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- EMDB-33474: Structure of ATP7B C983S/C985S/D1027A mutant with Cu+ in presence... -

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Basic information

Entry
Database: EMDB / ID: EMD-33474
TitleStructure of ATP7B C983S/C985S/D1027A mutant with Cu+ in presence of ATOX1
Map data
Sample
  • Organelle or cellular component: ATP7B
    • Protein or peptide: Copper-transporting ATPase 2
  • Ligand: COPPER (II) ION
KeywordsP-type Cu(+) transporter / Translocase / METAL TRANSPORT / TRANSLOCATE
Function / homology
Function and homology information


protein maturation by copper ion transfer / P-type divalent copper transporter activity / copper ion export / copper ion transmembrane transporter activity / copper ion import / P-type Cu+ transporter / P-type monovalent copper transporter activity / sequestering of calcium ion / copper ion transport / xenobiotic detoxification by transmembrane export across the plasma membrane ...protein maturation by copper ion transfer / P-type divalent copper transporter activity / copper ion export / copper ion transmembrane transporter activity / copper ion import / P-type Cu+ transporter / P-type monovalent copper transporter activity / sequestering of calcium ion / 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 / lactation / trans-Golgi network membrane / establishment of localization in cell / late endosome / monoatomic ion transmembrane transport / copper ion binding / viral translational frameshifting / 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: 3.8 Å
AuthorsYang G / Xu L / Chang S / 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) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33474.png

Downloads & links

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Map

FileDownload / File: emd_33474.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.026281001 - 0.04320205
Average (Standard dev.)-0.0000029402129 (±0.0010359742)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_33474_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_33474_half_map_2.map
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Sample components

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Entire : ATP7B

EntireName: ATP7B
Components
  • Organelle or cellular component: ATP7B
    • Protein or peptide: Copper-transporting ATPase 2
  • Ligand: COPPER (II) ION

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Supramolecule #1: ATP7B

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

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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

UniProtKB: Copper-transporting ATPase 2

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Macromolecule #2: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 167790
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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