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- PDB-4byf: Crystal structure of human Myosin 1c in complex with calmodulin i... -

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Basic information

Entry
Database: PDB / ID: 4byf
TitleCrystal structure of human Myosin 1c in complex with calmodulin in the pre-power stroke state
Components
  • CALMODULIN
  • UNCONVENTIONAL MYOSIN-IC
KeywordsHYDROLASE / MYO1C / GLUT4 EXOCYTOSIS / ATPASE / MOTOR PROTEIN
Function / homology
Function and homology information


positive regulation of cell migration by vascular endothelial growth factor signaling pathway / stereocilium membrane / small GTPase binding => GO:0031267 / positive regulation of cellular response to insulin stimulus / microfilament motor activity => GO:0000146 / unconventional myosin complex / : / positive regulation of vascular endothelial growth factor signaling pathway / : / establishment of protein localization to mitochondrial membrane ...positive regulation of cell migration by vascular endothelial growth factor signaling pathway / stereocilium membrane / small GTPase binding => GO:0031267 / positive regulation of cellular response to insulin stimulus / microfilament motor activity => GO:0000146 / unconventional myosin complex / : / positive regulation of vascular endothelial growth factor signaling pathway / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / vesicle transport along actin filament / regulation of bicellular tight junction assembly / CaM pathway / protein targeting to membrane / Cam-PDE 1 activation / Sodium/Calcium exchangers / regulation of synaptic vesicle endocytosis / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / 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) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / response to corticosterone / microfilament motor activity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / filamentous actin / RHO GTPases activate PAKs / brush border / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / microvillus / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / lateral plasma membrane / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / positive regulation of protein targeting to membrane / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / mRNA transport / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / protein targeting / Protein methylation / phosphatidylinositol 3-kinase binding / eNOS activation / nuclear pore / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of protein dephosphorylation / Ion homeostasis / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / transcription initiation-coupled chromatin remodeling / calcium channel complex / response to amphetamine / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity
Similarity search - Function
Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. ...Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADP ORTHOVANADATE / Unconventional myosin-Ic / Calmodulin-1 / Calmodulin-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsMunnich, S. / Taft, M.H. / Pathan-Chhatbar, S. / Manstein, D.J.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Crystal Structure of Human Myosin 1C-the Motor in Glut4 Exocytosis: Implications for Ca(2+) Regulation and 14-3-3 Binding.
Authors: Munnich, S. / Taft, M.H. / Manstein, D.J.
History
DepositionJul 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UNCONVENTIONAL MYOSIN-IC
B: CALMODULIN
C: UNCONVENTIONAL MYOSIN-IC
D: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,7469
Polymers201,5844
Non-polymers1,1615
Water3,495194
1
C: UNCONVENTIONAL MYOSIN-IC
D: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3855
Polymers100,7922
Non-polymers5933
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-28.7 kcal/mol
Surface area38380 Å2
MethodPISA
2
A: UNCONVENTIONAL MYOSIN-IC
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3614
Polymers100,7922
Non-polymers5682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-19.7 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.580, 158.450, 114.340
Angle α, β, γ (deg.)90.00, 91.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UNCONVENTIONAL MYOSIN-IC / MYOSIN I BETA / MMI-BETA / MMIB


Mass: 83939.688 Da / Num. of mol.: 2 / Fragment: MOTOR DOMAIN, RESIDUES 36-760
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC DUAL / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O00159, EC: 3.6.4.1
#2: Protein CALMODULIN / CAM


Mass: 16852.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC DUAL / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-AOV / ADP ORTHOVANADATE


Mass: 544.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N5O14P2V / Comment: energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 51.2 % / Description: NONE
Crystal growDetails: 18% PEG3350, 0.2 M SODIUM MALONATE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0645
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2013
RadiationMonochromator: SILICON (1 1 1) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0645 Å / Relative weight: 1
ReflectionResolution: 2.74→47.94 Å / Num. obs: 51985 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 62.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.4
Reflection shellResolution: 2.74→2.84 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.15 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LKX

1lkx


Resolution: 2.74→47.94 Å / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 -5 %
Rwork0.183 --
obs-51985 94 %
Solvent computationShrinkage radii: 2 Å / VDW probe radii: 2 Å
Displacement parametersBiso mean: 58.8 Å2
Refinement stepCycle: LAST / Resolution: 2.74→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13722 0 67 194 13983
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.834
X-RAY DIFFRACTIONf_angle_d0.0048
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr

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