[English] 日本語
Yorodumi
- EMDB-1966: CFTR map generated from 2D crystals grown using the epitaxial method. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1966
TitleCFTR map generated from 2D crystals grown using the epitaxial method.
Map dataEM map generated from 2D crystals of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR or ABCC7).
Sample
  • Sample: Cystic fibrosis transmembrane conductance regulator
  • Protein or peptide: Cystic fibrosis transmembrane conductance regulator
KeywordsCystic fibrosis / CFTR / ion channel / ATP binding cassette protein
Function / homology
Function and homology information


ATPase-coupled lipid transmembrane transporter activity / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type transporter activity / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Cystic fibrosis transmembrane conductance regulator / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...Cystic fibrosis transmembrane conductance regulator / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Putative multidrug export ATP-binding/permease protein SAV1866
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodelectron crystallography / cryo EM / negative staining / Resolution: 9.0 Å
AuthorsRosenberg MF / ORyan LP / Hughes G / Zhao Z / Aleksandrov LA / Riordan JR / Ford RC
CitationJournal: J Biol Chem / Year: 2011
Title: The cystic fibrosis transmembrane conductance regulator (CFTR): three-dimensional structure and localization of a channel gate.
Authors: Mark F Rosenberg / Liam P O'Ryan / Guy Hughes / Zhefeng Zhao / Luba A Aleksandrov / John R Riordan / Robert C Ford /
Abstract: Cystic fibrosis affects about 1 in 2500 live births and involves loss of transmembrane chloride flux due to a lack of a membrane protein channel termed the cystic fibrosis transmembrane conductance ...Cystic fibrosis affects about 1 in 2500 live births and involves loss of transmembrane chloride flux due to a lack of a membrane protein channel termed the cystic fibrosis transmembrane conductance regulator (CFTR). We have studied CFTR structure by electron crystallography. The data were compared with existing structures of other ATP-binding cassette transporters. The protein was crystallized in the outward facing state and resembled the well characterized Sav1866 transporter. We identified regions in the CFTR map, not accounted for by Sav1866, which were potential locations for the regulatory region as well as the channel gate. In this analysis, we were aided by the fact that the unit cell was composed of two molecules not related by crystallographic symmetry. We also identified regions in the fitted Sav1866 model that were missing from the map, hence regions that were either disordered in CFTR or differently organized compared with Sav1866. Apart from the N and C termini, this indicated that in CFTR, the cytoplasmic end of transmembrane helix 5/11 and its associated loop could be partly disordered (or alternatively located).
History
DepositionSep 12, 2011-
Header (metadata) releaseJan 6, 2012-
Map releaseJan 6, 2012-
UpdateMar 7, 2012-
Current statusMar 7, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 60
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 60
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4a82
  • Surface level: 60
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4a82
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1966.png

Downloads & links

-
Map

FileDownload / File: emd_1966.map.gz / Format: CCP4 / Size: 15.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map generated from 2D crystals of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR or ABCC7).
Voxel sizeX: 0.7 Å / Y: 0.76 Å / Z: 2.5 Å
Density
Contour LevelBy AUTHOR: 60.0 / Movie #1: 60
Minimum - Maximum-212.549000000000007 - 212.882000000000005
Average (Standard dev.)-0.205385 (±56.310499999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions20920199
Spacing20920199
CellA: 140.7 Å / B: 158.84 Å / C: 247.5 Å
α: 90 ° / β: 90 ° / γ: 125 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.70.762.5
M x/y/z20120999
origin x/y/z0.0000.0000.000
length x/y/z140.700158.840247.500
α/β/γ90.00090.000125.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS20120999
D min/max/mean-212.549212.882-0.205

-
Supplemental data

-
Sample components

-
Entire : Cystic fibrosis transmembrane conductance regulator

EntireName: Cystic fibrosis transmembrane conductance regulator
Components
  • Sample: Cystic fibrosis transmembrane conductance regulator
  • Protein or peptide: Cystic fibrosis transmembrane conductance regulator

-
Supramolecule #1000: Cystic fibrosis transmembrane conductance regulator

SupramoleculeName: Cystic fibrosis transmembrane conductance regulator / type: sample / ID: 1000
Details: Human ortholog. Sample was glycosylated and mostly dephosphorylated. No nucleotide was added.
Oligomeric state: 2 Monomers / Number unique components: 1
Molecular weightExperimental: 200 KDa / Theoretical: 168.142 KDa / Method: SDS-PAGE

-
Macromolecule #1: Cystic fibrosis transmembrane conductance regulator

MacromoleculeName: Cystic fibrosis transmembrane conductance regulator / type: protein_or_peptide / ID: 1 / Name.synonym: CFTR
Details: Human protein is glycosylated but non-phosphorylated, as expressed and purified from BHK cells. No nucleotide is present during purification and crystallisation.
Number of copies: 2 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: BHK
Molecular weightExperimental: 200 KDa / Theoretical: 168 KDa
Recombinant expressionOrganism: Chinese Hamster Kidney cells
SequenceGO: membrane => GO:0016020
InterPro: Cystic fibrosis transmembrane conductance regulator

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingelectron crystallography
Aggregation state2D array

-
Sample preparation

Concentration0.05 mg/mL
BufferpH: 8
Details: 0.05% dodecyl maltoside, polyethylene glycol 4000 (10% w/v), 100mM ammonium sulphate, 50 mM Tris-HCl.
StainingType: NEGATIVE / Details: Unstained
GridDetails: 400 mesh carbon, gold
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 80 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: 10 seconds
Detailson carbon (epitaxial)
Crystal formationDetails: on carbon (epitaxial)

-
Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 97 K / Max: 97 K / Average: 97 K
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 1.9 µm / Number real images: 121 / Bits/pixel: 16
Tilt angle min0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.1 µm
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN HELIUM / Tilt angle max: 70 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 70 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: MRC
Details: Lattice unbending and origin refinement were carried out with 2dx and 2dxmerge software.
Crystal parametersUnit cell - A: 72.300 Å / Unit cell - B: 75.800 Å / Unit cell - C: 300.000 Å / Unit cell - γ: 125.00 ° / Unit cell - α: 90.00 ° / Unit cell - β: 90.00 ° / Plane group: P 1
CTF correctionDetails: TTREFINE

-
Atomic model buiding 1

Initial modelPDB ID:

2hyd

SoftwareName: Chimera
DetailsProtocol: Rigid Body. Initial manual docking then refinement using Chimera fir-in-map routine.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Target criteria: Cross-correlation between calculated map vs experimental map
Output model

PDB-4a82:
Fitted model of staphylococcus aureus sav1866 model ABC transporter in the human cystic fibrosis transmembrane conductance regulator volume map EMD-1966.

+
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://pdbjlvh1.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