[English] 日本語
Yorodumi
- PDB-4e53: Calmodulin and Nm peptide complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4.0E+53
TitleCalmodulin and Nm peptide complex
ComponentsCalmodulin, Linker, IQ motif of Neuromodulin
KeywordsPROTEIN BINDING / Calmodulin (CaM) / Intrinsically unstructured proteins / Protein kinase C (PKC) / Neuromodulin / Growth associated protein -43 (GAP-43) / Long Term Potentiation (LTP) / Long Term Depression (LTD) / IQ motif
Function / homology
Function and homology information


L1CAM interactions / axon choice point recognition / CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor ...L1CAM interactions / axon choice point recognition / CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / CLEC7A (Dectin-1) induces NFAT activation / regulation of postsynaptic specialization assembly / Synthesis of IP3 and IP4 in the cytosol / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Calcineurin activates NFAT / eNOS activation / Ion transport by P-type ATPases / Unblocking of NMDA receptors, glutamate binding and activation / Protein methylation / RAF activation / VEGFR2 mediated vascular permeability / lysophosphatidic acid binding / RAS processing / Smooth Muscle Contraction / phosphatidylinositol phosphate binding / Ca2+ pathway / negative regulation of calcium ion transmembrane transporter activity / FCERI mediated Ca+2 mobilization / RAF/MAP kinase cascade / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / PKA activation / growth cone membrane / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Platelet degranulation / glial cell differentiation / : / tissue regeneration / regulation of filopodium assembly / establishment of protein localization to mitochondrial membrane / Stimuli-sensing channels / Ion homeostasis / type 3 metabotropic glutamate receptor binding / filopodium membrane / regulation of growth / axon regeneration / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / response to corticosterone / phosphatidylserine binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / protein phosphatase activator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / GABA-ergic synapse / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / cell fate commitment / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / 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 / potassium ion transmembrane transport / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / cell periphery / axon guidance / calcium-mediated signaling / spindle microtubule / mitochondrial membrane
Similarity search - Function
Neuromodulin (GAP-43) / Neuromodulin (GAP-43), C-terminal / Neuromodulin, palmitoylation site / Neuromodulin gap junction N-terminal / Neuromodulin, phosphorylation site / Neuromodulin / Gap junction protein N-terminal region / Neuromodulin (GAP-43) signature 1. / Neuromodulin (GAP-43) signature 2. / IQ calmodulin-binding motif ...Neuromodulin (GAP-43) / Neuromodulin (GAP-43), C-terminal / Neuromodulin, palmitoylation site / Neuromodulin gap junction N-terminal / Neuromodulin, phosphorylation site / Neuromodulin / Gap junction protein N-terminal region / Neuromodulin (GAP-43) signature 1. / Neuromodulin (GAP-43) signature 2. / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site / EF-hand / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Neuromodulin / Calmodulin-1 / Calmodulin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.69 Å
AuthorsKumar, V. / Sivaraman, J.
CitationJournal: Sci Rep / Year: 2013
Title: Structural basis for the interaction of unstructured neuron specific substrates neuromodulin and neurogranin with calmodulin
Authors: Kumar, V. / Chichili, V.P.R. / Zhong, L. / Tang, X. / Velazquez-Campoy, A. / Sheu, F.-S. / Seetharaman, J. / Gerges, N.Z. / Sivaraman, J.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calmodulin, Linker, IQ motif of Neuromodulin
B: Calmodulin, Linker, IQ motif of Neuromodulin


Theoretical massNumber of molelcules
Total (without water)41,4862
Polymers41,4862
Non-polymers00
Water1,24369
1
A: Calmodulin, Linker, IQ motif of Neuromodulin


Theoretical massNumber of molelcules
Total (without water)20,7431
Polymers20,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calmodulin, Linker, IQ motif of Neuromodulin


Theoretical massNumber of molelcules
Total (without water)20,7431
Polymers20,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.386, 79.285, 136.064
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Calmodulin, Linker, IQ motif of Neuromodulin /


Mass: 20743.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chimera of Calmodulin, Linker, IQ motif of Neuromodulin
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGS21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P62204, UniProt: P06837, UniProt: P0DP26*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 5.16 Å3/Da / Density % sol: 76.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.12mM MgAcO, 8% PEG 3350, 10% EtOH, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSRRC BL13B110.978
ROTATING ANODEBRUKER AXS MICROSTAR21.541
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 15, 2011
Bruker Platinum 1352CCDJun 7, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
21.5411
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.255
11-K, -H, -L20.247
11K, H, -L30.241
11-h,-k,l40.257
ReflectionResolution: 2.69→50 Å / Num. all: 23563 / Num. obs: 23563 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.69→2.74 Å / % possible all: 85.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.69→30 Å / Cor.coef. Fo:Fc: 0.787 / Cor.coef. Fo:Fc free: 0.664 / SU B: 7.702 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31817 1278 5.7 %RANDOM
Rwork0.27604 ---
obs0.2785 21094 94.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.101 Å2
Baniso -1Baniso -2Baniso -3
1-12.47 Å20 Å2-0.51 Å2
2--23.17 Å20 Å2
3----35.64 Å2
Refinement stepCycle: LAST / Resolution: 2.69→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2646 0 0 69 2715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222672
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9623576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.99426.027146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.01815516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9811516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022022
X-RAY DIFFRACTIONr_mcbond_it0.2231.51654
X-RAY DIFFRACTIONr_mcangle_it0.41422646
X-RAY DIFFRACTIONr_scbond_it0.64231018
X-RAY DIFFRACTIONr_scangle_it1.0624.5930
LS refinement shellResolution: 2.69→2.759 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 75 -
Rwork0.176 1191 -
obs--73.65 %

+
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