[English] 日本語
Yorodumi
- PDB-8ovk: Lipidic amyloid-beta(1-40) fibril - polymorph L1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ovk
TitleLipidic amyloid-beta(1-40) fibril - polymorph L1
ComponentsAmyloid-beta A4 protein
KeywordsPROTEIN FIBRIL / amyloid-beta / fibril / lipids
Function / homology
Function and homology information


signaling receptor activator activity / Golgi-associated vesicle / clathrin-coated pit / axonogenesis / central nervous system development / heparin binding / growth cone / perikaryon / early endosome / membrane raft ...signaling receptor activator activity / Golgi-associated vesicle / clathrin-coated pit / axonogenesis / central nervous system development / heparin binding / growth cone / perikaryon / early endosome / membrane raft / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular region / nucleus / plasma membrane
Similarity search - Function
Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain ...Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta A4 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsFrieg, B. / Han, M. / Giller, K. / Dienemann, C. / Riedel, D. / Becker, S. / Andreas, L.B. / Griesinger, C. / Schroeder, G.F.
Funding support Germany, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
Helmholtz Association Germany
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM structures of lipidic fibrils of amyloid-β (1-40).
Authors: Benedikt Frieg / Mookyoung Han / Karin Giller / Christian Dienemann / Dietmar Riedel / Stefan Becker / Loren B Andreas / Christian Griesinger / Gunnar F Schröder /
Abstract: Alzheimer's disease (AD) is a progressive and incurable neurodegenerative disease characterized by the extracellular deposition of amyloid plaques. Investigation into the composition of these plaques ...Alzheimer's disease (AD) is a progressive and incurable neurodegenerative disease characterized by the extracellular deposition of amyloid plaques. Investigation into the composition of these plaques revealed a high amount of amyloid-β (Aβ) fibrils and a high concentration of lipids, suggesting that fibril-lipid interactions may also be relevant for the pathogenesis of AD. Therefore, we grew Aβ40 fibrils in the presence of lipid vesicles and determined their structure by cryo-electron microscopy (cryo-EM) to high resolution. The fold of the major polymorph is similar to the structure of brain-seeded fibrils reported previously. The majority of the lipids are bound to the fibrils, as we show by cryo-EM and NMR spectroscopy. This apparent lipid extraction from vesicles observed here in vitro provides structural insights into potentially disease-relevant fibril-lipid interactions.
History
DepositionApr 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amyloid-beta A4 protein
B: Amyloid-beta A4 protein
C: Amyloid-beta A4 protein
D: Amyloid-beta A4 protein
E: Amyloid-beta A4 protein
F: Amyloid-beta A4 protein
G: Amyloid-beta A4 protein
H: Amyloid-beta A4 protein
I: Amyloid-beta A4 protein
J: Amyloid-beta A4 protein


Theoretical massNumber of molelcules
Total (without water)43,35910
Polymers43,35910
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 1 - 40 / Label seq-ID: 1 - 40

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ

NCS oper:
IDCodeMatrixVector
1given(-0.999979625167, -0.00638351379226, -1.58447446576E-6), (0.00638351379046, -0.999979625168, 1.13669287577E-6), (-1.59169827701E-6, 1.12655520124E-6, 0.999999999998)263.335301109, 261.659431174, 2.35406956139
2given(0.999918462707, 0.0127698057151, 2.94819113667E-7), (-0.012769805715, 0.999918462707, -1.72334373857E-7), (-2.96995751386E-7, 1.68555539376E-7, 1)-1.6653862979, 1.68674381601, 4.70801901666
3given(-0.999816522698, -0.0191551804872, 5.39434350673E-7), (0.019155180487, -0.999816522698, -3.45079670686E-7), (5.45945440088E-7, -3.34683394051E-7, 1)264.990024285, 259.961823921, 7.06196864379
4given(0.999673846278, 0.0255382275664, 5.23560991709E-7), (-0.0255382275662, 0.999673846278, -3.69162549949E-7), (-5.32817987552E-7, 3.55671326459E-7, 1)-3.30914189772, 3.39472738606, 9.41602639345
5given(-0.999490415397, -0.0319203622959, -6.57430584007E-8), (0.0319203622959, -0.999490415397, 4.10408542331E-8), (-6.70195956865E-8, 3.89213982031E-8, 1)266.622672151, 258.243587024, 11.7700041629
6given(0.999266203188, 0.0383021561541, -4.71191318447E-7), (-0.0383021561539, 0.999266203188, 4.03227411581E-7), (4.86290039044E-7, -3.84883881134E-7, 1)-4.93079306626, 5.12339590915, 14.123984648
7given(-0.999001321354, -0.0446806438328, 3.35972975111E-7), (0.0446806438327, -0.999001321354, -2.64649671855E-7), (3.47462163804E-7, -2.49373883041E-7, 1)268.233227167, 256.504639909, 16.4779853153
8given(0.998695612014, 0.0510595196101, 5.21538025175E-7), (-0.0510595196099, 0.998695612015, -4.05299906078E-7), (-5.41552155743E-7, 3.78141756726E-7, 1)-6.53038743516, 6.87277861203, 18.832024414
9given(-0.998349222146, -0.0574354475775, 1.07220656569E-6), (0.0574354475766, -0.998349222147, -8.30895194549E-7), (1.11815942822E-6, -7.67940907168E-7, 0.999999999999)269.821616456, 254.745049496, 21.1859477334

-
Components

#1: Protein/peptide
Amyloid-beta A4 protein


Mass: 4335.852 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4DM00

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: The L1 amyloid-beta(1-40) fibril in complex with lipids
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 179.63 ° / Axial rise/subunit: 2.35 Å / Axial symmetry: C1
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 177981 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 70.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01193120
ELECTRON MICROSCOPYf_angle_d1.80264190
ELECTRON MICROSCOPYf_chiral_restr0.1089440
ELECTRON MICROSCOPYf_plane_restr0.0112560
ELECTRON MICROSCOPYf_dihedral_angle_d14.9921070
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000549176059939
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000548937927437
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000562954865371
ens_1d_5AELECTRON MICROSCOPYNCS constraints0.000560356967677
ens_1d_6AELECTRON MICROSCOPYNCS constraints0.000390260693101
ens_1d_7AELECTRON MICROSCOPYNCS constraints0.000565650356439
ens_1d_8AELECTRON MICROSCOPYNCS constraints0.000544973584342
ens_1d_9AELECTRON MICROSCOPYNCS constraints0.00056014746907
ens_1d_10AELECTRON MICROSCOPYNCS constraints0.000584970647023

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more