HEADER PROTEIN FIBRIL 10-JUN-21 7F29 TITLE CRYO-EM STRUCTURE OF THE FIBRIL FORMED BY DISACCHARIDE-MODIFIED TITLE 2 AMYLOID-BETA(1-42) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA A4 PROTEIN; COMPND 3 CHAIN: E, C, D, F, A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS AMYLOID FIBRIL, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR W.C.XIA,Y.P.SUN,C.LIU REVDAT 1 13-JUL-22 7F29 0 JRNL AUTH D.LIU,Q.WEI,W.XIA,C.HE,Q.ZHANG,L.HUANG,X.WANG,Y.SUN,Y.MA, JRNL AUTH 2 X.ZHANG,Y.WANG,X.SHI,C.LIU,S.DONG JRNL TITL O-GLYCOSYLATION INDUCES AMYLOID-BETA TO FORM NEW FIBRIL JRNL TITL 2 POLYMORPHS VULNERABLE FOR DEGRADATION JRNL REF J.AM.CHEM.SOC. V. 143 20216 2021 JRNL REFN ESSN 1520-5126 JRNL DOI 10.1021/JACS.1C08607 REMARK 2 REMARK 2 RESOLUTION. 3.10 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 92523 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 7F29 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022621. 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 : CRYO-EM STRUCTURE OF THE FIBRIL REMARK 245 FORMED BY DISACCHARIDE-MODIFIED REMARK 245 AMYLOID-BETA(1-42) 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 : 4.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, C, D, F, A, B, G, H, I, J, REMARK 350 AND CHAINS: K, L 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR E 10 OH REMARK 470 TYR C 10 OH REMARK 470 TYR D 10 OH REMARK 470 TYR F 10 OH REMARK 470 TYR A 10 OH REMARK 470 TYR B 10 OH 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 CZ TYR F 10 O1 X6X J 1 1.37 REMARK 500 CZ TYR A 10 O1 X6X K 1 1.37 REMARK 500 CZ TYR E 10 O1 X6X G 1 1.37 REMARK 500 CZ TYR D 10 O1 X6X I 1 1.37 REMARK 500 CZ TYR B 10 O1 X6X L 1 1.37 REMARK 500 CZ TYR C 10 O1 X6X H 1 1.37 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 GLU E 22 -61.78 -93.87 REMARK 500 GLU C 22 -61.74 -93.91 REMARK 500 GLU D 22 -61.74 -93.87 REMARK 500 GLU F 22 -61.76 -93.90 REMARK 500 GLU A 22 -61.80 -93.88 REMARK 500 GLU B 22 -61.81 -93.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-31428 RELATED DB: EMDB DBREF 7F29 E 6 42 UNP B4DM00 B4DM00_HUMAN 435 471 DBREF 7F29 C 6 42 UNP B4DM00 B4DM00_HUMAN 435 471 DBREF 7F29 D 6 42 UNP B4DM00 B4DM00_HUMAN 435 471 DBREF 7F29 F 6 42 UNP B4DM00 B4DM00_HUMAN 435 471 DBREF 7F29 A 6 42 UNP B4DM00 B4DM00_HUMAN 435 471 DBREF 7F29 B 6 42 UNP B4DM00 B4DM00_HUMAN 435 471 SEQRES 1 E 37 HIS ASP SER GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL SEQRES 2 E 37 PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY ALA ILE SEQRES 3 E 37 ILE GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 C 37 HIS ASP SER GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL SEQRES 2 C 37 PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY ALA ILE SEQRES 3 C 37 ILE GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 D 37 HIS ASP SER GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL SEQRES 2 D 37 PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY ALA ILE SEQRES 3 D 37 ILE GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 F 37 HIS ASP SER GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL SEQRES 2 F 37 PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY ALA ILE SEQRES 3 F 37 ILE GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 A 37 HIS ASP SER GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL SEQRES 2 A 37 PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY ALA ILE SEQRES 3 A 37 ILE GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 B 37 HIS ASP SER GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL SEQRES 2 B 37 PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY ALA ILE SEQRES 3 B 37 ILE GLY LEU MET VAL GLY GLY VAL VAL ILE ALA HET X6X G 1 12 HET GAL G 2 11 HET X6X H 1 12 HET GAL H 2 11 HET X6X I 1 12 HET GAL I 2 11 HET X6X J 1 12 HET GAL J 2 11 HET X6X K 1 12 HET GAL K 2 11 HET X6X L 1 12 HET GAL L 2 11 HET ACY E 101 3 HET ACY C 101 3 HET ACY D 101 3 HET ACY F 101 3 HET ACY A 101 3 HET ACY B 101 3 HETNAM X6X 2-AMINO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM ACY ACETIC ACID HETSYN X6X ALPHA-D-GALACTOSAMINE; 2-AMINO-2-DEOXY-ALPHA-D- HETSYN 2 X6X GALACTOSE; 2-AMINO-2-DEOXY-D-GALACTOSE; 2-AMINO-2- HETSYN 3 X6X DEOXY-GALACTOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 7 X6X 6(C6 H13 N O5) FORMUL 7 GAL 6(C6 H12 O6) FORMUL 13 ACY 6(C2 H4 O2) SHEET 1 AA1 3 GLU C 11 VAL C 12 0 SHEET 2 AA1 3 GLU E 11 VAL E 12 1 N GLU E 11 O VAL C 12 SHEET 3 AA1 3 GLU D 11 VAL D 12 1 O GLU D 11 N VAL E 12 SHEET 1 AA2 3 GLN C 15 ASN C 27 0 SHEET 2 AA2 3 GLN E 15 ASN E 27 1 N ASP E 23 O GLU C 22 SHEET 3 AA2 3 GLN D 15 ASN D 27 1 O ASP D 23 N GLU E 22 SHEET 1 AA3 3 ALA C 30 MET C 35 0 SHEET 2 AA3 3 ALA E 30 MET E 35 1 N MET E 35 O LEU C 34 SHEET 3 AA3 3 ALA D 30 MET D 35 1 O MET D 35 N LEU E 34 SHEET 1 AA4 3 VAL C 39 ILE C 41 0 SHEET 2 AA4 3 VAL E 39 ILE E 41 1 N VAL E 40 O ILE C 41 SHEET 3 AA4 3 VAL D 39 ILE D 41 1 O VAL D 40 N ILE E 41 SHEET 1 AA5 3 GLU A 11 VAL A 12 0 SHEET 2 AA5 3 GLU F 11 VAL F 12 1 N GLU F 11 O VAL A 12 SHEET 3 AA5 3 GLU B 11 VAL B 12 1 O GLU B 11 N VAL F 12 SHEET 1 AA6 3 GLN A 15 ASN A 27 0 SHEET 2 AA6 3 GLN F 15 ASN F 27 1 N ASP F 23 O GLU A 22 SHEET 3 AA6 3 GLN B 15 ASN B 27 1 O ASP B 23 N GLU F 22 SHEET 1 AA7 3 ALA A 30 MET A 35 0 SHEET 2 AA7 3 ALA F 30 MET F 35 1 N MET F 35 O LEU A 34 SHEET 3 AA7 3 ALA B 30 MET B 35 1 O MET B 35 N LEU F 34 SHEET 1 AA8 3 VAL A 39 ILE A 41 0 SHEET 2 AA8 3 VAL F 39 ILE F 41 1 N VAL F 40 O ILE A 41 SHEET 3 AA8 3 VAL B 39 ILE B 41 1 O VAL B 40 N ILE F 41 LINK C ACY E 101 N2 X6X G 1 1555 1555 1.46 LINK C ACY C 101 N2 X6X H 1 1555 1555 1.46 LINK C ACY D 101 N2 X6X I 1 1555 1555 1.46 LINK C ACY F 101 N2 X6X J 1 1555 1555 1.46 LINK C ACY A 101 N2 X6X K 1 1555 1555 1.46 LINK C ACY B 101 N2 X6X L 1 1555 1555 1.46 LINK O3 X6X G 1 C1 GAL G 2 1555 1555 1.40 LINK O3 X6X H 1 C1 GAL H 2 1555 1555 1.40 LINK O3 X6X I 1 C1 GAL I 2 1555 1555 1.40 LINK O3 X6X J 1 C1 GAL J 2 1555 1555 1.40 LINK O3 X6X K 1 C1 GAL K 2 1555 1555 1.40 LINK O3 X6X L 1 C1 GAL L 2 1555 1555 1.40 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