[English] 日本語
Yorodumi
- PDB-6xxx: 1.25 Angstrom crystal structure of Ca/CaM A102V:RyR2 peptide complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xxx
Title1.25 Angstrom crystal structure of Ca/CaM A102V:RyR2 peptide complex
Components
  • Calmodulin-1
  • LYS-LYS-ALA-VAL-TRP-HIS-LYS-LEU-LEU-SER-LYS-GLN-ARG-LYS-ARG-ALA-VAL-VAL-ALA-CYS-PHE
KeywordsMETAL BINDING PROTEIN / calcium-binding protein / cardiac muscle contraction / RyR2
Function / homology
Function and homology information


CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation ...CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Platelet degranulation / myelin sheath / Ca2+ pathway / RAF/MAP kinase cascade / vesicle / transmembrane transporter binding / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway
Similarity search - Function
EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsAntonyuk, S. / Helassa, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationFS/17/56/32925 United Kingdom
CitationJournal: J.Cell.Sci. / Year: 2022
Title: CPVT-associated calmodulin variants N53I and A102V dysregulate Ca2+ signalling via different mechanisms.
Authors: Prakash, O. / Held, M. / McCormick, L.F. / Gupta, N. / Lian, L.Y. / Antonyuk, S. / Haynes, L.P. / Thomas, N.L. / Helassa, N.
History
DepositionJan 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Calmodulin-1
BBB: LYS-LYS-ALA-VAL-TRP-HIS-LYS-LEU-LEU-SER-LYS-GLN-ARG-LYS-ARG-ALA-VAL-VAL-ALA-CYS-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5466
Polymers19,3862
Non-polymers1604
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-74 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.110, 41.800, 86.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Calmodulin-1 /


Mass: 16880.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#2: Protein/peptide LYS-LYS-ALA-VAL-TRP-HIS-LYS-LEU-LEU-SER-LYS-GLN-ARG-LYS-ARG-ALA-VAL-VAL-ALA-CYS-PHE


Mass: 2505.123 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate trihydrate pH 4.0, 25% w/v Polyethylene glycol 1,500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.23→41.8 Å / Num. obs: 42088 / % possible obs: 98.37 % / Redundancy: 5.6 % / Biso Wilson estimate: 16.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.017 / Rrim(I) all: 0.042 / Net I/σ(I): 18.4
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1739 / CC1/2: 0.473 / Rpim(I) all: 0.553 / Rrim(I) all: 0.971 / % possible all: 83.25

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XXF

6xxf


Resolution: 1.25→37.624 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.152 / SU B: 3.229 / SU ML: 0.057 / Average fsc free: 0.9421 / Average fsc work: 0.962 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1892 2015 4.988 %
Rwork0.1417 38384 -
all0.144 --
obs-40399 98.952 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.636 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2--3.864 Å20 Å2
3----2.594 Å2
Refinement stepCycle: LAST / Resolution: 1.25→37.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 4 209 1540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131426
X-RAY DIFFRACTIONr_bond_other_d0.0060.0181319
X-RAY DIFFRACTIONr_angle_refined_deg2.0651.6571927
X-RAY DIFFRACTIONr_angle_other_deg1.6811.5933085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2875186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71823.69692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63915285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1971511
X-RAY DIFFRACTIONr_chiral_restr0.1090.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021648
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02293
X-RAY DIFFRACTIONr_nbd_refined0.2420.2418
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21219
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2709
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2557
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2126
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2070.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.150.221
X-RAY DIFFRACTIONr_nbd_other0.2440.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.240
X-RAY DIFFRACTIONr_mcbond_it3.3392.118691
X-RAY DIFFRACTIONr_mcbond_other3.3372.117690
X-RAY DIFFRACTIONr_mcangle_it3.673.184867
X-RAY DIFFRACTIONr_mcangle_other3.6693.185868
X-RAY DIFFRACTIONr_scbond_it5.4792.586735
X-RAY DIFFRACTIONr_scbond_other5.4792.585735
X-RAY DIFFRACTIONr_scangle_it6.1943.7221050
X-RAY DIFFRACTIONr_scangle_other6.1943.7211050
X-RAY DIFFRACTIONr_lrange_it6.0927.761829
X-RAY DIFFRACTIONr_lrange_other5.76727.1381783
X-RAY DIFFRACTIONr_rigid_bond_restr13.18732745
LS refinement shellResolution: 1.25→1.282 Å
RfactorNum. reflection% reflection
Rfree0.286 113 -
Rwork0.275 2572 -
obs--90.9553 %

+
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