HEADER PROTEIN FIBRIL 02-SEP-25 9WL5 TITLE ALECT2 TYPE IA FILAMENT FROM RENAL BIOPSY TISSUE OF AN INDIVIDUAL WITH TITLE 2 ALECT2 AMYLOIDOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUKOCYTE CELL-DERIVED CHEMOTAXIN-2; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: LECT-2,HLECT2; COMPND 5 OTHER_DETAILS: LEUKOCYTE CHEMOTACTIC FACTOR 2 WITH A I40V MUTATION SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS LEUKOCYTE CHEMOTACTIC FACTOR 2 AMYLOID FILAMENT, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR J.ZHENG,Y.ZHENG,Y.SHI REVDAT 1 03-JUN-26 9WL5 0 JRNL AUTH J.L.ZHENG,Y.X.ZHENG,K.CHEN,S.WANG,J.W.LIANG,S.X.WANG,L.YANG, JRNL AUTH 2 Y.SHI JRNL TITL CRYO-EM STRUCTURES OF ALECT2 FILAMENTS FROM HUMAN RENAL JRNL TITL 2 BIOPSIES. JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 42173881 JRNL DOI 10.1038/S41467-026-73602-2 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, PHENIX, 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 : 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) : 1.960 REMARK 3 NUMBER OF PARTICLES : 453143 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 9WL5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 05-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1300063037. 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 : LEUKOCYTE CHEMOTACTIC FACTOR 2 REMARK 245 AMYLOID FILAMENTS 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 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) : 4200.00 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: A, B, C 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 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 ASN A 5 -67.83 -98.53 REMARK 500 ASP A 39 -61.41 -94.03 REMARK 500 ALA A 44 77.82 60.19 REMARK 500 CYS A 81 78.84 62.47 REMARK 500 HIS A 118 75.05 67.06 REMARK 500 ASN B 5 -67.82 -98.55 REMARK 500 ASP B 39 -61.43 -94.08 REMARK 500 ALA B 44 77.86 60.21 REMARK 500 CYS B 81 78.83 62.48 REMARK 500 HIS B 118 75.06 67.08 REMARK 500 ASN C 5 -67.84 -98.52 REMARK 500 ASP C 39 -61.45 -94.01 REMARK 500 ALA C 44 77.87 60.16 REMARK 500 CYS C 81 78.81 62.51 REMARK 500 HIS C 118 74.99 67.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-66046 RELATED DB: EMDB REMARK 900 ALECT2 TYPE IA FILAMENT FROM RENAL BIOPSY TISSUE OF AN INDIVIDUAL REMARK 900 WITH ALECT2 AMYLOIDOSIS DBREF 9WL5 A 1 133 UNP O14960 LECT2_HUMAN 19 151 DBREF 9WL5 B 1 133 UNP O14960 LECT2_HUMAN 19 151 DBREF 9WL5 C 1 133 UNP O14960 LECT2_HUMAN 19 151 SEQADV 9WL5 VAL A 40 UNP O14960 ILE 58 VARIANT SEQADV 9WL5 VAL B 40 UNP O14960 ILE 58 VARIANT SEQADV 9WL5 VAL C 40 UNP O14960 ILE 58 VARIANT SEQRES 1 A 133 GLY PRO TRP ALA ASN ILE CYS ALA GLY LYS SER SER ASN SEQRES 2 A 133 GLU ILE ARG THR CYS ASP ARG HIS GLY CYS GLY GLN TYR SEQRES 3 A 133 SER ALA GLN ARG SER GLN ARG PRO HIS GLN GLY VAL ASP SEQRES 4 A 133 VAL LEU CYS SER ALA GLY SER THR VAL TYR ALA PRO PHE SEQRES 5 A 133 THR GLY MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN SEQRES 6 A 133 LYS ASN ALA ILE ASN ASN GLY VAL ARG ILE SER GLY ARG SEQRES 7 A 133 GLY PHE CYS VAL LYS MET PHE TYR ILE LYS PRO ILE LYS SEQRES 8 A 133 TYR LYS GLY PRO ILE LYS LYS GLY GLU LYS LEU GLY THR SEQRES 9 A 133 LEU LEU PRO LEU GLN LYS VAL TYR PRO GLY ILE GLN SER SEQRES 10 A 133 HIS VAL HIS ILE GLU ASN CYS ASP SER SER ASP PRO THR SEQRES 11 A 133 ALA TYR LEU SEQRES 1 B 133 GLY PRO TRP ALA ASN ILE CYS ALA GLY LYS SER SER ASN SEQRES 2 B 133 GLU ILE ARG THR CYS ASP ARG HIS GLY CYS GLY GLN TYR SEQRES 3 B 133 SER ALA GLN ARG SER GLN ARG PRO HIS GLN GLY VAL ASP SEQRES 4 B 133 VAL LEU CYS SER ALA GLY SER THR VAL TYR ALA PRO PHE SEQRES 5 B 133 THR GLY MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN SEQRES 6 B 133 LYS ASN ALA ILE ASN ASN GLY VAL ARG ILE SER GLY ARG SEQRES 7 B 133 GLY PHE CYS VAL LYS MET PHE TYR ILE LYS PRO ILE LYS SEQRES 8 B 133 TYR LYS GLY PRO ILE LYS LYS GLY GLU LYS LEU GLY THR SEQRES 9 B 133 LEU LEU PRO LEU GLN LYS VAL TYR PRO GLY ILE GLN SER SEQRES 10 B 133 HIS VAL HIS ILE GLU ASN CYS ASP SER SER ASP PRO THR SEQRES 11 B 133 ALA TYR LEU SEQRES 1 C 133 GLY PRO TRP ALA ASN ILE CYS ALA GLY LYS SER SER ASN SEQRES 2 C 133 GLU ILE ARG THR CYS ASP ARG HIS GLY CYS GLY GLN TYR SEQRES 3 C 133 SER ALA GLN ARG SER GLN ARG PRO HIS GLN GLY VAL ASP SEQRES 4 C 133 VAL LEU CYS SER ALA GLY SER THR VAL TYR ALA PRO PHE SEQRES 5 C 133 THR GLY MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN SEQRES 6 C 133 LYS ASN ALA ILE ASN ASN GLY VAL ARG ILE SER GLY ARG SEQRES 7 C 133 GLY PHE CYS VAL LYS MET PHE TYR ILE LYS PRO ILE LYS SEQRES 8 C 133 TYR LYS GLY PRO ILE LYS LYS GLY GLU LYS LEU GLY THR SEQRES 9 C 133 LEU LEU PRO LEU GLN LYS VAL TYR PRO GLY ILE GLN SER SEQRES 10 C 133 HIS VAL HIS ILE GLU ASN CYS ASP SER SER ASP PRO THR SEQRES 11 C 133 ALA TYR LEU SHEET 1 AA1 3 TRP B 3 ILE B 6 0 SHEET 2 AA1 3 TRP A 3 ILE A 6 1 N ASN A 5 O ILE B 6 SHEET 3 AA1 3 TRP C 3 ILE C 6 1 O ASN C 5 N ILE A 6 SHEET 1 AA2 3 SER B 12 ASP B 19 0 SHEET 2 AA2 3 SER A 12 ASP A 19 1 N SER A 12 O ASN B 13 SHEET 3 AA2 3 SER C 12 ASP C 19 1 O SER C 12 N ASN A 13 SHEET 1 AA3 3 TYR B 26 GLN B 29 0 SHEET 2 AA3 3 TYR A 26 GLN A 29 1 N GLN A 29 O ALA B 28 SHEET 3 AA3 3 TYR C 26 GLN C 29 1 O GLN C 29 N ALA A 28 SHEET 1 AA4 3 HIS B 35 LEU B 41 0 SHEET 2 AA4 3 HIS A 35 LEU A 41 1 N VAL A 40 O ASP B 39 SHEET 3 AA4 3 HIS C 35 LEU C 41 1 O VAL C 40 N ASP A 39 SHEET 1 AA5 3 THR B 47 TYR B 49 0 SHEET 2 AA5 3 THR A 47 TYR A 49 1 N VAL A 48 O TYR B 49 SHEET 3 AA5 3 THR C 47 TYR C 49 1 O VAL C 48 N TYR A 49 SHEET 1 AA6 3 PHE B 52 GLU B 60 0 SHEET 2 AA6 3 PHE A 52 GLU A 60 1 N GLU A 60 O GLN B 59 SHEET 3 AA6 3 PHE C 52 GLU C 60 1 O GLU C 60 N GLN A 59 SHEET 1 AA7 3 LYS B 66 ILE B 75 0 SHEET 2 AA7 3 LYS A 66 ILE A 75 1 N ASN A 70 O ILE B 69 SHEET 3 AA7 3 LYS C 66 ILE C 75 1 O ASN C 70 N ILE A 69 SHEET 1 AA8 3 ARG B 78 GLY B 79 0 SHEET 2 AA8 3 ARG A 78 GLY A 79 1 N ARG A 78 O GLY B 79 SHEET 3 AA8 3 ARG C 78 GLY C 79 1 O ARG C 78 N GLY A 79 SHEET 1 AA9 3 LYS B 83 ILE B 87 0 SHEET 2 AA9 3 LYS A 83 ILE A 87 1 N PHE A 85 O MET B 84 SHEET 3 AA9 3 LYS C 83 ILE C 87 1 O PHE C 85 N MET A 84 SHEET 1 AB1 3 ILE B 96 LYS B 98 0 SHEET 2 AB1 3 ILE A 96 LYS A 98 1 N ILE A 96 O LYS B 97 SHEET 3 AB1 3 ILE C 96 LYS C 98 1 O ILE C 96 N LYS A 97 SHEET 1 AB2 3 THR B 104 LEU B 105 0 SHEET 2 AB2 3 THR A 104 LEU A 105 1 N THR A 104 O LEU B 105 SHEET 3 AB2 3 THR C 104 LEU C 105 1 O THR C 104 N LEU A 105 SHEET 1 AB3 3 LEU B 108 VAL B 111 0 SHEET 2 AB3 3 LEU A 108 VAL A 111 1 N LEU A 108 O GLN B 109 SHEET 3 AB3 3 LEU C 108 VAL C 111 1 O LEU C 108 N GLN A 109 SHEET 1 AB4 3 GLY B 114 ILE B 115 0 SHEET 2 AB4 3 GLY A 114 ILE A 115 1 N ILE A 115 O GLY B 114 SHEET 3 AB4 3 GLY C 114 ILE C 115 1 O ILE C 115 N GLY A 114 SHEET 1 AB5 3 VAL B 119 ASN B 123 0 SHEET 2 AB5 3 VAL A 119 ASN A 123 1 N ASN A 123 O GLU B 122 SHEET 3 AB5 3 VAL C 119 ASN C 123 1 O ASN C 123 N GLU A 122 SHEET 1 AB6 3 THR B 130 TYR B 132 0 SHEET 2 AB6 3 THR A 130 TYR A 132 1 N THR A 130 O ALA B 131 SHEET 3 AB6 3 THR C 130 TYR C 132 1 O THR C 130 N ALA A 131 SSBOND 1 CYS A 7 CYS A 42 1555 1555 2.04 SSBOND 2 CYS A 18 CYS A 23 1555 1555 2.03 SSBOND 3 CYS A 81 CYS A 124 1555 1555 2.02 SSBOND 4 CYS B 7 CYS B 42 1555 1555 2.04 SSBOND 5 CYS B 18 CYS B 23 1555 1555 2.03 SSBOND 6 CYS B 81 CYS B 124 1555 1555 2.02 SSBOND 7 CYS C 7 CYS C 42 1555 1555 2.04 SSBOND 8 CYS C 18 CYS C 23 1555 1555 2.03 SSBOND 9 CYS C 81 CYS C 124 1555 1555 2.02 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 CONECT 52 318 CONECT 131 170 CONECT 170 131 CONECT 318 52 CONECT 607 954 CONECT 954 607 CONECT 1075 1341 CONECT 1154 1193 CONECT 1193 1154 CONECT 1341 1075 CONECT 1630 1977 CONECT 1977 1630 CONECT 2098 2364 CONECT 2177 2216 CONECT 2216 2177 CONECT 2364 2098 CONECT 2653 3000 CONECT 3000 2653 MASTER 131 0 0 0 45 0 0 6 3066 3 18 33 END