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- PDB-2ix7: Structure of apo-calmodulin bound to unconventional myosin V -

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Basic information

Entry
Database: PDB / ID: 2ix7
TitleStructure of apo-calmodulin bound to unconventional myosin V
Components
  • CALMODULIN
  • MYOSIN-5A
KeywordsCONTRACTILE PROTEIN/METAL BINDING / ACTIN-BINDING / UBL CONJUGATION / CA2+ REGULATION / MYOSIN / CALCIUM / IQ MOTIF / CALMODULIN / ACETYLATION / NUCLEOTIDE- BINDING / CONTRACTILE PROTEIN / COMPLEX / PHOSPHORYLATION / CALMODULIN-BINDING / METAL BINDING / METHYLATION / COILED COIL / ATP-BINDING / MOTOR PROTEIN / CONTRACTILE PROTEIN-METAL BINDING complex
Function / homology
Function and homology information


establishment of endoplasmic reticulum localization to postsynapse / regulation of postsynaptic cytosolic calcium ion concentration / 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 / melanosome localization / endoplasmic reticulum localization / Reduction of cytosolic Ca++ levels ...establishment of endoplasmic reticulum localization to postsynapse / regulation of postsynaptic cytosolic calcium ion concentration / 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 / melanosome localization / endoplasmic reticulum localization / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / Synthesis of IP3 and IP4 in the cytosol / CLEC7A (Dectin-1) induces NFAT activation / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Ion transport by P-type ATPases / Calcineurin activates NFAT / Unblocking of NMDA receptors, glutamate binding and activation / locomotion involved in locomotory behavior / Protein methylation / melanin metabolic process / RAF activation / negative regulation of calcium ion transmembrane transporter activity / VEGFR2 mediated vascular permeability / vesicle transport along actin filament / RAS processing / unconventional myosin complex / insulin-responsive compartment / FCERI mediated Ca+2 mobilization / Ca2+ pathway / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / RAF/MAP kinase cascade / PKA activation / developmental pigmentation / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / melanosome transport / secretory granule localization / Smooth Muscle Contraction / Regulation of MITF-M-dependent genes involved in pigmentation / Regulation of actin dynamics for phagocytic cup formation / actin filament-based movement / : / : / melanin biosynthetic process / hair follicle maturation / positive regulation of cyclic-nucleotide phosphodiesterase activity / Platelet degranulation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / : / melanocyte differentiation / establishment of protein localization to mitochondrial membrane / actomyosin / Stimuli-sensing channels / type 3 metabotropic glutamate receptor binding / Ion homeostasis / long-chain fatty acid biosynthetic process / myosin complex / insulin secretion / odontogenesis / intermediate filament / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / nitric-oxide synthase binding / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / mitochondrion-endoplasmic reticulum membrane tethering / pigmentation / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / microfilament motor activity / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / calcineurin-mediated signaling / exocytosis / regulation of synaptic vesicle endocytosis / cytoskeletal motor activity / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / photoreceptor outer segment / detection of calcium ion / regulation of cardiac muscle contraction / phosphatidylinositol 3-kinase binding / smooth endoplasmic reticulum / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / activation of adenylate cyclase activity / vesicle-mediated transport / enzyme regulator activity
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #190 / Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #190 / Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / EF-hand / : / Recoverin; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYSTEINE / Calmodulin-1 / Calmodulin-2 / Unconventional myosin-Va
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å
AuthorsHoudusse, A. / Gaucher, J.F. / Mui, S. / Krementsova, E. / Trybus, K.M. / Cohen, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Crystal Structure of Apo-Calmodulin Bound to the First Two Iq Motifs of Myosin V Reveals Essential Recognition Features.
Authors: Houdusse, A. / Gaucher, J.F. / Krementsova, E. / Mui, S. / Trybus, K.M. / Cohen, C.
History
DepositionJul 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Feb 27, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALMODULIN
B: CALMODULIN
C: MYOSIN-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4259
Polymers39,8233
Non-polymers6016
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-51.1 kcal/mol
Surface area22810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)112.000, 112.000, 102.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-1148-

SO4

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Components

#1: Protein CALMODULIN / CAM


Mass: 16450.014 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-146
Source method: isolated from a genetically manipulated source
Details: APO-CALMODULIN / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGP1-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P62204, UniProt: P0DP26*PLUS
#2: Protein MYOSIN-5A / MYOSIN VA / DILUTE MYOSIN HEAVY CHAIN / NON-MUSCLE


Mass: 6923.355 Da / Num. of mol.: 1 / Fragment: RESIDUES 763-820
Source method: isolated from a genetically manipulated source
Details: IQ MOTIFS / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q99104
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.6 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5
Details: VAPOR DIFFUSION METHOD (4 C) PROTEIN SOLUTION; 10MG/ML IN 10MM IMIDAZOL PH7.0, 20MM NACL. RESERVOIR; 1.8M SA, 50MM MES PH5.0, 5% MPD, 5MM EGTA, 2MM NAN3, pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9134
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9134 Å / Relative weight: 1
ReflectionResolution: 2.5→29.8 Å / Num. obs: 25837 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 48.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS0.9refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS
Starting model: PDB ENTRY 1WCD

1wcd


Resolution: 2.5→29.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3356211.51 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. THE STRUCTURE WAS FIRST SOLVED BY MIRAS AND THEN REFINED WITH A NON ISOMORPHOUS NATIVE DATA SET.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2570 9.9 %RANDOM
Rwork0.216 ---
obs0.216 25977 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.0899 Å2 / ksol: 0.365848 e/Å3
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.34 Å23.99 Å20 Å2
2--5.34 Å20 Å2
3----10.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-6 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 32 144 2935
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.081.5
X-RAY DIFFRACTIONc_mcangle_it5.592
X-RAY DIFFRACTIONc_scbond_it6.582
X-RAY DIFFRACTIONc_scangle_it8.492.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 430 10 %
Rwork0.27 3860 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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