HEADER PROTEIN FIBRIL 29-AUG-15 5AEF TITLE ELECTRON CRYO-MICROSCOPY OF AN ABETA(1-42)AMYLOID FIBRIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ABETA, UNP RESIDUES 630-657; COMPND 5 SYNONYM: ABETA17-42; COMPND 6 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 PROTEIN FIBRIL, ALZHEIMER'S DISEASE, AMYLOID FIBRIL, PROTEIN KEYWDS 2 AGGREGATION, PROTEIN FOLDING, CROSS-BETA, FREALIX EXPDTA ELECTRON MICROSCOPY AUTHOR M.SCHMIDT,A.ROHOU,K.LASKER,J.K.YADAV,C.SCHIENE-FISCHER,M.FANDRICH, AUTHOR 2 N.GRIGORIEFF REVDAT 6 23-OCT-19 5AEF 1 CRYST1 REVDAT 5 02-OCT-19 5AEF 1 CRYST1 SCALE REVDAT 4 03-OCT-18 5AEF 1 REMARK REVDAT 3 30-AUG-17 5AEF 1 REMARK REVDAT 2 21-OCT-15 5AEF 1 JRNL REVDAT 1 14-OCT-15 5AEF 0 JRNL AUTH M.SCHMIDT,A.ROHOU,K.LASKER,J.K.YADAV,C.SCHIENE-FISCHER, JRNL AUTH 2 M.FANDRICH,N.GRIGORIE JRNL TITL PEPTIDE DIMER STRUCTURE IN AN ABETA(1-42) FIBRIL VISUALIZED JRNL TITL 2 WITH CRYO-EM JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 11858 2015 JRNL REFN ISSN 0027-8424 JRNL PMID 26351699 JRNL DOI 10.1073/PNAS.1503455112 REMARK 2 REMARK 2 RESOLUTION. 5.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : FREALIX 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 : OTHER REMARK 3 REFINEMENT TARGET : ELECTRON DENSITY REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--DIREX REFINEMENT PROTOCOL--PEPTIDE REMARK 3 CHAIN 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) : 5.000 REMARK 3 NUMBER OF PARTICLES : 62320 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: FINAL MAP WAS CALCULATED FROM 29 SINGLE FILAMENT REMARK 3 RECONSTRUCTIONS. DATA USED FOR REFINEMENT WAS NEVER BELOW 10 REMARK 3 ANGSTROM RESOLUTION. RESOLUTION OF FIBRIL CORE IS ABOUT 5 REMARK 3 ANGSTROM. 3 POSSIBLE MODELS FOR THE CENTRAL REGION OF A ABETA(1- REMARK 3 42) FIBRIL RECONSTRUCTION. MODEL1 ABETA(17-42) MODEL2 ABETA( 16- REMARK 3 41) MODEL3 ABETA(15-40) SUBMISSION BASED ON EXPERIMENTAL DATA REMARK 3 FROM EMDB EMD-3132. (DEPOSITION ID: 13698). REMARK 4 REMARK 4 5AEF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1290064853. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : VITREOUS ICE CRYO EM REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : ABETA(1-42) AMYLOID-LIKE FIBRIL REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : 4 SEC BACKSIDE BLOTTING REMARK 245 SAMPLE BUFFER : 50MM TRIS-HCL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : FIBRIL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 05-FEB-10 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 100.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F30 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1750.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 30.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 59000 REMARK 245 CALIBRATED MAGNIFICATION : 58333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ILE A 31 CD1 REMARK 470 ILE A 32 CD1 REMARK 470 ILE A 41 CD1 REMARK 470 ALA A 42 O REMARK 470 ILE B 31 CD1 REMARK 470 ILE B 32 CD1 REMARK 470 ILE B 41 CD1 REMARK 470 ALA B 42 O 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 C GLN A 15 N LEU A 17 0.59 REMARK 500 C GLN B 15 CD1 LEU B 17 0.64 REMARK 500 O VAL A 39 C ALA A 42 0.67 REMARK 500 C VAL A 39 C ALA A 42 0.79 REMARK 500 C GLN B 15 N LEU B 17 0.80 REMARK 500 CG2 ILE B 41 CB ALA B 42 0.83 REMARK 500 N VAL A 39 N ALA A 42 0.98 REMARK 500 CG2 ILE B 41 CA ALA B 42 1.03 REMARK 500 O VAL A 39 CA ALA A 42 1.03 REMARK 500 O GLN B 15 CD1 LEU B 17 1.12 REMARK 500 CA GLN B 15 CD1 LEU B 17 1.31 REMARK 500 CB GLN B 15 CD2 LEU B 17 1.33 REMARK 500 C GLN B 15 C LYS B 16 1.35 REMARK 500 O GLN B 15 N LEU B 17 1.38 REMARK 500 C GLN A 15 C LYS A 16 1.41 REMARK 500 CA VAL A 39 N ALA A 42 1.44 REMARK 500 O GLN A 15 N LEU A 17 1.45 REMARK 500 C GLN A 15 CA LEU A 17 1.60 REMARK 500 CB GLN B 15 CG LEU B 17 1.64 REMARK 500 N VAL A 40 C ALA A 42 1.67 REMARK 500 C GLN B 15 CG LEU B 17 1.68 REMARK 500 C VAL A 39 CA ALA A 42 1.70 REMARK 500 CG1 ILE B 41 N ALA B 42 1.73 REMARK 500 CB GLN A 15 CB LEU A 17 1.83 REMARK 500 CA GLN B 15 CG LEU B 17 1.92 REMARK 500 C GLN B 15 CA LEU B 17 1.94 REMARK 500 CB VAL A 39 N ALA A 42 1.97 REMARK 500 O VAL A 39 CB ALA A 42 2.00 REMARK 500 CA GLN A 15 N LEU A 17 2.03 REMARK 500 CB GLN B 15 CD1 LEU B 17 2.08 REMARK 500 CB GLN B 15 CB LEU B 17 2.10 REMARK 500 N GLN B 15 CD1 LEU B 17 2.16 REMARK 500 CA VAL A 39 CA ALA A 42 2.16 REMARK 500 C GLN A 15 CB LEU A 17 2.17 REMARK 500 C VAL A 39 N ALA A 42 2.17 REMARK 500 N VAL A 39 CA ALA A 42 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ILE A 41 C ILE A 41 O 6.112 REMARK 500 ILE B 41 C ILE B 41 O 2.952 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE A 41 CA - C - O ANGL. DEV. = -70.8 DEGREES REMARK 500 ILE B 41 CA - C - O ANGL. DEV. = -88.3 DEGREES 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 PHE A 20 53.81 -116.54 REMARK 500 LYS A 28 89.34 -156.59 REMARK 500 VAL A 36 111.69 80.71 REMARK 500 LYS B 28 117.87 -174.89 REMARK 500 ALA B 30 54.44 -99.17 REMARK 500 VAL B 36 116.96 67.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 26 ASN A 27 -149.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 3-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 4-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-3132 RELATED DB: EMDB DBREF 5AEF A 15 42 UNP E9PG40 E9PG40_HUMAN 630 657 DBREF 5AEF B 15 42 UNP E9PG40 E9PG40_HUMAN 630 657 SEQRES 1 A 28 GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN SEQRES 2 A 28 LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL VAL SEQRES 3 A 28 ILE ALA SEQRES 1 B 28 GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN SEQRES 2 B 28 LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL VAL SEQRES 3 B 28 ILE ALA SHEET 1 AA 2 LYS A 16 VAL A 18 0 SHEET 2 AA 2 LEU A 17 PHE A 19 1 O LEU A 17 N LEU A 17 SHEET 1 AB 2 GLY A 33 LEU A 34 0 SHEET 2 AB 2 ALA A 30 GLY A 37 1 O GLY A 33 N LEU A 34 SHEET 1 AC 2 ALA A 30 ILE A 32 0 SHEET 2 AC 2 ALA A 30 GLY A 37 1 O ALA A 30 N ILE A 31 SHEET 1 AD 2 MET A 35 VAL A 40 0 SHEET 2 AD 2 ALA A 30 GLY A 37 1 O MET A 35 N VAL A 36 SHEET 1 BA 4 LYS B 16 PHE B 19 0 SHEET 2 BA 4 LEU B 17 PHE B 20 1 O LEU B 17 N LEU B 17 SHEET 3 BA 4 PHE B 19 PHE B 20 -1 O PHE B 19 N PHE B 19 SHEET 4 BA 4 LYS B 16 PHE B 19 -1 O LEU B 17 N PHE B 19 SHEET 1 BB 2 ASN B 27 LYS B 28 0 SHEET 2 BB 2 ASN B 27 LEU B 34 1 O ASN B 27 N LYS B 28 SHEET 1 BC 2 ILE B 32 GLY B 33 0 SHEET 2 BC 2 ASN B 27 LEU B 34 1 O ILE B 31 N ILE B 32 SHEET 1 BD 4 MET B 35 VAL B 36 0 SHEET 2 BD 4 LYS B 28 VAL B 36 1 O MET B 35 N MET B 35 SHEET 3 BD 4 ASN B 27 LEU B 34 1 O ASN B 27 N LYS B 28 SHEET 4 BD 4 ILE B 32 GLY B 33 1 O ILE B 32 N GLY B 33 SHEET 1 BE 4 MET B 35 VAL B 36 0 SHEET 2 BE 4 LYS B 28 VAL B 36 1 O MET B 35 N MET B 35 SHEET 3 BE 4 ASN B 27 LEU B 34 1 O ASN B 27 N LYS B 28 SHEET 4 BE 4 ASN B 27 LYS B 28 1 O ASN B 27 N LYS B 28 CISPEP 1 GLY A 37 GLY A 38 0 -25.15 CISPEP 2 GLY B 37 GLY B 38 0 -28.66 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