[English] 日本語
Yorodumi
- PDB-2lqb: Metal binding repeat 2 of the Wilson disease protein (ATP7B) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lqb
TitleMetal binding repeat 2 of the Wilson disease protein (ATP7B)
ComponentsCopper-transporting ATPase 2
KeywordsHYDROLASE / copper binding
Function / homology
Function and homology information


protein maturation by copper ion transfer / copper ion transmembrane transporter activity / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / 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 / copper ion transmembrane transporter activity / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / 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 / Alpha-Beta Plaits - #100 / E1-E2 ATPase ...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 / Alpha-Beta Plaits - #100 / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Copper-transporting ATPase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsNokhrin, S. / Dolgova, N.V. / Yu, C. / Dmitriev, O.Y.
CitationJournal: Biochem.J. / Year: 2013
Title: Copper chaperone Atox1 interacts with the metal-binding domain of Wilson's disease protein in cisplatin detoxification.
Authors: Dolgova, N.V. / Nokhrin, S. / Yu, C.H. / George, G.N. / Dmitriev, O.Y.
History
DepositionFeb 28, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Copper-transporting ATPase 2


Theoretical massNumber of molelcules
Total (without water)8,4281
Polymers8,4281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein Copper-transporting ATPase 2 / Copper pump 2 / Wilson disease-associated protein / WND/140 kDa


Mass: 8427.712 Da / Num. of mol.: 1 / Fragment: HMA 2 domain residues 141-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP7B, PWD, WC1, WND / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35670, Cu2+-exporting ATPase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D HN(COCA)CB
1613D C(CO)NH
1713D H(CCO)NH
1813D 1H-15N TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D HN(CA)CO

-
Sample preparation

DetailsContents: 50 mM [U-2H] Tris-Cl, 0.5 mM DSS, 0.05 mM sodium azide, 5 % [U-2H] D2O, 5 mM TCEP (tris(2-carboxyethyl)phosphine), 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMTris-Cl-1[U-2H]1
0.5 mMDSS-21
0.05 mMsodium azide-31
5 %D2O-4[U-2H]1
5 mMTCEP (tris(2-carboxyethyl)phosphine)-51
Sample conditionsIonic strength: 50 / pH: 7.4 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CARA1.9.0F. Damberger, R. Kellerchemical shift assignment
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.peak picking
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 894 / NOE intraresidue total count: 253 / NOE long range total count: 227 / NOE medium range total count: 145 / NOE sequential total count: 269 / Protein phi angle constraints total count: 66 / Protein psi angle constraints total count: 66
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.56 Å
NMR ensemble rmsDistance rms dev: 0.37 Å / Distance rms dev error: 0.12 Å

+
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://pdbjlvh1.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