HEADER PROTEIN FIBRIL 08-AUG-19 6SHS
TITLE ABETA FIBRIL (MORPHOLOGY I)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: AMYLOID-BETA PRECURSOR PROTEIN;
COMPND 3 CHAIN: A, B, C, H, D, I, E, J, F, K, G, L;
COMPND 4 SYNONYM: APP,ABPP,APPI,ALZHEIMER DISEASE AMYLOID PROTEIN,AMYLOID
COMPND 5 PRECURSOR PROTEIN,AMYLOID-BETA A4 PROTEIN,CEREBRAL VASCULAR AMYLOID
COMPND 6 PEPTIDE,CVAP,PREA4,PROTEASE NEXIN-II,PN-II
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 ORGAN: BRAIN;
SOURCE 6 TISSUE: MENINGES
KEYWDS FIBRIL, BETA AMYLOID, CRYO-EM, PROTEIN FIBRIL
EXPDTA ELECTRON MICROSCOPY
AUTHOR M.KOLLMER,M.FANDRICH
REVDAT 1 06-NOV-19 6SHS 0
JRNL AUTH M.KOLLMER,W.CLOSE,L.FUNK,J.RASMUSSEN,A.BSOUL,A.SCHIERHORN,
JRNL AUTH 2 M.SCHMIDT,C.J.SIGURDSON,M.JUCKER,M.FANDRICH
JRNL TITL CRYO-EM STRUCTURE AND POLYMORPHISM OF A BETA AMYLOID FIBRILS
JRNL TITL 2 PURIFIED FROM ALZHEIMER'S BRAIN TISSUE.
JRNL REF NAT COMMUN V. 10 4760 2019
JRNL REFN ESSN 2041-1723
JRNL PMID 31664019
JRNL DOI 10.1038/S41467-019-12683-8
REMARK 2
REMARK 2 RESOLUTION. 4.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 SOFTWARE PACKAGES : GCTF, COOT, PHENIX, RELION, 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) : 4.400
REMARK 3 NUMBER OF PARTICLES : 12282
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 6SHS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-AUG-19.
REMARK 100 THE DEPOSITION ID IS D_1292103770.
REMARK 245
REMARK 245 EXPERIMENTAL DETAILS
REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE
REMARK 245 SPECIMEN TYPE : NULL
REMARK 245
REMARK 245 ELECTRON MICROSCOPE SAMPLE
REMARK 245 SAMPLE TYPE : HELICAL ARRAY
REMARK 245 PARTICLE TYPE : POINT
REMARK 245 NAME OF SAMPLE : MENINGES
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 : 3027
REMARK 245 TEMPERATURE (KELVIN) : NULL
REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS
REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K)
REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00
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 : 2.70
REMARK 245 IMAGING MODE : BRIGHT FIELD
REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 40.90
REMARK 245 ILLUMINATION MODE : FLOOD BEAM
REMARK 245 NOMINAL MAGNIFICATION : 105000
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: DODECAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 36980 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 20920 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -147.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, H, D, I, E, J, F, K,
REMARK 350 AND CHAINS: G, 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 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 A 22 -53.60 -121.03
REMARK 500 ALA A 30 -39.44 -131.07
REMARK 500 GLU B 22 -53.57 -121.04
REMARK 500 ALA B 30 -39.46 -131.08
REMARK 500 GLU C 22 -53.56 -121.07
REMARK 500 ALA C 30 -39.41 -131.07
REMARK 500 GLU H 22 -53.53 -121.02
REMARK 500 ALA H 30 -39.47 -131.07
REMARK 500 GLU D 22 -53.58 -121.05
REMARK 500 ALA D 30 -39.39 -131.09
REMARK 500 GLU I 22 -53.56 -121.07
REMARK 500 ALA I 30 -39.49 -131.10
REMARK 500 GLU E 22 -53.61 -121.04
REMARK 500 ALA E 30 -39.44 -131.08
REMARK 500 GLU J 22 -53.58 -121.04
REMARK 500 ALA J 30 -39.47 -131.06
REMARK 500 GLU F 22 -53.62 -121.06
REMARK 500 ALA F 30 -39.47 -131.11
REMARK 500 GLU K 22 -53.63 -121.06
REMARK 500 ALA K 30 -39.49 -131.06
REMARK 500 GLU G 22 -53.64 -121.05
REMARK 500 ALA G 30 -39.44 -131.09
REMARK 500 GLU L 22 -53.60 -121.04
REMARK 500 ALA L 30 -39.46 -131.09
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: EMD-4864 RELATED DB: EMDB
REMARK 900 RELATED ID: EMD-4866 RELATED DB: EMDB
REMARK 900 RELATED ID: EMD-10204 RELATED DB: EMDB
REMARK 900 ABETA FIBRIL (MORPHOLOGY I)
DBREF 6SHS A 1 40 UNP P05067 A4_HUMAN 616 655
DBREF 6SHS B 1 40 UNP P05067 A4_HUMAN 616 655
DBREF 6SHS C 1 40 UNP P05067 A4_HUMAN 616 655
DBREF 6SHS H 1 40 UNP P05067 A4_HUMAN 616 655
DBREF 6SHS D 1 40 UNP P05067 A4_HUMAN 616 655
DBREF 6SHS I 1 40 UNP P05067 A4_HUMAN 616 655
DBREF 6SHS E 1 40 UNP P05067 A4_HUMAN 616 655
DBREF 6SHS J 1 40 UNP P05067 A4_HUMAN 616 655
DBREF 6SHS F 1 40 UNP P05067 A4_HUMAN 616 655
DBREF 6SHS K 1 40 UNP P05067 A4_HUMAN 616 655
DBREF 6SHS G 1 40 UNP P05067 A4_HUMAN 616 655
DBREF 6SHS L 1 40 UNP P05067 A4_HUMAN 616 655
SEQRES 1 A 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS
SEQRES 2 A 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER
SEQRES 3 A 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL
SEQRES 4 A 40 VAL
SEQRES 1 B 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS
SEQRES 2 B 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER
SEQRES 3 B 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL
SEQRES 4 B 40 VAL
SEQRES 1 C 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS
SEQRES 2 C 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER
SEQRES 3 C 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL
SEQRES 4 C 40 VAL
SEQRES 1 H 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS
SEQRES 2 H 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER
SEQRES 3 H 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL
SEQRES 4 H 40 VAL
SEQRES 1 D 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS
SEQRES 2 D 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER
SEQRES 3 D 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL
SEQRES 4 D 40 VAL
SEQRES 1 I 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS
SEQRES 2 I 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER
SEQRES 3 I 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL
SEQRES 4 I 40 VAL
SEQRES 1 E 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS
SEQRES 2 E 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER
SEQRES 3 E 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL
SEQRES 4 E 40 VAL
SEQRES 1 J 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS
SEQRES 2 J 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER
SEQRES 3 J 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL
SEQRES 4 J 40 VAL
SEQRES 1 F 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS
SEQRES 2 F 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER
SEQRES 3 F 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL
SEQRES 4 F 40 VAL
SEQRES 1 K 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS
SEQRES 2 K 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER
SEQRES 3 K 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL
SEQRES 4 K 40 VAL
SEQRES 1 G 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS
SEQRES 2 G 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER
SEQRES 3 G 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL
SEQRES 4 G 40 VAL
SEQRES 1 L 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS
SEQRES 2 L 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER
SEQRES 3 L 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL
SEQRES 4 L 40 VAL
SHEET 1 AA1 6 ALA D 2 VAL D 12 0
SHEET 2 AA1 6 ALA C 2 VAL C 12 1 N ASP C 7 O HIS D 6
SHEET 3 AA1 6 ALA A 2 VAL A 12 1 N ASP A 7 O HIS C 6
SHEET 4 AA1 6 ALA E 2 VAL E 12 1 O ASP E 7 N HIS A 6
SHEET 5 AA1 6 ALA F 2 VAL F 12 1 O ASP F 7 N HIS E 6
SHEET 6 AA1 6 ALA G 2 VAL G 12 1 O ASP G 7 N HIS F 6
SHEET 1 AA2 6 GLN D 15 PHE D 19 0
SHEET 2 AA2 6 GLN C 15 PHE C 19 1 N LEU C 17 O LYS D 16
SHEET 3 AA2 6 GLN A 15 PHE A 19 1 N LEU A 17 O LYS C 16
SHEET 4 AA2 6 GLN E 15 PHE E 19 1 O LEU E 17 N LYS A 16
SHEET 5 AA2 6 GLN F 15 PHE F 19 1 O LEU F 17 N LYS E 16
SHEET 6 AA2 6 GLN G 15 PHE G 19 1 O LEU G 17 N LYS F 16
SHEET 1 AA3 6 GLY D 33 LEU D 34 0
SHEET 2 AA3 6 GLY C 33 LEU C 34 1 N GLY C 33 O LEU D 34
SHEET 3 AA3 6 GLY A 33 LEU A 34 1 N GLY A 33 O LEU C 34
SHEET 4 AA3 6 GLY E 33 LEU E 34 1 O GLY E 33 N LEU A 34
SHEET 5 AA3 6 GLY F 33 LEU F 34 1 O GLY F 33 N LEU E 34
SHEET 6 AA3 6 GLY G 33 LEU G 34 1 O GLY G 33 N LEU F 34
SHEET 1 AA4 6 GLU I 3 VAL I 12 0
SHEET 2 AA4 6 GLU H 3 VAL H 12 1 N GLU H 3 O PHE I 4
SHEET 3 AA4 6 GLU B 3 VAL B 12 1 N GLU B 3 O PHE H 4
SHEET 4 AA4 6 GLU J 3 VAL J 12 1 O GLU J 3 N PHE B 4
SHEET 5 AA4 6 GLU K 3 VAL K 12 1 O GLU K 3 N PHE J 4
SHEET 6 AA4 6 GLU L 3 VAL L 12 1 O GLU L 3 N PHE K 4
SHEET 1 AA5 6 GLN I 15 PHE I 19 0
SHEET 2 AA5 6 GLN H 15 PHE H 19 1 N LEU H 17 O LYS I 16
SHEET 3 AA5 6 GLN B 15 PHE B 19 1 N LEU B 17 O LYS H 16
SHEET 4 AA5 6 GLN J 15 PHE J 19 1 O LEU J 17 N LYS B 16
SHEET 5 AA5 6 GLN K 15 PHE K 19 1 O LEU K 17 N LYS J 16
SHEET 6 AA5 6 GLN L 15 PHE L 19 1 O LEU L 17 N LYS K 16
SHEET 1 AA6 6 GLY I 33 LEU I 34 0
SHEET 2 AA6 6 GLY H 33 LEU H 34 1 N GLY H 33 O LEU I 34
SHEET 3 AA6 6 GLY B 33 LEU B 34 1 N GLY B 33 O LEU H 34
SHEET 4 AA6 6 GLY J 33 LEU J 34 1 O GLY J 33 N LEU B 34
SHEET 5 AA6 6 GLY K 33 LEU K 34 1 O GLY K 33 N LEU J 34
SHEET 6 AA6 6 GLY L 33 LEU L 34 1 O GLY L 33 N LEU K 34
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
(ATOM LINES ARE NOT SHOWN.)
END
