[English] 日本語
Yorodumi
- EMDB-18204: Copper-transporting ATPase HMA4 in E2P state with AlF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18204
TitleCopper-transporting ATPase HMA4 in E2P state with AlF
Map data
Sample
  • Complex: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica
    • Protein or peptide: Copper-transporting ATPase HMA4
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: MAGNESIUM ION
KeywordsP-ATPase / TRANSPORT PROTEIN
Function / homology
Function and homology information


P-type Cu+ transporter / P-type monovalent copper transporter activity / detoxification of copper ion / vacuolar membrane / transmembrane transport / copper ion binding / ATP hydrolysis activity / ATP 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 / E1-E2 ATPase / 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 / 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
Copper-transporting ATPase HMA4
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGuo Z / Gourdon P / Wang K
Funding support Denmark, 2 items
OrganizationGrant numberCountry
LundbeckfondenR133-A12689 Denmark
LundbeckfondenR324-2019-1855 Denmark
CitationJournal: Nat Commun / Year: 2024
Title: Diverse roles of the metal binding domains and transport mechanism of copper transporting P-type ATPases.
Authors: Zongxin Guo / Fredrik Orädd / Viktoria Bågenholm / Christina Grønberg / Jian Feng Ma / Peter Ott / Yong Wang / Magnus Andersson / Per Amstrup Pedersen / Kaituo Wang / Pontus Gourdon /
Abstract: Copper transporting P-type (P-) ATPases are essential for cellular homeostasis. Nonetheless, the E1-E1P-E2P-E2 states mechanism of P-ATPases remains poorly understood. In particular, the role of the ...Copper transporting P-type (P-) ATPases are essential for cellular homeostasis. Nonetheless, the E1-E1P-E2P-E2 states mechanism of P-ATPases remains poorly understood. In particular, the role of the intrinsic metal binding domains (MBDs) is enigmatic. Here, four cryo-EM structures and molecular dynamics simulations of a P-ATPase are combined to reveal that in many eukaryotes the MBD immediately prior to the ATPase core, MBD, serves a structural role, remodeling the ion-uptake region. In contrast, the MBD prior to MBD, MBD, likely assists in copper delivery to the ATPase core. Invariant Tyr, Asn and Ser residues in the transmembrane domain assist in positioning sulfur-providing copper-binding amino acids, allowing for copper uptake, binding and release. As such, our findings unify previously conflicting data on the transport and regulation of P-ATPases. The results are critical for a fundamental understanding of cellular copper homeostasis and for comprehension of the molecular bases of P-disorders and ongoing clinical trials.
History
DepositionAug 15, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18204.png

Downloads & links

-
Map

FileDownload / File: emd_18204.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.96433777 - 2.0576298
Average (Standard dev.)-0.0015997632 (±0.046944518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_18204_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_18204_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica

EntireName: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica
Components
  • Complex: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica
    • Protein or peptide: Copper-transporting ATPase HMA4
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica

SupramoleculeName: Copper-transporting ATPase HMA4 from Oryza sativa subsp. japonica
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

-
Macromolecule #1: Copper-transporting ATPase HMA4

MacromoleculeName: Copper-transporting ATPase HMA4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 94.744531 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: EVDELQEQEI AVCRLQIKGM ACTSCSESVE RALQMVPGVK KAAVGLALEE AKVHFDPNIT SRDLIIEAIE DAGFGADLIS SGDDVNKVH LKLEGVSSPE DIKLIQSRLE SVEGVNNVEC DTAGQTIIVA YDPDVTGPRL LIQCIQDAAQ PPKYFNASLY S PPKQREAE ...String:
EVDELQEQEI AVCRLQIKGM ACTSCSESVE RALQMVPGVK KAAVGLALEE AKVHFDPNIT SRDLIIEAIE DAGFGADLIS SGDDVNKVH LKLEGVSSPE DIKLIQSRLE SVEGVNNVEC DTAGQTIIVA YDPDVTGPRL LIQCIQDAAQ PPKYFNASLY S PPKQREAE RHHEIRNYRN QFLWSCLFSV PVFMFSMVLP MISPFGDWLF YKVCNNMTIG MLLRWLLCSP VQFIIGWRFY VG AYHALKR GYSNMDVLVA LGTNAAYFYS VYIVLKALTS ESFEGQDFFE TSAMLISFIL LGKYLEVVAK GKTSDALSKL TEL APETAC LLTLDKDGNA ISETEISTQL LQRNDVIKIV PGEKVPVDGV VIKGQSHVNE SMITGEARPI AKKPGDKVIG GTVN DNGCI IVKVTHVGSE TALSQIVQLV EAAQLARAPV QKLADRISRF FVPTVVVAAF LTWLGWFVAG QFDIYPREWI PKAMD SFEL ALQFGISVLV VACPCALGLA TPTAVMVATG KGASQGVLIK GGNALEKAHK VKAIIFDKTG TLTVGKPSVV QTKVFS KIP LLELCDLAAG AEANSEHPLS KAIVEYTKKL REQYGSHSDH IMESKDFEVH PGAGVSANVE GKLVLVGNKR LMQEFEV PI SSEVEGHMSE TEELARTCVL VAIDRTICGA LSVSDPLKPE AGRAISYLSS MGISSIMVTG DNWATAKSIA KEVGIGTV F AEIDPVGKAE KIKDLQMKGL TVAMVGDGIN DSPALAAADV GLAIGAGTDV AIEAADIVLM RSSLEDVITA IDLSRKTLS RIRLNYVWAL GYNVLGMPVA AGVLFPFTGI RLPPWLAGAC MAASSVSVVC SSLLLQLYKK PLHVEEVAAG PKNDPDLV

UniProtKB: Copper-transporting ATPase HMA4

-
Macromolecule #2: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 184854
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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