[English] 日本語
Yorodumi
- EMDB-33475: Structure of ATP7B C983S/C985S/D1027A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33475
TitleStructure of ATP7B C983S/C985S/D1027A mutant
Map data
Sample
  • Organelle or cellular component: ATP7BWilson disease protein
    • Protein or peptide: Copper-transporting ATPase 2
Function / homology
Function and homology information


protein maturation by copper ion transfer / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion transmembrane transporter activity / sequestering of calcium ion / copper ion export / copper ion import / copper ion transport / xenobiotic detoxification by transmembrane export across the plasma membrane ...protein maturation by copper ion transfer / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion transmembrane transporter activity / sequestering of calcium ion / copper ion export / copper ion import / copper ion transport / xenobiotic detoxification by transmembrane export across the plasma membrane / intracellular zinc ion homeostasis / response to copper ion / Ion transport by P-type ATPases / intracellular copper ion homeostasis / monoatomic ion transmembrane transport / lactation / trans-Golgi network membrane / establishment of localization in cell / late endosome / copper ion binding / Golgi membrane / Golgi apparatus / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYang G / Xu L / Guo J / Wu Z
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0908501 China
Ministry of Science and Technology (MoST, China)2018YFA0508100 China
National Natural Science Foundation of China (NSFC)31870724 China
National Natural Science Foundation of China (NSFC)81125009 China
CitationJournal: Cell Rep / Year: 2023
Title: Structures of the human Wilson disease copper transporter ATP7B.
Authors: Guo-Min Yang / Lingyi Xu / Rou-Min Wang / Xin Tao / Zi-Wei Zheng / Shenghai Chang / Demin Ma / Cheng Zhao / Yi Dong / Shan Wu / Jiangtao Guo / Zhi-Ying Wu /
Abstract: The P-type ATPase ATP7B exports cytosolic copper and plays an essential role in the regulation of cellular copper homeostasis. Mutants of ATP7B cause Wilson disease (WD), an autosomal recessive ...The P-type ATPase ATP7B exports cytosolic copper and plays an essential role in the regulation of cellular copper homeostasis. Mutants of ATP7B cause Wilson disease (WD), an autosomal recessive disorder of copper metabolism. Here, we present cryoelectron microscopy (cryo-EM) structures of human ATP7B in the E1 state in the apo, the putative copper-bound, and the putative cisplatin-bound forms. In ATP7B, the N-terminal sixth metal-binding domain (MBD6) binds at the cytosolic copper entry site of the transmembrane domain (TMD), facilitating the delivery of copper from the MBD6 to the TMD. The sulfur-containing residues in the TMD of ATP7B mark the copper transport pathway. By comparing structures of the E1 state human ATP7B and E2-P state frog ATP7B, we propose the ATP-driving copper transport model of ATP7B. These structures not only advance our understanding of the mechanisms of ATP7B-mediated copper export but can also guide the development of therapeutics for the treatment of WD.
History
DepositionMay 19, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateMay 3, 2023-
Current statusMay 3, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33475.png

Downloads & links

-
Map

FileDownload / File: emd_33475.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.045117978 - 0.08274373
Average (Standard dev.)7.149173e-05 (±0.0014079765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 243.36002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_33475_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_33475_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ATP7B

EntireName: ATP7BWilson disease protein
Components
  • Organelle or cellular component: ATP7BWilson disease protein
    • Protein or peptide: Copper-transporting ATPase 2

-
Supramolecule #1: ATP7B

SupramoleculeName: ATP7B / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Copper-transporting ATPase 2

MacromoleculeName: Copper-transporting ATPase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type Cu+ transporter
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 162.033516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPEQERQITA REGASRKILS KLSLPTRAWE PAMKKSFAFD NVGYEGGLDG LGPSSQVATS TVRILGMTCQ SCVKSIEDRI SNLKGIISM KVSLEQGSAT VKYVPSVVCL QQVCHQIGDM GFEASIAEGK AASWPSRSLP AQEAVVKLRV EGMTCQSCVS S IEGKVRKL ...String:
MPEQERQITA REGASRKILS KLSLPTRAWE PAMKKSFAFD NVGYEGGLDG LGPSSQVATS TVRILGMTCQ SCVKSIEDRI SNLKGIISM KVSLEQGSAT VKYVPSVVCL QQVCHQIGDM GFEASIAEGK AASWPSRSLP AQEAVVKLRV EGMTCQSCVS S IEGKVRKL QGVVRVKVSL SNQEAVITYQ PYLIQPEDLR DHVNDMGFEA AIKSKVAPLS LGPIDIERLQ STNPKRPLSS AN QNFNNSE TLGHQGSHVV TLQLRIDGMH CKSCVLNIEE NIGQLLGVQS IQVSLENKTA QVKYDPSCTS PVALQRAIEA LPP GNFKVS LPDGAEGSGT DHRSSSSHSP GSPPRNQVQG TCSTTLIAIA GMTCASCVHS IEGMISQLEG VQQISVSLAE GTAT VLYNP SVISPEELRA AIEDMGFEAS VVSESCSTNP LGNHSAGNSM VQTTDGTPTS VQEVAPHTGR LPANHAPDIL AKSPQ STRA VAPQKCFLQI KGMTCASCVS NIERNLQKEA GVLSVLVALM AGKAEIKYDP EVIQPLEIAQ FIQDLGFEAA VMEDYA GSD GNIELTITGM TCASCVHNIE SKLTRTNGIT YASVALATSK ALVKFDPEII GPRDIIKIIE EIGFHASLAQ RNPNAHH LD HKMEIKQWKK SFLCSLVFGI PVMALMIYML IPSNEPHQSM VLDHNIIPGL SILNLIFFIL CTFVQLLGGW YFYVQAYK S LRHRSANMDV LIVLATSIAY VYSLVILVVA VAEKAERSPV TFFDTPPMLF VFIALGRWLE HLAKSKTSEA LAKLMSLQA TEATVVTLGE DNLIIREEQV PMELVQRGDI VKVVPGGKFP VDGKVLEGNT MADESLITGE AMPVTKKPGS TVIAGSINAH GSVLIKATH VGNDTTLAQI VKLVEEAQMS KAPIQQLADR FSGYFVPFII IMSTLTLVVW IVIGFIDFGV VQRYFPNPNK H ISQTEVII RFAFQTSITV LCIASPSSLG LATPTAVMVG TGVAAQNGIL IKGGKPLEMA HKIKTVMFAK TGTITHGVPR VM RVLLLGD VATLPLRKVL AVVGTAEASS EHPLGVAVTK YCKEELGTET LGYCTDFQAV PGCGIGCKVS NVEGILAHSE RPL SAPASH LNEAGSLPAE KDAVPQTFSV LIGNREWLRR NGLTISSDVS DAMTDHEMKG QTAILVAIDG VLCGMIAIAD AVKQ EAALA VHTLQSMGVD VVLITGDNRK TARAIATQVG INKVFAEVLP SHKVAKVQEL QNKGKKVAMV GDGVNDSPAL AQADM GVAI GTGTDVAIEA ADVVLIRNDL LDVVASIHLS KRTVRRIRIN LVLALIYNLV GIPIAAGVFM PIGIVLQPWM GSAAMA ASS VSVVLSSLQL KCYKKPDLER YEAQAHGHMK PLTASQVSVH IGMDDRWRDS PRATPWDQVS YVSQVSLSSL TSDKPSR HS AAADDDGDKW SLLLNGRDEE QYIVDELTSR GRDYKDDDDK WSHPQFEKGG GGSGGSAWSH PQFEK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.3 µm / Nominal defocus min: 1.1 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 338254

+
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