[English] 日本語
Yorodumi
- PDB-9hx4: Amyloid fibril of apolipoprotein A-IV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hx4
TitleAmyloid fibril of apolipoprotein A-IV
ComponentsApolipoprotein A-IV
KeywordsPROTEIN FIBRIL / Amyloid / Apolipoprotein / Fibril
Function / homology
Function and homology information


protein-lipid complex assembly / response to triglyceride / chylomicron assembly / negative regulation of plasma lipoprotein oxidation / positive regulation of triglyceride catabolic process / response to lipid hydroperoxide / chylomicron remodeling / response to stilbenoid / peripheral nervous system axon regeneration / regulation of intestinal cholesterol absorption ...protein-lipid complex assembly / response to triglyceride / chylomicron assembly / negative regulation of plasma lipoprotein oxidation / positive regulation of triglyceride catabolic process / response to lipid hydroperoxide / chylomicron remodeling / response to stilbenoid / peripheral nervous system axon regeneration / regulation of intestinal cholesterol absorption / Assembly of active LPL and LIPC lipase complexes / regulation of cholesterol transport / phosphatidylcholine metabolic process / acylglycerol homeostasis / very-low-density lipoprotein particle remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron remodeling / lipid transporter activity / Chylomicron assembly / lipoprotein metabolic process / phospholipid efflux / chylomicron / high-density lipoprotein particle remodeling / positive regulation of fatty acid biosynthetic process / reverse cholesterol transport / low-density lipoprotein particle / phosphatidylcholine binding / cholesterol transfer activity / high-density lipoprotein particle / very-low-density lipoprotein particle / cholesterol efflux / leukocyte cell-cell adhesion / lipid transport / antioxidant activity / lipid homeostasis / Retinoid metabolism and transport / cholesterol metabolic process / lipid catabolic process / removal of superoxide radicals / cholesterol homeostasis / innate immune response in mucosa / hydrogen peroxide catabolic process / phospholipid binding / extracellular vesicle / : / blood microparticle / early endosome / endoplasmic reticulum lumen / Amyloid fiber formation / copper ion binding / synapse / lipid binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / cytosol
Similarity search - Function
Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAibara, S. / Kassner, A. / Wong, E. / Klingel, K. / Papworth, M. / Althage, M. / Wang, Q.D. / Correia, C. / Milting, H. / Oliveira, T.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Apolipoprotein A-IV fibrils: structural diagnosis of mixed cardiac amyloidosis.
Authors: Shintaro Aibara / Astrid Kassner / Edmond Wong / Karin Klingel / Monika Papworth / Magnus Althage / Qing-Dong Wang / Claudia Correia / Hendrik Milting / Taiana Maia de Oliveira /
Abstract: Cardiac amyloidosis (CA) occurs when misfolded proteins deposit as fibrils in the extracellular space of the heart. The fibrillogenic properties of apolipoprotein A-IV (ApoAIV) have been ...Cardiac amyloidosis (CA) occurs when misfolded proteins deposit as fibrils in the extracellular space of the heart. The fibrillogenic properties of apolipoprotein A-IV (ApoAIV) have been histologically observed and associated with CA pathogenesis. We report the structure of an ApoAIV amyloid from a patient's heart, which coexist amongst transthyretin (TTR) amyloids. These cases of undetected mixed CA highlight the importance of developing broad-spectrum anti-amyloid treatments to improve outcomes in patients.
History
DepositionJan 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Apolipoprotein A-IV
E: Apolipoprotein A-IV
B: Apolipoprotein A-IV
A: Apolipoprotein A-IV
C: Apolipoprotein A-IV
D: Apolipoprotein A-IV
G: Apolipoprotein A-IV
H: Apolipoprotein A-IV
I: Apolipoprotein A-IV
J: Apolipoprotein A-IV


Theoretical massNumber of molelcules
Total (without water)454,34010
Polymers454,34010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Apolipoprotein A-IV / Apo-AIV / ApoA-IV / Apolipoprotein A4


Mass: 45433.961 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P06727
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Amyloid fibril of apolipoprotein A-IV / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.21.1_5286: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.04 ° / Axial rise/subunit: 4.76 Å / Axial symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36124 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0014900
ELECTRON MICROSCOPYf_angle_d0.3536620
ELECTRON MICROSCOPYf_dihedral_angle_d3.993620
ELECTRON MICROSCOPYf_chiral_restr0.041760
ELECTRON MICROSCOPYf_plane_restr0.001860

+
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