[English] 日本語
Yorodumi
- PDB-5y4d: Crystal Structure of AnkB Ankyrin Repeats in Complex with AnkR/An... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5y4d
TitleCrystal Structure of AnkB Ankyrin Repeats in Complex with AnkR/AnkB Chimeric Autoinhibition Segment
ComponentsAnkyrin-1,Ankyrin-2,Ankyrin-2
KeywordsPROTEIN BINDING / ANK REPEAT / PROTEIN-PROTEIN INTERACTION / STRUCTURAL PROTEIN / AUTO-INHIBITION
Function / homology
Function and homology information


protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / regulation of calcium ion transmembrane transporter activity / positive regulation of calcium ion transmembrane transporter activity / protein localization to M-band / positive regulation of potassium ion transmembrane transporter activity / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential ...protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / regulation of calcium ion transmembrane transporter activity / positive regulation of calcium ion transmembrane transporter activity / protein localization to M-band / positive regulation of potassium ion transmembrane transporter activity / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential / protein localization to organelle / paranodal junction assembly / phosphorylation-dependent protein binding / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / positive regulation of cation channel activity / atrial cardiac muscle cell action potential / protein localization to endoplasmic reticulum / sarcoplasmic reticulum calcium ion transport / cytoskeletal anchor activity / atrial septum development / positive regulation of potassium ion transport / ventricular cardiac muscle cell action potential / costamere / response to methylmercury / regulation of release of sequestered calcium ion into cytosol / positive regulation of calcium ion transport / regulation of ventricular cardiac muscle cell membrane repolarization / M band / regulation of cardiac muscle cell contraction / regulation of cardiac muscle contraction by calcium ion signaling / protein localization to cell surface / Interaction between L1 and Ankyrins / A band / spectrin binding / regulation of heart rate by cardiac conduction / regulation of calcium ion transport / intercalated disc / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / COPI-mediated anterograde transport / T-tubule / regulation of heart rate / protein localization to plasma membrane / regulation of protein stability / protein localization / recycling endosome / structural constituent of cytoskeleton / sarcolemma / Z disc / intracellular calcium ion homeostasis / endocytosis / protein transport / protein-macromolecule adaptor activity / ATPase binding / basolateral plasma membrane / postsynaptic membrane / transmembrane transporter binding / early endosome / lysosome / cytoskeleton / protein stabilization / neuron projection / apical plasma membrane / positive regulation of gene expression / protein kinase binding / enzyme binding / signal transduction / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
Ankyrin, UPA domain / UPA domain / Domain of unknown function DUF3447 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain ...Ankyrin, UPA domain / UPA domain / Domain of unknown function DUF3447 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Ankyrin repeats (many copies) / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Ankyrin-1 / Ankyrin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsChen, K. / Li, J. / Wang, C. / Wei, Z. / Zhang, M.
CitationJournal: Elife / Year: 2017
Title: Autoinhibition of ankyrin-B/G membrane target bindings by intrinsically disordered segments from the tail regions.
Authors: Chen, K. / Li, J. / Wang, C. / Wei, Z. / Zhang, M.
History
DepositionAug 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ankyrin-1,Ankyrin-2,Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,98811
Polymers78,0271
Non-polymers96110
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Heterodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-120 kcal/mol
Surface area29060 Å2
Unit cell
Length a, b, c (Å)179.787, 179.787, 227.098
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Ankyrin-1,Ankyrin-2,Ankyrin-2 / ANK-2 / Ankyrin-B / Brain ankyrin / Non-erythroid ankyrin


Mass: 78026.922 Da / Num. of mol.: 1
Fragment: UNP RESIDUES 1577-1613,UNP RESIDUES 3707-3718,UNP RESIDUES 28-693
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Ank1, ANK2 / Production host: Escherichia coli (E. coli) / References: UniProt: D3Z5M4, UniProt: Q01484
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.53 Å3/Da / Density % sol: 72.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4 M ammonium acetate, 0.1 M Bis-Tris propane (pH 7.0)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 20949 / % possible obs: 97.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 92.57 Å2 / Rmerge(I) obs: 0.103 / Χ2: 1.993 / Net I/σ(I): 9.3 / Num. measured all: 111753
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.3-3.365.50.72110251.436198.9
3.36-3.425.40.6510451.466198.9
3.42-3.485.40.51810521.535198.6
3.48-3.555.40.41610431.557198.4
3.55-3.635.40.32710401.545198.9
3.63-3.725.40.28710541.622198.5
3.72-3.815.40.24310651.797198.4
3.81-3.915.40.18510491.755198.3
3.91-4.035.40.1810401.813198.4
4.03-4.165.40.14710421.971198.1
4.16-4.315.40.12610482.011198.1
4.31-4.485.40.11210512.101197.9
4.48-4.685.40.10610442.066197.9
4.68-4.935.30.10310552.336197.7
4.93-5.245.30.10610452.442197.6
5.24-5.645.30.10710422.38197.1
5.64-6.215.30.09810552.178196.7
6.21-7.15.10.06610522.242196.2
7.1-8.945.10.04710452.836195.5
8.94-504.90.04310572.971191.8

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RLV

4rlv


Resolution: 3.3→42.806 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.9 / Phase error: 27.83
RfactorNum. reflection% reflection
Rfree0.229 1980 9.46 %
Rwork0.1834 --
obs0.1878 20932 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 194.51 Å2 / Biso mean: 102.7773 Å2 / Biso min: 44.73 Å2
Refinement stepCycle: final / Resolution: 3.3→42.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5019 0 50 0 5069
Biso mean--141.2 --
Num. residues----695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075138
X-RAY DIFFRACTIONf_angle_d1.0117016
X-RAY DIFFRACTIONf_chiral_restr0.054859
X-RAY DIFFRACTIONf_plane_restr0.008910
X-RAY DIFFRACTIONf_dihedral_angle_d6.8893048
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2978-3.38020.30641370.27171358149599
3.3802-3.47160.3151470.24911344149199
3.4716-3.57370.28661370.21651357149499
3.5737-3.6890.2591420.20651342148499
3.689-3.82070.24661400.18711362150298
3.8207-3.97360.24091430.18141348149198
3.9736-4.15430.24721430.17791352149598
4.1543-4.37310.22681360.16621355149198
4.3731-4.64680.19831410.16811345148698
4.6468-5.00510.24521440.1661365150998
5.0051-5.50780.25011430.19481344148797
5.5078-6.30270.25151390.2231365150497
6.3027-7.93240.22021450.17771350149596
7.9324-42.80920.17421430.1541365150893

+
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