[English] 日本語
Yorodumi
- PDB-4a82: Fitted model of staphylococcus aureus sav1866 model ABC transport... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a82
TitleFitted model of staphylococcus aureus sav1866 model ABC transporter in the human cystic fibrosis transmembrane conductance regulator volume map EMD-1966.
ComponentsCYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR
KeywordsTRANSPORT PROTEIN / CYSTIC FIBROSIS / CFTR / ION CHANNEL / CASSETTE PROTEIN
Function / homology
Function and homology information


Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / 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 transmembrane region fold / ABC transporter type 1, transmembrane domain / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative multidrug export ATP-binding/permease protein SAV1866
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 9 Å
AuthorsRosenberg, M.F. / ORyan, L.P. / Hughes, G. / Zhao, Z. / Aleksandrov, L.A. / Riordan, J.R. / Ford, R.C.
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
DepositionNov 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Derived calculations / Other

-
Structure visualization

Movie
  • Biological unit as author_defined_assembly
  • Imaged by Jmol
  • Download
  • Biological unit as author_defined_assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1966
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1966
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR
B: CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR
C: CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR
D: CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR


Theoretical massNumber of molelcules
Total (without water)259,7364
Polymers259,7364
Non-polymers00
Water0
1
A: CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR
B: CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR


Theoretical massNumber of molelcules
Total (without water)129,8682
Polymers129,8682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR
D: CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR


Theoretical massNumber of molelcules
Total (without water)129,8682
Polymers129,8682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.300, 75.800, 300.000
Angle α, β, γ (deg.)90.00, 90.00, 125.00
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR


Mass: 64933.965 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: STABLY TRANSFECTED BHK CELLS. / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q99T13*PLUS
Sequence detailsTHE FITTED MODEL IS DERIVED FROM THE PDB ENTRY 2HYD WHICH COMES FROM A BACTERIAL SOURCE ...THE FITTED MODEL IS DERIVED FROM THE PDB ENTRY 2HYD WHICH COMES FROM A BACTERIAL SOURCE (STAPHYLOCOCCUS AUREUS), BUT THE EXPERIMENTAL SOURCE FOR THE ELECTROM MICROSCOPY VOLUME MAP 1966 IS FROM HUMAN.

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 140
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

-
Sample preparation

ComponentName: staphylococcus aureus sav1866 model ABC transporter in the human cystic fibrosis transmembrane conductance regulator
Type: COMPLEX
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Crystal growpH: 8 / Details: pH 8.0

-
Data collection

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 100 nm
Image recordingFilm or detector model: GENERIC GATAN (4k x 4k)
DiffractionMean temperature: 97 K
Radiation wavelengthRelative weight: 1
ReflectionResolution: 7→300 Å / Num. obs: 13694 / % possible obs: 91 % / Redundancy: 4 %

-
Processing

Software
NameClassification
2DXmodel building
2DXrefinement
2DXdata scaling
2DXphasing
3D reconstructionResolution: 9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 2D CRYSTAL
RefinementResolution: 2→5 Å / σ(F): 2
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1966. (DEPOSITION ID: 10250). IN ORDER TO PROVIDE A DENSITY MAP FOR EMDB THAT THEY COULD HANDLE, AUTHORS DEPOSITED A MAP WHICH HAD BEEN ...Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1966. (DEPOSITION ID: 10250). IN ORDER TO PROVIDE A DENSITY MAP FOR EMDB THAT THEY COULD HANDLE, AUTHORS DEPOSITED A MAP WHICH HAD BEEN EXTENDED ALONG A AND B AND THEN CROPPED TO CONTAIN ROUGHLY 2 UNIT CELLS. HENCE THE DIMENSIONS 140.7, 158.84, 247.5 REPRESENT ROUGHLY (NOT EXACTLY) 2 UNIT CELLS. IN ELECTRON CRYSTALLOGRAPHY THE C DIMENSION IS SET TO BE LARGER THA THE EXPECTED THICKNESS OF THE CRYSTAL (IN THIS CASE 300 ANGSTROM WA USED) AS THE CRYSTAL IS A SINGLE UNIT CELL THICK. THE THICKNESS OF 247.5 ANGSTROM ENCLOSES THE SIGNIFICANT DENSITY IN THE MAP WITH A FEW ANGSTROMS TO SPARE ON EACH SIDE OF THE CRYSTAL.
RfactorNum. reflection% reflection
Rwork0.37 --
obs-3097 60.8 %
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9248 0 0 0 9248
Refine LS restraints
Refine-IDTypeDev ideal
ELECTRON CRYSTALLOGRAPHYo_bond_d0.007
ELECTRON CRYSTALLOGRAPHYo_bond_d_na
ELECTRON CRYSTALLOGRAPHYo_bond_d_prot
ELECTRON CRYSTALLOGRAPHYo_angle_d
ELECTRON CRYSTALLOGRAPHYo_angle_d_na
ELECTRON CRYSTALLOGRAPHYo_angle_d_prot
ELECTRON CRYSTALLOGRAPHYo_angle_deg1
ELECTRON CRYSTALLOGRAPHYo_angle_deg_na
ELECTRON CRYSTALLOGRAPHYo_angle_deg_prot
ELECTRON CRYSTALLOGRAPHYo_dihedral_angle_d
ELECTRON CRYSTALLOGRAPHYo_dihedral_angle_d_na
ELECTRON CRYSTALLOGRAPHYo_dihedral_angle_d_prot
ELECTRON CRYSTALLOGRAPHYo_improper_angle_d
ELECTRON CRYSTALLOGRAPHYo_improper_angle_d_na
ELECTRON CRYSTALLOGRAPHYo_improper_angle_d_prot
ELECTRON CRYSTALLOGRAPHYo_mcbond_it
ELECTRON CRYSTALLOGRAPHYo_mcangle_it
ELECTRON CRYSTALLOGRAPHYo_scbond_it
ELECTRON CRYSTALLOGRAPHYo_scangle_it

+
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