PROTEIN 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
Method 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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.31817
1278
5.7 %
RANDOM
Rwork
0.27604
-
-
-
obs
0.2785
21094
94.74 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 57.101 Å2
Baniso -1
Baniso -2
Baniso -3
1-
12.47 Å2
0 Å2
-0.51 Å2
2-
-
23.17 Å2
0 Å2
3-
-
-
-35.64 Å2
Refinement step
Cycle: LAST / Resolution: 2.69→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2646
0
0
69
2715
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.022
2672
X-RAY DIFFRACTION
r_angle_refined_deg
1.195
1.962
3576
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.844
5
332
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
45.994
26.027
146
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
21.018
15
516
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.981
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.079
0.2
392
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2022
X-RAY DIFFRACTION
r_mcbond_it
0.223
1.5
1654
X-RAY DIFFRACTION
r_mcangle_it
0.414
2
2646
X-RAY DIFFRACTION
r_scbond_it
0.642
3
1018
X-RAY DIFFRACTION
r_scangle_it
1.062
4.5
930
LS refinement shell
Resolution: 2.69→2.759 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.199
75
-
Rwork
0.176
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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