[English] 日本語
Yorodumi
- PDB-3j09: High resolution helical reconstruction of the bacterial p-type AT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3j09
TitleHigh resolution helical reconstruction of the bacterial p-type ATPase copper transporter CopA
Componentscopper-exporting P-type ATPase A
KeywordsHYDROLASE / METAL TRANSPORT / p-type ATPase / copper transporter / CopA / adenosine triphosphatases / archaeal proteins / cation transport proteins / cryoelectron microscopy
Function / homology
Function and homology information


P-type divalent copper transporter activity / P-type Cu+ transporter / P-type monovalent copper transporter activity / copper ion homeostasis / copper ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain ...Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Probable copper-exporting P-type ATPase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10 Å
AuthorsWu, C. / Allen, G.S. / Cardozo, T. / Stokes, D.L.
CitationJournal: Structure / Year: 2011
Title: The architecture of CopA from Archeaoglobus fulgidus studied by cryo-electron microscopy and computational docking.
Authors: Gregory S Allen / Chen-Chou Wu / Tim Cardozo / David L Stokes /
Abstract: CopA uses ATP to pump Cu(+) across cell membranes. X-ray crystallography has defined atomic structures of several related P-type ATPases. We have determined a structure of CopA at 10 Å resolution ...CopA uses ATP to pump Cu(+) across cell membranes. X-ray crystallography has defined atomic structures of several related P-type ATPases. We have determined a structure of CopA at 10 Å resolution by cryo-electron microscopy of a new crystal form and used computational molecular docking to study the interactions between the N-terminal metal-binding domain (NMBD) and other elements of the molecule. We found that the shorter-chain lipids used to produce these crystals are associated with movements of the cytoplasmic domains, with a novel dimer interface and with disordering of the NMBD, thus offering evidence for the transience of its interaction with the other cytoplasmic domains. Docking identified a binding site that matched the location of the NMBD in our previous structure by cryo-electron microscopy, allowing a more detailed view of its binding configuration and further support for its role in autoinhibition.
History
DepositionMay 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection
Category: em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5004
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: copper-exporting P-type ATPase A
B: copper-exporting P-type ATPase A


Theoretical massNumber of molelcules
Total (without water)155,6312
Polymers155,6312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein copper-exporting P-type ATPase A / CopA


Mass: 77815.648 Da / Num. of mol.: 2 / Fragment: deltaC-CopA (UNP residues 15-737)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: copA, pacS, AF_0473 / Production host: Escherichia coli (E. coli)
References: UniProt: O29777, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: deltaC-CopA in DOPC lipids / Type: COMPLEX
Details: DeltaC-CopA tubular crystals were grown with DOPC at a protein concentration of 1 mg/mL and at a lipid-to-protein weight ratio of 0.4. Dialysis was carried out for 5 days in 50 uL dialysis ...Details: DeltaC-CopA tubular crystals were grown with DOPC at a protein concentration of 1 mg/mL and at a lipid-to-protein weight ratio of 0.4. Dialysis was carried out for 5 days in 50 uL dialysis buttons at 303K against 500 mL of 50 mM MES, pH 6.1, 25 mM Na2SO4, 25 mM K2SO4, 200 uM BCDS, 10 mM MgSO4, and 2 mM beta-mercaptoethanol. Stock solutions of lipid were made in dodecyl octaethylene glycol ether (C12E8) at 1 mg lipid per 2 mg detergent.
Molecular weightValue: 0.077 MDa / Experimental value: NO
Buffer solutionpH: 6.1
Details: 50 mM MES, pH 6.1, 25 mM Na2SO4, 25 mM K2SO4, 200 uM BCDS, 10 mM MgSO4, 2 mM beta-mercaptoethanol
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 50 mM MES, pH 6.1, 25 mM Na2SO4, 25 mM K2SO4, 200 uM BCDS, 10 mM MgSO4, 2 mM beta-mercaptoethanol
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 77 K / Method: blot for 5 seconds before plunging

-
Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Jan 1, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: CT3500 / Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM softwareName: EMIP / Category: 3D reconstruction
CTF correctionDetails: each tube-crystal
3D reconstructionMethod: Fourier-Bessel / Resolution: 10 Å / Resolution method: OTHER / Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 0 0 10932

+
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