[English] 日本語
Yorodumi
- EMDB-5271: High resolution helical reconstruction of the bacterial p-type AT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5271
TitleHigh resolution helical reconstruction of the bacterial p-type ATPase copper transporter CopA.
Map dataThis is a cubic section encompassing the unit cell of a Fourier-Bessel reconstructed map of tubular vesicles - crystals of deltaC-CopA from Archaeoglobus fulgidus.
Sample
  • Sample: deltaC-CopA in DMPC-DOPE lipids
  • Protein or peptide: membrane protein
Keywordsp-type ATPase / copper transporter / CopA / Adenosine Triphosphatases / Archaeal Proteins / Archaeoglobus fulgidus / 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 transport / 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 ...: / 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)
Methodhelical reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsWu C / Allen GS / Cardozo T / Stokes DL
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
DepositionApr 4, 2011-
Header (metadata) releaseJun 23, 2011-
Map releaseAug 16, 2011-
UpdateNov 16, 2011-
Current statusNov 16, 2011Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 130
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 130
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j08
  • Surface level: 130
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5271_1.png

Downloads & links

-
Map

FileDownload / File: emd_5271.map.gz / Format: CCP4 / Size: 789.1 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a cubic section encompassing the unit cell of a Fourier-Bessel reconstructed map of tubular vesicles - crystals of deltaC-CopA from Archaeoglobus fulgidus.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 81 pix.
= 162. Å		2 Å/pix.
x 51 pix.
= 102. Å		2 Å/pix.
x 50 pix.
= 100. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 130.0 / Movie #1: 130
Minimum - Maximum-30.964200000000002 - 199.592999999999989
Average (Standard dev.)104.631 (±38.0715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions515081
Spacing515081
CellA: 100 Å / B: 102 Å / C: 162 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z505181
origin x/y/z0.0000.0000.000
length x/y/z100.000102.000162.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS505181
D min/max/mean-30.964199.593104.631

-
Supplemental data

-
Sample components

-
Entire : deltaC-CopA in DMPC-DOPE lipids

EntireName: deltaC-CopA in DMPC-DOPE lipids
Components
  • Sample: deltaC-CopA in DMPC-DOPE lipids
  • Protein or peptide: membrane protein

-
Supramolecule #1000: deltaC-CopA in DMPC-DOPE lipids

SupramoleculeName: deltaC-CopA in DMPC-DOPE lipids / type: sample / ID: 1000
Details: deltaC-CopA tubular crystals were grown with a 4-to-1 mixture of DMPC-DOPE at a protein concentration of 1 mg per mL and at a lipid-to-protein weight ratio of 0.4. Dialysis was carried out ...Details: deltaC-CopA tubular crystals were grown with a 4-to-1 mixture of DMPC-DOPE at a protein concentration of 1 mg per 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 30 degrees C 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.
Number unique components: 1
Molecular weightTheoretical: 77 KDa

-
Macromolecule #1: membrane protein

MacromoleculeName: membrane protein / type: protein_or_peptide / ID: 1 / Name.synonym: membrane protein / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes
Source (natural)Organism: Archaeoglobus fulgidus (archaea) / Cell: E. coli / Location in cell: plasma membrane
Molecular weightTheoretical: 77 KDa
Recombinant expressionOrganism: Escherichia coli strain LMG 1940 / Recombinant plasmid: pBAD
SequenceGO: copper ion transport / InterPro: INTERPRO: IPR006403

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

Concentration1 mg/mL
BufferpH: 6.1
Details: 50 mM MES, pH 6.1, 25 mM Na2SO4, 25 mM K2SO4, 200 uM BCDS, 10 mM MgSO4, and 2 mM beta-mercaptoethanol.
GridDetails: holey carbon grid
VitrificationCryogen name: ETHANE / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: blot for 5 seconds before plunging
Detailsdialysis buttons

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 100 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: CT3500 / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Software - Name: EMIP
CTF correctionDetails: each tube-crystal

+
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