[English] 日本語
Yorodumi
- PDB-6m3r: Crystal structure of AnkG/beta4-spectrin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m3r
TitleCrystal structure of AnkG/beta4-spectrin complex
Components
  • Ankyrin-3
  • Spectrin beta chain
KeywordsSTRUCTURAL PROTEIN / PROTEIN BINDING
Function / homology
Function and homology information


Interaction between L1 and Ankyrins / regulation of protein targeting / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / maintenance of protein location in plasma membrane / positive regulation of sodium ion import across plasma membrane / NCAM signaling for neurite out-growth / membrane assembly / protein localization to axon / clustering of voltage-gated sodium channels ...Interaction between L1 and Ankyrins / regulation of protein targeting / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / maintenance of protein location in plasma membrane / positive regulation of sodium ion import across plasma membrane / NCAM signaling for neurite out-growth / membrane assembly / protein localization to axon / clustering of voltage-gated sodium channels / spectrin / spectrin-associated cytoskeleton / establishment or maintenance of microtubule cytoskeleton polarity / COPI-mediated anterograde transport / central nervous system projection neuron axonogenesis / magnesium ion homeostasis / regulation of potassium ion transport / RAF/MAP kinase cascade / positive regulation of membrane potential / plasma membrane organization / negative regulation of delayed rectifier potassium channel activity / cell body fiber / channel activator activity / maintenance of protein location in cell / phosphorylation-dependent protein binding / cardiac conduction / positive regulation of homotypic cell-cell adhesion / paranode region of axon / positive regulation of sodium ion transport / axon hillock / regulation of modification of postsynaptic structure / negative regulation of endocytosis / axon initial segment / costamere / anterograde axonal transport / actin filament capping / cellular response to magnesium ion / positive regulation of multicellular organism growth / juxtaparanode region of axon / Golgi to plasma membrane protein transport / node of Ranvier / fertilization / adult walking behavior / ankyrin binding / negative regulation of heart rate / neuromuscular process / cortical actin cytoskeleton / spectrin binding / neuromuscular junction development / axon development / adult behavior / response to immobilization stress / transmission of nerve impulse / mitotic cytokinesis / intercalated disc / lateral plasma membrane / sodium channel regulator activity / positive regulation of protein targeting to membrane / bicellular tight junction / phosphatase binding / neuronal action potential / cytoskeletal protein binding / regulation of sodium ion transport / axon cytoplasm / T-tubule / axonogenesis / axon guidance / basal plasma membrane / sarcoplasmic reticulum / protein localization to plasma membrane / cell projection / neuromuscular junction / establishment of protein localization / sensory perception of sound / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / PML body / sarcolemma / phospholipid binding / structural constituent of cytoskeleton / nuclear matrix / Z disc / actin filament binding / cell junction / intracellular protein localization / actin binding / actin cytoskeleton organization / protein-containing complex assembly / protein-macromolecule adaptor activity / basolateral plasma membrane / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / postsynaptic membrane / cytoskeleton / lysosome / postsynapse / neuron projection / postsynaptic density / cadherin binding / axon
Similarity search - Function
Ankyrin-3, death domain / Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Ankyrin, UPA domain / UPA domain / : / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain ...Ankyrin-3, death domain / Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Ankyrin, UPA domain / UPA domain / : / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Death-like domain superfamily / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Spectrin beta chain / Ankyrin-3 / Spectrin beta chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.313 Å
AuthorsLi, J. / Chen, K. / Zhu, R. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)16100517 Hong Kong
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Basis Underlying Strong Interactions between Ankyrins and Spectrins.
Authors: Li, J. / Chen, K. / Zhu, R. / Zhang, M.
History
DepositionMar 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Ankyrin-3
F: Spectrin beta chain


Theoretical massNumber of molelcules
Total (without water)91,4382
Polymers91,4382
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-10 kcal/mol
Surface area37340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.591, 139.591, 211.317
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Ankyrin-3 / ANK-3 / Ankyrin-G


Mass: 54560.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ank3 / Production host: Escherichia coli (E. coli) / References: UniProt: O70511
#2: Protein Spectrin beta chain


Mass: 36877.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sptbn4, Spnb4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VIE5, UniProt: E9PX29*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.5 Å3/Da / Density % sol: 81.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 0.8 M potassium sodium tartrate tetrahydrate, 0.1 M Tris, pH 8.5 and 0.5% w/v polyethylene glycol monomethyl ether 5,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 4.3→50 Å / Num. obs: 16538 / % possible obs: 99.9 % / Redundancy: 15.7 % / Biso Wilson estimate: 77.93 Å2 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.059 / Rrim(I) all: 0.142 / Χ2: 0.961 / Net I/σ(I): 2.2 / Num. measured all: 259971
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
4.3-4.3716.18050.510.6021.013100
4.37-4.4515.88220.5970.5710.981100
4.45-4.5416.17890.6740.5370.975100
4.54-4.6315.88350.6990.4331.022100
4.63-4.7316.17890.7710.3640.988100
4.73-4.84168230.8070.3150.985100
4.84-4.9615.88210.8660.2460.9581000.994
4.96-5.116.18100.9120.2430.9961000.991
5.1-5.2516.38260.9090.1940.9721000.7950.819
5.25-5.4216.48130.9150.1830.9921000.7480.771
5.42-5.6116.28260.9390.1750.9871000.710.732
5.61-5.8315.98200.9430.1620.9631000.6510.672
5.83-6.115.98180.9650.1340.961000.5380.555
6.1-6.4215.68270.9620.1150.9521000.4580.472
6.42-6.8215.38400.9810.0820.9621000.3250.335
6.82-7.3514.88260.9880.0610.9441000.2350.243
7.35-8.0812.48310.9880.0410.93999.30.1420.148
8.08-9.2516.28450.9980.0210.95899.50.0850.088
9.25-11.6316.88580.9990.0140.89999.90.060.061
11.63-5014.89140.9990.0130.78199.50.0530.054

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D8O, 3KBT

4d8o

3kbt


Resolution: 4.313→39.896 Å / SU ML: 0.74 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.9
RfactorNum. reflection% reflection
Rfree0.2952 763 4.83 %
Rwork0.2564 --
obs0.2583 15782 95.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 349.62 Å2 / Biso mean: 87.6322 Å2 / Biso min: 3.08 Å2
Refinement stepCycle: final / Resolution: 4.313→39.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 0 0 4999
Num. residues----711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085091
X-RAY DIFFRACTIONf_angle_d1.316972
X-RAY DIFFRACTIONf_chiral_restr0.063857
X-RAY DIFFRACTIONf_plane_restr0.013904
X-RAY DIFFRACTIONf_dihedral_angle_d16.1163023
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.3133-4.64590.38061330.3291255782
4.6459-5.11260.34361560.27253068100
5.1126-5.85040.33031590.2743312499
5.8504-7.36330.32031600.2613312099
7.3633-39.8960.19161550.2008315096

+
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