[English] 日本語
Yorodumi
- EMDB-5004: Structure of the Copper Transporting ATPase of A. fulgidus by Cry... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5004
TitleStructure of the Copper Transporting ATPase of A. fulgidus by Cryo-electron microscopy.
Map dataThis is one unit cell masked from CopA DeltaC tubular crystals imaged by cryo-EM
Sample
  • Sample: DeltaC construct of CopA, the copper transporting ATPase of A. fulgidus
  • Protein or peptide: P-type ATPase
KeywordsP-type ATPase / copper / metal binding domain / helical reconstruction
Function / homology
Function and homology information


P-type divalent copper transporter activity => GO:0043682 / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / regulation of striated muscle contraction ...P-type divalent copper transporter activity => GO:0043682 / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / regulation of striated muscle contraction / negative regulation of striated muscle contraction / copper ion homeostasis / positive regulation of ATPase-coupled calcium transmembrane transporter activity / P-type Ca2+ transporter / P-type calcium transporter activity / I band / endoplasmic reticulum-Golgi intermediate compartment / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / calcium ion transport / copper ion binding / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
: / Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / P-type ATPase, subfamily IIA, SERCA-type / 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 ...: / Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / P-type ATPase, subfamily IIA, SERCA-type / 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 / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / 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 / Copper-exporting P-type ATPase / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Methodhelical reconstruction / cryo EM / Resolution: 17.5 Å
AuthorsWu C / Rice WJ / Stokes DL
CitationJournal: Structure / Year: 2008
Title: Structure of a copper pump suggests a regulatory role for its metal-binding domain.
Authors: Chen-Chou Wu / William J Rice / David L Stokes /
Abstract: P-type ATPases play an important role in Cu homeostasis, which provides sufficient Cu for metalloenzyme biosynthesis but prevents oxidative damage of free Cu to the cell. The P(IB) group of P-type ...P-type ATPases play an important role in Cu homeostasis, which provides sufficient Cu for metalloenzyme biosynthesis but prevents oxidative damage of free Cu to the cell. The P(IB) group of P-type ATPases includes ATP-dependent pumps of Cu and other transition metal ions, and it is distinguished from other family members by the presence of N-terminal metal-binding domains (MBD). We have determined structures of two constructs of a Cu pump from Archaeoglobus fulgidus (CopA) by cryoelectron microscopy of tubular crystals, which reveal the overall architecture and domain organization of the molecule. By comparing these structures, we localized its N-terminal MBD within the cytoplasmic domains that use ATP hydrolysis to drive the transport cycle. We have built a pseudoatomic model by fitting existing crystallographic structures into the cryoelectron microscopy maps for CopA, which suggest a Cu-dependent regulatory role for the MBD.
History
DepositionFeb 14, 2008-
Header (metadata) releaseFeb 26, 2008-
Map releaseApr 22, 2009-
UpdateApr 23, 2009-
Current statusApr 23, 2009Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 13
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 13
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j09
  • Surface level: 13
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2voy
  • Surface level: 13
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5004_1.gif

Downloads & links

-
Map

FileDownload / File: emd_5004.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is one unit cell masked from CopA DeltaC tubular crystals imaged by cryo-EM
Voxel sizeX=Y=Z: 2 Å
Density
Contour Level1: 10.0 / Movie #1: 13
Minimum - Maximum-48.613700000000001 - 75.387500000000003
Average (Standard dev.)0.528807 (±4.943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions101101101
Spacing101101101
CellA=B=C: 202 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z101101101
origin x/y/z0.0000.0000.000
length x/y/z202.000202.000202.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS101101101
D min/max/mean-48.61475.3870.529

-
Supplemental data

-
Sample components

-
Entire : DeltaC construct of CopA, the copper transporting ATPase of A. fu...

EntireName: DeltaC construct of CopA, the copper transporting ATPase of A. fulgidus
Components
  • Sample: DeltaC construct of CopA, the copper transporting ATPase of A. fulgidus
  • Protein or peptide: P-type ATPase

-
Supramolecule #1000: DeltaC construct of CopA, the copper transporting ATPase of A. fu...

SupramoleculeName: DeltaC construct of CopA, the copper transporting ATPase of A. fulgidus
type: sample / ID: 1000 / Oligomeric state: homodimer / Number unique components: 1
Molecular weightTheoretical: 80 KDa / Method: SDS-PAGE

-
Macromolecule #1: P-type ATPase

MacromoleculeName: P-type ATPase / type: protein_or_peptide / ID: 1 / Name.synonym: Cu pump / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Strain: Archaeoglobus fulgidus / Location in cell: plasma membrane
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pBAD
SequenceGO: P-type divalent copper transporter activity => GO:0043682
InterPro: INTERPRO: IPR001756

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 6.1
Details: 50 mM MES, 25 mM Na2SO4, 25 mM K2SO4, 10 mM MgSO4, 2 mM 2-mercaptoethanol, 200 uM BCDS,
GridDetails: 300 mesh holey carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home made plunger
Method: Blot for 2-5 seconds before plunging. Plunge in cold room.
Detailscrystals grown at 45 to 55 C

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/UT
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51300 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Oxford / Specimen holder model: OTHER
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: objective astigmatism corrected at 200,000X mag
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 24 / Average electron dose: 10 e/Å2 / Bits/pixel: 8

-
Image processing

CTF correctionDetails: each tube
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.5 Å / Resolution method: FSC 0.5 CUT-OFF

-
Atomic model buiding 1

Initial modelPDB ID:

2b8e

DetailsDomains separately fitted by manual docking using O and Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2voy:
CryoEM model of CopA, the copper transporting ATPase from Archaeoglobus fulgidus

PDB-3j09:
High resolution helical reconstruction of the bacterial p-type ATPase copper transporter CopA

+
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