 6 REMARK 465 PRO A 7 REMARK 465 PRO A 8 REMARK 465 SER A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 GLY A 12 REMARK 465 THR A 13 REMARK 465 PRO A 14 REMARK 465 GLY A 15 REMARK 465 GLN A 16 REMARK 465 LEU A 111 REMARK 465 SER A 112 REMARK 465 GLN A 113 REMARK 465 PRO A 114 REMARK 465 LYS A 115 REMARK 465 ALA A 116 REMARK 465 ASN A 117 REMARK 465 PRO A 118 REMARK 465 THR A 119 REMARK 465 VAL A 120 REMARK 465 THR A 121 REMARK 465 LEU A 122 REMARK 465 PHE A 123 REMARK 465 PRO A 124 REMARK 465 PRO A 125 REMARK 465 SER A 126 REMARK 465 SER A 127 REMARK 465 GLU A 128 REMARK 465 GLU A 129 REMARK 465 GLN B 1 REMARK 465 SER B 2 REMARK 465 VAL B 3 REMARK 465 LEU B 4 REMARK 465 THR B 5 REMARK 465 GLN B 6 REMARK 465 PRO B 7 REMARK 465 PRO B 8 REMARK 465 SER B 9 REMARK 465 ALA B 10 REMARK 465 SER B 11 REMARK 465 GLY B 12 REMARK 465 THR B 13 REMARK 465 PRO B 14 REMARK 465 GLY B 15 REMARK 465 GLN B 16 REMARK 465 LEU B 111 REMARK 465 SER B 112 REMARK 465 GLN B 113 REMARK 465 PRO B 114 REMARK 465 LYS B 115 REMARK 465 ALA B 116 REMARK 465 ASN B 117 REMARK 465 PRO B 118 REMARK 465 THR B 119 REMARK 465 VAL B 120 REMARK 465 THR B 121 REMARK 465 LEU B 122 REMARK 465 PHE B 123 REMARK 465 PRO B 124 REMARK 465 PRO B 125 REMARK 465 SER B 126 REMARK 465 SER B 127 REMARK 465 GLU B 128 REMARK 465 GLU B 129 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 ARG C 62 70.47 58.32 REMARK 500 PHE C 63 42.86 70.37 REMARK 500 ASP C 83 96.36 -160.72 REMARK 500 ARG A 62 70.46 58.31 REMARK 500 PHE A 63 42.89 70.34 REMARK 500 ASP A 83 96.40 -160.74 REMARK 500 ARG B 62 70.48 58.33 REMARK 500 PHE B 63 42.88 70.34 REMARK 500 ASP B 83 96.37 -160.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-63129 RELATED DB: EMDB REMARK 900 THE CRYO-EM STRUCTURE OF AMYLOID FIBRILS FROM ABDOMINAL FAT OF AN REMARK 900 AL AMYLOIDOSIS PATIENT (CASE 3). DBREF 9LJ0 C 1 129 PDB 9LJ0 9LJ0 1 129 DBREF 9LJ0 A 1 129 PDB 9LJ0 9LJ0 1 129 DBREF 9LJ0 B 1 129 PDB 9LJ0 9LJ0 1 129 SEQRES 1 C 129 GLN SER VAL LEU THR GLN PRO PRO SER ALA SER GLY THR SEQRES 2 C 129 PRO GLY GLN ARG VAL THR ILE SER CYS SER GLY SER SER SEQRES 3 C 129 SER ASN ILE GLY SER ASN ASN VAL TYR TRP TYR GLN GLN SEQRES 4 C 129 LEU PRO GLY MET ALA PRO LYS LEU LEU ILE TYR ASN ASN SEQRES 5 C 129 PHE GLN ARG PRO SER GLY VAL SER ASP ARG PHE SER GLY SEQRES 6 C 129 SER LYS SER GLY THR SER ALA SER LEU ALA ILE SER GLY SEQRES 7 C 129 LEU ARG SER GLU ASP GLU ALA ASP TYR TYR CYS ALA ALA SEQRES 8 C 129 TRP ASP ASP SER LEU SER GLY LEU TYR VAL PHE GLY THR SEQRES 9 C 129 ALA THR LYS VAL THR VAL LEU SER GLN PRO LYS ALA ASN SEQRES 10 C 129 PRO THR VAL THR LEU PHE PRO PRO SER SER GLU GLU SEQRES 1 A 129 GLN SER VAL LEU THR GLN PRO PRO SER ALA SER GLY THR SEQRES 2 A 129 PRO GLY GLN ARG VAL THR ILE SER CYS SER GLY SER SER SEQRES 3 A 129 SER ASN ILE GLY SER ASN ASN VAL TYR TRP TYR GLN GLN SEQRES 4 A 129 LEU PRO GLY MET ALA PRO LYS LEU LEU ILE TYR ASN ASN SEQRES 5 A 129 PHE GLN ARG PRO SER GLY VAL SER ASP ARG PHE SER GLY SEQRES 6 A 129 SER LYS SER GLY THR SER ALA SER LEU ALA ILE SER GLY SEQRES 7 A 129 LEU ARG SER GLU ASP GLU ALA ASP TYR TYR CYS ALA ALA SEQRES 8 A 129 TRP ASP ASP SER LEU SER GLY LEU TYR VAL PHE GLY THR SEQRES 9 A 129 ALA THR LYS VAL THR VAL LEU SER GLN PRO LYS ALA ASN SEQRES 10 A 129 PRO THR VAL THR LEU PHE PRO PRO SER SER GLU GLU SEQRES 1 B 129 GLN SER VAL LEU THR GLN PRO PRO SER ALA SER GLY THR SEQRES 2 B 129 PRO GLY GLN ARG VAL THR ILE SER CYS SER GLY SER SER SEQRES 3 B 129 SER ASN ILE GLY SER ASN ASN VAL TYR TRP TYR GLN GLN SEQRES 4 B 129 LEU PRO GLY MET ALA PRO LYS LEU LEU ILE TYR ASN ASN SEQRES 5 B 129 PHE GLN ARG PRO SER GLY VAL SER ASP ARG PHE SER GLY SEQRES 6 B 129 SER LYS SER GLY THR SER ALA SER LEU ALA ILE SER GLY SEQRES 7 B 129 LEU ARG SER GLU ASP GLU ALA ASP TYR TYR CYS ALA ALA SEQRES 8 B 129 TRP ASP ASP SER LEU SER GLY LEU TYR VAL PHE GLY THR SEQRES 9 B 129 ALA THR LYS VAL THR VAL LEU SER GLN PRO LYS ALA ASN SEQRES 10 B 129 PRO THR VAL THR LEU PHE PRO PRO SER SER GLU GLU SHEET 1 AA1 3 VAL C 18 CYS C 22 0 SHEET 2 AA1 3 VAL A 18 CYS A 22 1 O ILE A 20 N THR C 19 SHEET 3 AA1 3 VAL B 18 CYS B 22 1 O ILE B 20 N THR A 19 SHEET 1 AA2 3 ASN C 32 GLN C 39 0 SHEET 2 AA2 3 ASN A 32 GLN A 39 1 O ASN A 32 N ASN C 33 SHEET 3 AA2 3 ASN B 32 GLN B 39 1 O ASN B 32 N ASN A 33 SHEET 1 AA3 3 GLY C 42 MET C 43 0 SHEET 2 AA3 3 GLY A 42 MET A 43 1 O GLY A 42 N MET C 43 SHEET 3 AA3 3 GLY B 42 MET B 43 1 O GLY B 42 N MET A 43 SHEET 1 AA4 3 ILE C 49 GLN C 54 0 SHEET 2 AA4 3 ILE A 49 GLN A 54 1 O ASN A 51 N ASN C 52 SHEET 3 AA4 3 ILE B 49 GLN B 54 1 O ASN B 51 N ASN A 52 SHEET 1 AA5 3 SER C 57 ASP C 61 0 SHEET 2 AA5 3 SER A 57 ASP A 61 1 O SER A 60 N VAL C 59 SHEET 3 AA5 3 SER B 57 ASP B 61 1 O SER B 60 N VAL A 59 SHEET 1 AA6 3 SER C 68 LEU C 74 0 SHEET 2 AA6 3 SER A 68 LEU A 74 1 O THR A 70 N GLY C 69 SHEET 3 AA6 3 SER B 68 LEU B 74 1 O THR B 70 N GLY A 69 SHEET 1 AA7 3 GLU C 84 ASP C 86 0 SHEET 2 AA7 3 GLU A 84 ASP A 86 1 O GLU A 84 N ALA C 85 SHEET 3 AA7 3 GLU B 84 ASP B 86 1 O GLU B 84 N ALA A 85 SHEET 1 AA8 3 ALA C 91 ASP C 93 0 SHEET 2 AA8 3 ALA A 91 ASP A 93 1 O ALA A 91 N TRP C 92 SHEET 3 AA8 3 ALA B 91 ASP B 93 1 O ALA B 91 N TRP A 92 SHEET 1 AA9 3 TYR C 100 PHE C 102 0 SHEET 2 AA9 3 TYR A 100 PHE A 102 1 O VAL A 101 N PHE C 102 SHEET 3 AA9 3 TYR B 100 PHE B 102 1 O VAL B 101 N PHE A 102 SHEET 1 AB1 3 ALA C 105 THR C 109 0 SHEET 2 AB1 3 ALA A 105 THR A 109 1 O VAL A 108 N LYS C 107 SHEET 3 AB1 3 ALA B 105 THR B 109 1 O VAL B 108 N LYS A 107 SSBOND 1 CYS C 22 CYS C 89 1555 1555 2.03 SSBOND 2 CYS A 22 CYS A 89 1555 1555 2.03 SSBOND 3 CYS B 22 CYS B 89 1555 1555 2.03 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 TER 709 VAL C 110 TER 1418 VAL A 110 TER 2127 VAL B 110 CONECT 45 553 CONECT 553 45 CONECT 754 1262 CONECT 1262 754 CONECT 1463 1971 CONECT 1971 1463 MASTER 236 0 0 0 30 0 0 6 2124 3 6 30 END