[English] 日本語
Yorodumi
- PDB-2aw0: FOURTH METAL-BINDING DOMAIN OF THE MENKES COPPER-TRANSPORTING ATP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2aw0
TitleFOURTH METAL-BINDING DOMAIN OF THE MENKES COPPER-TRANSPORTING ATPASE, NMR, 20 STRUCTURES
ComponentsMENKES COPPER-TRANSPORTING ATPASE
KeywordsCOPPER TRANSPORT / COPPER-TRANSPORTING ATPASE / COPPER-BINDING DOMAIN / HYDROLASE
Function / homology
Function and homology information


peptidyl-lysine modification / epinephrine metabolic process / elastin biosynthetic process / positive regulation of response to wounding / tryptophan metabolic process / cellular response to cobalt ion / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding / cerebellar Purkinje cell differentiation ...peptidyl-lysine modification / epinephrine metabolic process / elastin biosynthetic process / positive regulation of response to wounding / tryptophan metabolic process / cellular response to cobalt ion / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding / cerebellar Purkinje cell differentiation / elastic fiber assembly / response to iron(III) ion / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion import / copper ion transmembrane transporter activity / positive regulation of melanin biosynthetic process / superoxide dismutase copper chaperone activity / cellular response to lead ion / pyramidal neuron development / copper ion homeostasis / copper ion transport / melanosome membrane / serotonin metabolic process / catecholamine metabolic process / detoxification of copper ion / trans-Golgi network transport vesicle / regulation of oxidative phosphorylation / norepinephrine metabolic process / T-helper cell differentiation / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / cartilage development / response to manganese ion / negative regulation of iron ion transmembrane transport / pigmentation / skin development / cellular response to antibiotic / hair follicle morphogenesis / dopamine metabolic process / lung alveolus development / response to zinc ion / positive regulation of catalytic activity / central nervous system neuron development / cellular response to platelet-derived growth factor stimulus / Detoxification of Reactive Oxygen Species / blood vessel development / cuprous ion binding / cell leading edge / microvillus / Ion transport by P-type ATPases / intracellular copper ion homeostasis / positive regulation of cell size / blood vessel remodeling / positive regulation of lamellipodium assembly / cellular response to copper ion / cellular response to cadmium ion / lactation / removal of superoxide radicals / mitochondrion organization / extracellular matrix organization / neuron projection morphogenesis / trans-Golgi network membrane / locomotory behavior / liver development / secretory granule / female pregnancy / positive regulation of epithelial cell proliferation / brush border membrane / cellular response to amino acid stimulus / trans-Golgi network / cellular response to iron ion / small GTPase binding / phagocytic vesicle membrane / late endosome / cellular response to hypoxia / protein-folding chaperone binding / perikaryon / early endosome membrane / basolateral plasma membrane / in utero embryonic development / postsynaptic density / neuron projection / copper ion binding / apical plasma membrane / axon / dendrite / neuronal cell body / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol
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
SILVER ION / Copper-transporting ATPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsGitschier, J. / Fairbrother, W.J.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Solution structure of the fourth metal-binding domain from the Menkes copper-transporting ATPase.
Authors: Gitschier, J. / Moffat, B. / Reilly, D. / Wood, W.I. / Fairbrother, W.J.
History
DepositionOct 8, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MENKES COPPER-TRANSPORTING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7442
Polymers7,6371
Non-polymers1081
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40LOWEST RESIDUAL RESTRAINT VIOLATION ENERGIES
Representative

-
Components

#1: Protein MENKES COPPER-TRANSPORTING ATPASE


Mass: 7636.557 Da / Num. of mol.: 1 / Fragment: FOURTH METAL-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: AG(I)-BOUND STATE / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q04656, EC: 3.6.1.36
#2: Chemical ChemComp-AG / SILVER ION / Silver


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112QF COSY
121TOCSY (30 AND 70 MS)
131NOESY(100 AND 200 MS)
141ROESY(40 MS)
151COSY-35

-
Sample preparation

Sample conditionspH: 6.8 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

-
Processing

NMR software
NameDeveloperClassification
DISCOVERMSIrefinement
DGIIstructure solution
DISCOVERstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST RESIDUAL RESTRAINT VIOLATION ENERGIES
Conformers calculated total number: 40 / Conformers submitted total number: 20

+
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