[English] 日本語
Yorodumi
- PDB-4x3i: The crystal structure of Arc N-lobe complexed with CAMK2A fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x3i
TitleThe crystal structure of Arc N-lobe complexed with CAMK2A fragment
Components
  • Activity-regulated cytoskeleton-associated protein
  • CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II SUBUNIT ALPHA
KeywordsSIGNALING PROTEIN / ENDOCYTOSIS MEDIATOR
Function / homology
Function and homology information


regulation of synaptic vesicle docking / positive regulation of AMPA receptor activity / HSF1-dependent transactivation / Interferon gamma signaling / virus-like capsid / vesicle-mediated intercellular transport / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / postsynaptic endosome ...regulation of synaptic vesicle docking / positive regulation of AMPA receptor activity / HSF1-dependent transactivation / Interferon gamma signaling / virus-like capsid / vesicle-mediated intercellular transport / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / postsynaptic endosome / neuronal ribonucleoprotein granule / regulation of endocannabinoid signaling pathway / RAF activation / calcium- and calmodulin-dependent protein kinase complex / Trafficking of AMPA receptors / Ca2+ pathway / RAF/MAP kinase cascade / Ca2+/calmodulin-dependent protein kinase / clathrin-coated vesicle membrane / negative regulation of hydrolase activity / dendritic spine development / regulation of neuron migration / regulation of neurotransmitter secretion / endoderm development / regulation of dendritic spine morphogenesis / Ion homeostasis / positive regulation of calcium ion transport / regulation of cell morphogenesis / calcium/calmodulin-dependent protein kinase activity / regulation of long-term synaptic potentiation / regulation of mitochondrial membrane permeability involved in apoptotic process / anterior/posterior pattern specification / dendrite morphogenesis / response to morphine / regulation of long-term synaptic depression / regulation of postsynaptic neurotransmitter receptor internalization / regulation of neuronal synaptic plasticity / long-term memory / mRNA transport / glutamate receptor binding / cellular response to interferon-beta / positive regulation of cardiac muscle cell apoptotic process / cytoskeleton organization / acrosomal vesicle / learning / response to ischemia / positive regulation of receptor signaling pathway via JAK-STAT / response to cocaine / modulation of chemical synaptic transmission / postsynaptic density membrane / Schaffer collateral - CA1 synapse / protein homooligomerization / G1/S transition of mitotic cell cycle / endocytosis / calcium ion transport / cell migration / extracellular vesicle / actin cytoskeleton / cell cortex / early endosome membrane / dendritic spine / response to ethanol / calmodulin binding / postsynaptic density / membrane raft / protein serine kinase activity / protein serine/threonine kinase activity / mRNA binding / synapse / dendrite / glutamatergic synapse / structural molecule activity / mitochondrion / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Activity-regulated cytoskeleton-associated protein, capsid domain / Activity-regulated cytoskeleton-associated protein / Activity-regulated cytoskeleton-associated protein, C-terminal domain / Activity-regulated cytoskeleton-associated protein, N-terminal domain / Arc C-lobe / Arc MA domain / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily ...: / Activity-regulated cytoskeleton-associated protein, capsid domain / Activity-regulated cytoskeleton-associated protein / Activity-regulated cytoskeleton-associated protein, C-terminal domain / Activity-regulated cytoskeleton-associated protein, N-terminal domain / Arc C-lobe / Arc MA domain / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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
Calcium/calmodulin-dependent protein kinase type II subunit alpha / Activity-regulated cytoskeleton-associated protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, W. / Ward, M. / Leahy, D. / Worley, P.
CitationJournal: Neuron / Year: 2015
Title: Structural basis of arc binding to synaptic proteins: implications for cognitive disease.
Authors: Zhang, W. / Wu, J. / Ward, M.D. / Yang, S. / Chuang, Y.A. / Xiao, M. / Li, R. / Leahy, D.J. / Worley, P.F.
History
DepositionNov 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _struct_keywords.text
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Activity-regulated cytoskeleton-associated protein
B: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II SUBUNIT ALPHA


Theoretical massNumber of molelcules
Total (without water)10,1462
Polymers10,1462
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-4 kcal/mol
Surface area5000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.527, 51.527, 69.929
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Activity-regulated cytoskeleton-associated protein / ARC/ARG3.1 / Activity-regulated gene 3.1 protein / Arg3.1


Mass: 9393.229 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 207-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arc / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q63053
#2: Protein/peptide CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II SUBUNIT ALPHA / CAM KINASE II SUBUNIT ALPHA / CAMK-II SUBUNIT ALPHA


Mass: 752.797 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 309-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CAMK2A / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P11798*PLUS, Ca2+/calmodulin-dependent protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2M AMMONIUM SULFATE AND 0.1 M TRIS, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9801 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.8→25.763 Å / Num. obs: 9807 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Net I/σ(I): 10.3
Reflection shellHighest resolution: 1.8 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→25.76 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 471 4.8 %
Rwork0.194 --
obs0.195 9807 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→25.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 0 0 70 740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007701
X-RAY DIFFRACTIONf_angle_d0.993946
X-RAY DIFFRACTIONf_dihedral_angle_d15.652257
X-RAY DIFFRACTIONf_chiral_restr0.07287
X-RAY DIFFRACTIONf_plane_restr0.004124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7999-2.06030.23681550.18693098X-RAY DIFFRACTION100
2.0603-2.59540.23131510.20663111X-RAY DIFFRACTION100
2.5954-25.76610.18791650.19033127X-RAY DIFFRACTION100

+
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