[English] 日本語
Yorodumi
- EMDB-2973: electron crystallographic structure of lens Aquaporin-0 (AQP0) (l... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2973
Titleelectron crystallographic structure of lens Aquaporin-0 (AQP0) (lens MIP) at 1.9A resolution, in a closed pore state
Map datacomplete unit cell. AQP0 2Fo-Fc map
Sample
  • Sample: Mammalian Aquaporin-0 (Sheep)
  • Protein or peptide: Aquaporin-0
KeywordsAquaporin-0 / electron crystallography / membrane channel
Function / homology
Function and homology information


gap junction-mediated intercellular transport / water channel activity / water transport / structural constituent of eye lens / gap junction / response to stimulus / lens development in camera-type eye / positive regulation of cell adhesion / visual perception / protein homotetramerization ...gap junction-mediated intercellular transport / water channel activity / water transport / structural constituent of eye lens / gap junction / response to stimulus / lens development in camera-type eye / positive regulation of cell adhesion / visual perception / protein homotetramerization / calmodulin binding / endoplasmic reticulum / plasma membrane
Similarity search - Function
Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
Lens fiber major intrinsic protein
Similarity search - Component
Biological speciesOvis aries (sheep)
Methodelectron crystallography / cryo EM / Resolution: 1.9 Å
AuthorsGonen T / Cheng Y / Sliz P / Hiroaki Y / Fujiyoshi Y / Harrison SC / Walz T
CitationJournal: Nature / Year: 2005
Title: Lipid-protein interactions in double-layered two-dimensional AQP0 crystals.
Authors: Tamir Gonen / Yifan Cheng / Piotr Sliz / Yoko Hiroaki / Yoshinori Fujiyoshi / Stephen C Harrison / Thomas Walz /
Abstract: Lens-specific aquaporin-0 (AQP0) functions as a specific water pore and forms the thin junctions between fibre cells. Here we describe a 1.9 A resolution structure of junctional AQP0, determined by ...Lens-specific aquaporin-0 (AQP0) functions as a specific water pore and forms the thin junctions between fibre cells. Here we describe a 1.9 A resolution structure of junctional AQP0, determined by electron crystallography of double-layered two-dimensional crystals. Comparison of junctional and non-junctional AQP0 structures shows that junction formation depends on a conformational switch in an extracellular loop, which may result from cleavage of the cytoplasmic amino and carboxy termini. In the centre of the water pathway, the closed pore in junctional AQP0 retains only three water molecules, which are too widely spaced to form hydrogen bonds with each other. Packing interactions between AQP0 tetramers in the crystalline array are mediated by lipid molecules, which assume preferred conformations. We were therefore able to build an atomic model for the lipid bilayer surrounding the AQP0 tetramers, and we describe lipid-protein interactions.
History
DepositionApr 1, 2015-
Header (metadata) releaseApr 15, 2015-
Map releaseApr 15, 2015-
UpdateApr 15, 2015-
Current statusApr 15, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2b6o
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2b6o
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2973.jpg

Downloads & links

-
Map

FileDownload / File: emd_2973.map.gz / Format: CCP4 / Size: 27.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomplete unit cell. AQP0 2Fo-Fc map
Voxel sizeX: 0.4618 Å / Y: 0.4618 Å / Z: 0.4444 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-5.73697138 - 7.43581915
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 89
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions144360144
Spacing144144360
CellA: 66.4992 Å / B: 66.4992 Å / C: 159.98401 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.461798611111110.461798611111110.4444
M x/y/z144144360
origin x/y/z0.0000.0000.000
length x/y/z66.49966.499159.984
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ144144360
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS360144144
D min/max/mean-5.7377.4360.000

-
Supplemental data

-
Segmentation: 2Fo-Fc map of AQP0 determined by electron crystallography...

Annotation2Fo-Fc map of AQP0 determined by electron crystallography - asymmetric unit only
Fileemd_2973_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mammalian Aquaporin-0 (Sheep)

EntireName: Mammalian Aquaporin-0 (Sheep)
Components
  • Sample: Mammalian Aquaporin-0 (Sheep)
  • Protein or peptide: Aquaporin-0

-
Supramolecule #1000: Mammalian Aquaporin-0 (Sheep)

SupramoleculeName: Mammalian Aquaporin-0 (Sheep) / type: sample / ID: 1000 / Oligomeric state: two tetramers / Number unique components: 1
Molecular weightExperimental: 120 KDa / Theoretical: 120 KDa / Method: SDS PAGE

-
Macromolecule #1: Aquaporin-0

MacromoleculeName: Aquaporin-0 / type: protein_or_peptide / ID: 1 / Name.synonym: Lens MIP, MP26 / Number of copies: 8 / Oligomeric state: two tetramers / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Ovis aries (sheep) / synonym: Sheep / Tissue: eye lens / Cell: lens fiber cells / Location in cell: plasma membrane
Molecular weightExperimental: 120 KDa / Theoretical: 120 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state2D array

-
Sample preparation

Concentration5 mg/mL
BufferpH: 8 / Details: 20mM Tris pH 8, 150mM NaCl, 25mM MgCl2
GridDetails: Mo hexagonal grids
VitrificationCryogen name: HELIUM / Chamber temperature: 4 K / Instrument: OTHER
Detailsdialysis into 2d sheets
Crystal formationDetails: dialysis into 2d sheets

-
Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Cs: 1.2 mm
Specialist opticsEnergy filter - Name: omega filter JEOL
Sample stageSpecimen holder: Helium Cooled / Specimen holder model: JEOL 3200FSC CRYOHOLDER / Tilt angle max: 70 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 70 °
TemperatureMin: 4 K / Max: 30 K / Average: 8 K
DateOct 9, 2004
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 286 / Average electron dose: 20 e/Å2 / Camera length: 1500
Tilt angle min0

-
Image processing

Crystal parametersUnit cell - A: 65.5 Å / Unit cell - B: 65.5 Å / Unit cell - C: 160 Å / Unit cell - γ: 90 ° / Unit cell - α: 90.0 ° / Unit cell - β: 90.0 ° / Plane group: P 4 2 2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Details: This submission corresponds to the PDB entry 2B6O.
DetailsData was processed in XDP. Model building in O and refinement in CNS.

+
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