[English] 日本語
Yorodumi
- PDB-6m3q: Crystal structure of AnkB/beta4-spectrin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m3q
TitleCrystal structure of AnkB/beta4-spectrin complex
Components
  • Ankyrin-2
  • Spectrin beta chain
KeywordsSTRUCTURAL PROTEIN / PROTEIN BINDING
Function / homology
Function and homology information


Interaction between L1 and Ankyrins / protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / : / : / NCAM signaling for neurite out-growth / positive regulation of potassium ion transmembrane transporter activity / spectrin / protein localization to M-band ...Interaction between L1 and Ankyrins / protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / : / : / NCAM signaling for neurite out-growth / positive regulation of potassium ion transmembrane transporter activity / spectrin / protein localization to M-band / clustering of voltage-gated sodium channels / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential / protein localization to organelle / COPI-mediated anterograde transport / paranodal junction assembly / central nervous system projection neuron axonogenesis / sarcoplasmic reticulum calcium ion transport / RAF/MAP kinase cascade / regulation of atrial cardiac muscle cell action potential / atrial cardiac muscle cell action potential / phosphorylation-dependent protein binding / positive regulation of cation channel activity / cell body fiber / regulation of SA node cell action potential / protein localization to endoplasmic reticulum / cardiac conduction / cytoskeletal anchor activity / paranode region of axon / atrial septum development / axon hillock / actin filament capping / axon initial segment / costamere / positive regulation of potassium ion transport / ventricular cardiac muscle cell action potential / response to methylmercury / positive regulation of multicellular organism growth / juxtaparanode region of axon / positive regulation of calcium ion transport / regulation of release of sequestered calcium ion into cytosol / regulation of ventricular cardiac muscle cell membrane repolarization / node of Ranvier / fertilization / regulation of cardiac muscle cell contraction / protein localization to cell surface / M band / A band / Interaction between L1 and Ankyrins / regulation of cardiac muscle contraction by calcium ion signaling / adult walking behavior / ankyrin binding / negative regulation of heart rate / neuromuscular process / spectrin binding / neuromuscular junction development / transmission of nerve impulse / adult behavior / 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 / phosphatase binding / regulation of sodium ion transport / COPI-mediated anterograde transport / T-tubule / axonogenesis / regulation of heart rate / protein localization to plasma membrane / sensory perception of sound / regulation of protein stability / sarcolemma / PML body / recycling endosome / phospholipid binding / structural constituent of cytoskeleton / Z disc / nuclear matrix / intracellular calcium ion homeostasis / endocytosis / intracellular protein localization / protein transport / actin binding / ATPase binding / protein-containing complex assembly / protein-macromolecule adaptor activity / basolateral plasma membrane / transmembrane transporter binding / postsynaptic membrane / cytoskeleton / early endosome / lysosome / neuron projection / protein stabilization / apical plasma membrane / axon / neuronal cell body / positive regulation of gene expression
Similarity search - Function
Immunoglobulin-like - #2660 / Chondroitinase Ac; Chain A, domain 3 - #30 / Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Ankyrin, UPA domain / UPA domain / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 ...Immunoglobulin-like - #2660 / Chondroitinase Ac; Chain A, domain 3 - #30 / Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Ankyrin, UPA domain / UPA domain / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Chondroitinase Ac; Chain A, domain 3 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Spectrin repeat / Spectrin repeat / Ankyrin repeats (many copies) / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Spectrin beta chain / Ankyrin-2 / Spectrin beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.436 Å
AuthorsLi, J. / Chen, K. / Zhu, R. / Zhang, M.
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-2
F: Spectrin beta chain


Theoretical massNumber of molelcules
Total (without water)90,1102
Polymers90,1102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-11 kcal/mol
Surface area37470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.900, 110.485, 131.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 53232.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK2, ANKB / Production host: Escherichia coli (E. coli) / References: UniProt: Q01484
#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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 25% w/v pentaerythritol propoxylate 629 (17/8 PO/OH), 50 mM magnesium chloride and 0.1 M HEPES, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97799 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97799 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 14141 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 62.23 Å2 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.106 / Rrim(I) all: 0.277 / Χ2: 1.799 / Net I/σ(I): 4.4 / Num. measured all: 94782
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.466.20.7676860.6610.3250.8351.56698.4
3.46-3.526.10.6326800.6530.2710.691.58597.4
3.52-3.596.20.5446860.7310.2330.5931.92999.7
3.59-3.6660.5186910.7930.230.5692.11199.1
3.66-3.745.80.5396820.7270.2440.5941.74798.6
3.74-3.836.30.6556890.7860.2810.7151.61899.9
3.83-3.926.80.6817050.8620.2820.7381.647100
3.92-4.036.90.5746980.9010.2350.6211.766100
4.03-4.156.80.4897200.9010.2020.531.873100
4.15-4.286.90.3466820.9580.1420.3742.028100
4.28-4.446.90.3077090.9570.1260.3332.21799.9
4.44-4.6170.3026890.9610.1230.3272.01100
4.61-4.827.20.2417090.9780.0970.261.87100
4.82-5.087.20.2297100.9680.0920.2471.796100
5.08-5.47.20.247230.9790.0960.2591.675100
5.4-5.817.20.2456990.9720.0980.2641.572100
5.81-6.47.10.2367340.9670.0950.2551.586100
6.4-7.327.10.1627200.9870.0650.1751.708100
7.32-9.216.80.0887410.9960.0360.0951.911100
9.21-506.30.0477880.9980.020.0511.76598.1

-
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: 3.436→35.357 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.18
RfactorNum. reflection% reflection
Rfree0.3071 667 4.75 %
Rwork0.2522 --
obs0.2548 14056 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 242.21 Å2 / Biso mean: 63.1711 Å2 / Biso min: 20.27 Å2
Refinement stepCycle: final / Resolution: 3.436→35.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5445 0 0 0 5445
Num. residues----754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055550
X-RAY DIFFRACTIONf_angle_d1.0647584
X-RAY DIFFRACTIONf_chiral_restr0.05915
X-RAY DIFFRACTIONf_plane_restr0.008984
X-RAY DIFFRACTIONf_dihedral_angle_d15.4973300
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4361-3.70120.36241240.3098245592
3.7012-4.07320.37951410.2974265399
4.0732-4.66140.29591150.24432721100
4.6614-5.86850.26161410.22942709100
5.8685-35.3570.28011460.22292851100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.42661.3710.14484.2453-1.17222.968-0.4634-0.81720.0411-0.22270.3113-0.42870.041-0.45580.01920.35040.0899-0.11020.4187-0.07590.350228.204-24.622-8.921
23.5001-1.00330.54630.86710.17162.17180.02550.1505-0.50290.06390.048-0.10780.250.2063-0.0740.42940.03560.02260.29850.03830.208618.506-18.316-22.137
31.1070.00040.28061.19750.46533.5711-0.0566-0.28520.3320.02660.01070.1126-0.0381-0.57030.05170.27140.05840.03870.37410.02640.2792-3.947-5.919-20.652
40.7132-0.92-0.29716.00581.73771.84930.1524-0.35160.2735-0.2423-0.14590.2797-0.5255-0.0650.00540.75870.0821-0.04490.7177-0.04320.441123.71722.0887.923
52.6207-0.354-1.69090.71530.85881.6708-0.18320.1803-0.37840.0444-0.0252-1.11550.41630.1848-0.30650.48730.1582-0.01280.5483-0.09150.970651.804-27.035-12.909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND RESID 954:993 )E954 - 993
2X-RAY DIFFRACTION2( CHAIN E AND RESID 994:1157 )E994 - 1157
3X-RAY DIFFRACTION3( CHAIN E AND RESID 1158:1458 )E1158 - 1458
4X-RAY DIFFRACTION4( CHAIN F AND RESID 1584:1762 )F1584 - 1762
5X-RAY DIFFRACTION5( CHAIN F AND RESID 1763:1897 )F1763 - 1897

+
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