HEADER PROTEIN FIBRIL 06-FEB-23 8G2V TITLE CRYO-EM STRUCTURE OF RECOMBINANT HUMAN LECT2 AMYLOID FIBRIL CORE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUKOCYTE CELL-DERIVED CHEMOTAXIN-2; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J; COMPND 4 SYNONYM: LECT-2,HLECT2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: LECT2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMYLOID, LECT2, HUMAN, RECOMBINANT, FIBRIL, PROTEIN, ALECT2, CRYO-EM, KEYWDS 2 PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR L.S.RICHARDS,M.D.FLORES,S.ZINK,N.A.SCHIBROWSKY,M.R.SAWAYA, AUTHOR 2 J.A.RODRIGUEZ REVDAT 3 15-NOV-23 8G2V 1 JRNL REVDAT 2 13-SEP-23 8G2V 1 JRNL REVDAT 1 16-AUG-23 8G2V 0 JRNL AUTH L.S.RICHARDS,M.D.FLORES,S.ZINK,N.A.SCHIBROWSKY,M.R.SAWAYA, JRNL AUTH 2 J.A.RODRIGUEZ JRNL TITL CRYO-EM STRUCTURE OF A HUMAN LECT2 AMYLOID FIBRIL REVEALS A JRNL TITL 2 NETWORK OF POLAR LADDERS AT ITS CORE. JRNL REF STRUCTURE V. 31 1386 2023 JRNL REFN ISSN 0969-2126 JRNL PMID 37657439 JRNL DOI 10.1016/J.STR.2023.08.007 REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOLO, EPU, CTFFIND, COOT, 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 : 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) : 2.715 REMARK 3 NUMBER OF PARTICLES : 24770 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 8G2V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000272110. 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 : RECOMBINANT HUMAN LECT2 AMYLOID REMARK 245 FIBRIL CORE. 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 : 6.50 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 130.00 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: 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-29682 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF RECOMBINANT HUMAN LECT2 AMYLOID FIBRIL CORE DBREF 8G2V A 55 75 UNP O14960 LECT2_HUMAN 73 93 DBREF 8G2V B 55 75 UNP O14960 LECT2_HUMAN 73 93 DBREF 8G2V C 55 75 UNP O14960 LECT2_HUMAN 73 93 DBREF 8G2V D 55 75 UNP O14960 LECT2_HUMAN 73 93 DBREF 8G2V E 55 75 UNP O14960 LECT2_HUMAN 73 93 DBREF 8G2V F 55 75 UNP O14960 LECT2_HUMAN 73 93 DBREF 8G2V G 55 75 UNP O14960 LECT2_HUMAN 73 93 DBREF 8G2V H 55 75 UNP O14960 LECT2_HUMAN 73 93 DBREF 8G2V I 55 75 UNP O14960 LECT2_HUMAN 73 93 DBREF 8G2V J 55 75 UNP O14960 LECT2_HUMAN 73 93 SEQRES 1 A 21 MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN LYS ASN SEQRES 2 A 21 ALA ILE ASN ASN GLY VAL ARG ILE SEQRES 1 B 21 MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN LYS ASN SEQRES 2 B 21 ALA ILE ASN ASN GLY VAL ARG ILE SEQRES 1 C 21 MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN LYS ASN SEQRES 2 C 21 ALA ILE ASN ASN GLY VAL ARG ILE SEQRES 1 D 21 MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN LYS ASN SEQRES 2 D 21 ALA ILE ASN ASN GLY VAL ARG ILE SEQRES 1 E 21 MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN LYS ASN SEQRES 2 E 21 ALA ILE ASN ASN GLY VAL ARG ILE SEQRES 1 F 21 MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN LYS ASN SEQRES 2 F 21 ALA ILE ASN ASN GLY VAL ARG ILE SEQRES 1 G 21 MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN LYS ASN SEQRES 2 G 21 ALA ILE ASN ASN GLY VAL ARG ILE SEQRES 1 H 21 MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN LYS ASN SEQRES 2 H 21 ALA ILE ASN ASN GLY VAL ARG ILE SEQRES 1 I 21 MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN LYS ASN SEQRES 2 I 21 ALA ILE ASN ASN GLY VAL ARG ILE SEQRES 1 J 21 MET ILE VAL GLY GLN GLU LYS PRO TYR GLN ASN LYS ASN SEQRES 2 J 21 ALA ILE ASN ASN GLY VAL ARG ILE SHEET 1 AA1 5 VAL H 57 GLU H 60 0 SHEET 2 AA1 5 VAL D 57 GLU D 60 1 N GLU D 60 O GLN H 59 SHEET 3 AA1 5 VAL A 57 GLU A 60 1 N GLY A 58 O GLN D 59 SHEET 4 AA1 5 VAL E 57 GLU E 60 1 O GLY E 58 N GLN A 59 SHEET 5 AA1 5 VAL I 57 GLU I 60 1 O GLY I 58 N GLN E 59 SHEET 1 AA2 5 ASN H 67 ASN H 70 0 SHEET 2 AA2 5 ASN D 67 ASN D 70 1 N ALA D 68 O ASN H 67 SHEET 3 AA2 5 ASN A 67 ASN A 70 1 N ALA A 68 O ASN D 67 SHEET 4 AA2 5 ASN E 67 ASN E 70 1 O ALA E 68 N ASN A 67 SHEET 5 AA2 5 ASN I 67 ALA I 68 1 O ALA I 68 N ASN E 67 SHEET 1 AA3 5 VAL H 73 ARG H 74 0 SHEET 2 AA3 5 VAL D 73 ARG D 74 1 N ARG D 74 O VAL H 73 SHEET 3 AA3 5 VAL A 73 ARG A 74 1 N ARG A 74 O VAL D 73 SHEET 4 AA3 5 VAL E 73 ARG E 74 1 O ARG E 74 N VAL A 73 SHEET 5 AA3 5 VAL I 73 ARG I 74 1 O ARG I 74 N VAL E 73 SHEET 1 AA4 5 VAL F 57 GLU F 60 0 SHEET 2 AA4 5 VAL B 57 GLU B 60 1 N GLY B 58 O GLN F 59 SHEET 3 AA4 5 VAL C 57 GLU C 60 1 O GLY C 58 N GLN B 59 SHEET 4 AA4 5 VAL G 57 GLU G 60 1 O GLY G 58 N GLN C 59 SHEET 5 AA4 5 VAL J 57 GLU J 60 1 O GLY J 58 N GLN G 59 SHEET 1 AA5 5 ASN F 67 ASN F 70 0 SHEET 2 AA5 5 ASN B 67 ASN B 70 1 N ALA B 68 O ASN F 67 SHEET 3 AA5 5 ASN C 67 ASN C 70 1 O ALA C 68 N ASN B 67 SHEET 4 AA5 5 ASN G 67 ASN G 70 1 O ALA G 68 N ASN C 67 SHEET 5 AA5 5 ASN J 67 ALA J 68 1 O ALA J 68 N ASN G 67 SHEET 1 AA6 5 VAL F 73 ARG F 74 0 SHEET 2 AA6 5 VAL B 73 ARG B 74 1 N ARG B 74 O VAL F 73 SHEET 3 AA6 5 VAL C 73 ARG C 74 1 O ARG C 74 N VAL B 73 SHEET 4 AA6 5 VAL G 73 ARG G 74 1 O ARG G 74 N VAL C 73 SHEET 5 AA6 5 VAL J 73 ARG J 74 1 O ARG J 74 N VAL G 73 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