[English] 日本語
Yorodumi
- PDB-6ts3: EF-hands 3 and 4 of alpha-actinin in complex with CaMKII regulato... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ts3
TitleEF-hands 3 and 4 of alpha-actinin in complex with CaMKII regulatory segment
Components
  • ACE-ASN-ALA-ARG-ARG-LYS-LEU-LYS-GLY-ALA-ILE-LEU-THR-THR-MET-LEU-ALA-THR-ARG-ASN-PHE
  • Alpha-actinin-2
KeywordsPEPTIDE BINDING PROTEIN / CaMKII-binding protein
Function / homology
Function and homology information


regulation of synaptic vesicle docking / actin filament uncapping / FATZ binding / titin Z domain binding / HSF1-dependent transactivation / Interferon gamma signaling / positive regulation of endocytic recycling / phospholipase C-activating angiotensin-activated signaling pathway / peptidyl-threonine autophosphorylation / Ion transport by P-type ATPases ...regulation of synaptic vesicle docking / actin filament uncapping / FATZ binding / titin Z domain binding / HSF1-dependent transactivation / Interferon gamma signaling / positive regulation of endocytic recycling / phospholipase C-activating angiotensin-activated signaling pathway / peptidyl-threonine autophosphorylation / Ion transport by P-type ATPases / RAF activation / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / neurotransmitter receptor transport to plasma membrane / Unblocking of NMDA receptors, glutamate binding and activation / Ca2+ pathway / Trafficking of AMPA receptors / Ca2+/calmodulin-dependent protein kinase / negative regulation of protein localization to cell surface / RAF/MAP kinase cascade / channel activator activity / LIM domain binding / microspike assembly / negative regulation of hydrolase activity / dendritic spine development / regulation of neurotransmitter secretion / focal adhesion assembly / structural constituent of postsynaptic actin cytoskeleton / positive regulation of potassium ion transport / muscle cell development / Ion homeostasis / positive regulation of calcium ion transport / regulation of neuron migration / postsynaptic actin cytoskeleton / Striated Muscle Contraction / calcium/calmodulin-dependent protein kinase activity / Nephrin family interactions / regulation of mitochondrial membrane permeability involved in apoptotic process / Assembly and cell surface presentation of NMDA receptors / GTPase activating protein binding / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / dendrite morphogenesis / cortical actin cytoskeleton / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ferroptosis / pseudopodium / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of potassium ion transport / Long-term potentiation / regulation of neuronal synaptic plasticity / glutamate receptor binding / postsynaptic cytosol / cell surface receptor signaling pathway via JAK-STAT / postsynaptic density, intracellular component / regulation of protein localization to plasma membrane / presynaptic cytosol / cellular response to interferon-beta / cytoskeletal protein binding / cell projection / phosphatidylinositol-4,5-bisphosphate binding / titin binding / positive regulation of cardiac muscle cell apoptotic process / ionotropic glutamate receptor signaling pathway / platelet alpha granule lumen / Ras activation upon Ca2+ influx through NMDA receptor / dendrite cytoplasm / response to ischemia / angiotensin-activated signaling pathway / protein localization to plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / filopodium / actin filament / regulation of membrane potential / G1/S transition of mitotic cell cycle / postsynaptic density membrane / cellular response to type II interferon / integrin binding / Schaffer collateral - CA1 synapse / Z disc / kinase activity / actin filament binding / calcium ion transport / cell junction / Platelet degranulation / RAF/MAP kinase cascade / actin cytoskeleton organization / regulation of apoptotic process / dendritic spine / cytoskeleton / transmembrane transporter binding / calmodulin binding / transcription coactivator activity / cell adhesion / neuron projection / postsynaptic density / protein domain specific binding / axon
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / 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 / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / NTF2-like domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ACETYL GROUP / Calcium/calmodulin-dependent protein kinase type II subunit alpha / Alpha-actinin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.28 Å
AuthorsZhu, J. / Gold, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)533303 United Kingdom
CitationJournal: To Be Published
Title: EF-hands 3 and 4 of alpha-actinin in complex with CaMKII regulatory segment
Authors: Zhu, J. / Gold, M.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-actinin-2
B: Alpha-actinin-2
C: ACE-ASN-ALA-ARG-ARG-LYS-LEU-LYS-GLY-ALA-ILE-LEU-THR-THR-MET-LEU-ALA-THR-ARG-ASN-PHE
D: ACE-ASN-ALA-ARG-ARG-LYS-LEU-LYS-GLY-ALA-ILE-LEU-THR-THR-MET-LEU-ALA-THR-ARG-ASN-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7456
Polymers20,6574
Non-polymers882
Water4,792266
1
A: Alpha-actinin-2
C: ACE-ASN-ALA-ARG-ARG-LYS-LEU-LYS-GLY-ALA-ILE-LEU-THR-THR-MET-LEU-ALA-THR-ARG-ASN-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3733
Polymers10,3292
Non-polymers441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-9 kcal/mol
Surface area5640 Å2
MethodPISA
2
B: Alpha-actinin-2
D: ACE-ASN-ALA-ARG-ARG-LYS-LEU-LYS-GLY-ALA-ILE-LEU-THR-THR-MET-LEU-ALA-THR-ARG-ASN-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3733
Polymers10,3292
Non-polymers441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-9 kcal/mol
Surface area5110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.355, 47.270, 47.472
Angle α, β, γ (deg.)90.000, 110.532, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Alpha-actinin-2 / Alpha-actinin skeletal muscle isoform 2 / F-actin cross-linking protein


Mass: 7903.778 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P35609
#2: Protein/peptide ACE-ASN-ALA-ARG-ARG-LYS-LEU-LYS-GLY-ALA-ILE-LEU-THR-THR-MET-LEU-ALA-THR-ARG-ASN-PHE


Mass: 2424.889 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P11798*PLUS
#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.28→44.46 Å / Num. obs: 46303 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.038 / Net I/σ(I): 19.7
Reflection shellResolution: 1.28→1.3 Å / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2152 / CC1/2: 0.94 / Rrim(I) all: 0.487

-
Processing

Software
NameVersionClassification
DIALS1.17.1_3660data collection
PHENIX1.17.1_3660refinement
DIALSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.28→44.46 Å / SU ML: 0.1249 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.6175
RfactorNum. reflection% reflection
Rfree0.1989 1996 4.32 %
Rwork0.1832 --
obs0.1839 46220 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.69 Å2
Refinement stepCycle: LAST / Resolution: 1.28→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 0 266 1618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511431
X-RAY DIFFRACTIONf_angle_d0.69821949
X-RAY DIFFRACTIONf_chiral_restr0.0699222
X-RAY DIFFRACTIONf_plane_restr0.005257
X-RAY DIFFRACTIONf_dihedral_angle_d13.0746214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.310.29581380.2523044X-RAY DIFFRACTION96.69
1.31-1.350.29071390.24273119X-RAY DIFFRACTION99.76
1.35-1.390.27231420.22973149X-RAY DIFFRACTION99.67
1.39-1.430.2451440.21273167X-RAY DIFFRACTION99.85
1.43-1.480.22141420.20523145X-RAY DIFFRACTION99.58
1.48-1.540.22621420.19783146X-RAY DIFFRACTION99.82
1.54-1.610.20031420.18813147X-RAY DIFFRACTION99.85
1.61-1.70.22291430.18883165X-RAY DIFFRACTION99.97
1.7-1.80.19321430.19453178X-RAY DIFFRACTION99.94
1.8-1.940.19821430.18963145X-RAY DIFFRACTION99.94
1.94-2.140.19111440.18063187X-RAY DIFFRACTION99.97
2.14-2.450.17451430.18193179X-RAY DIFFRACTION100
2.45-3.080.20841460.18593213X-RAY DIFFRACTION99.97
3.09-44.460.18481450.16573240X-RAY DIFFRACTION99.65
Refinement TLS params.Method: refined / Origin x: 15.1281362844 Å / Origin y: 21.9163990434 Å / Origin z: 51.1831683785 Å
111213212223313233
T0.121159552278 Å20.00884287218521 Å2-0.0138581632918 Å2-0.119212347253 Å20.0120755410377 Å2--0.156698327561 Å2
L1.04206130367 °2-0.438679642654 °2-0.297515697624 °2-0.485852111388 °2-0.0990778256617 °2--2.13401916637 °2
S0.0436904734155 Å °-0.0496646452414 Å °-0.0649457729327 Å °-0.00654105398861 Å °0.0328064869885 Å °0.0391085940183 Å °-0.0135063513924 Å °-0.289520261344 Å °-0.0432803874475 Å °
Refinement TLS groupSelection details: all

+
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