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- PDB-4l79: Crystal Structure of nucleotide-free Myosin 1b residues 1-728 wit... -

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Basic information

Entry
Database: PDB / ID: 4l79
TitleCrystal Structure of nucleotide-free Myosin 1b residues 1-728 with bound Calmodulin
Components
  • Calmodulin
  • Unconventional myosin-Ib
KeywordsMOTOR PROTEIN/METAL BINDING PROTEIN / myosin motor / actin binding / nucleotide hydrolysis / cargo / membrane binding / ca2+ binding / MOTOR PROTEIN-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


post-Golgi vesicle-mediated transport / transferrin transport / actin filament-based movement / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / negative regulation of peptidyl-threonine phosphorylation / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding ...post-Golgi vesicle-mediated transport / transferrin transport / actin filament-based movement / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / negative regulation of peptidyl-threonine phosphorylation / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / myosin complex / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of peptidyl-threonine phosphorylation / positive regulation of ryanodine-sensitive calcium-release channel activity / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / positive regulation of DNA binding / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / response to corticosterone / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / negative regulation of ryanodine-sensitive calcium-release channel activity / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / microfilament motor activity / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of synaptic vesicle exocytosis / microvillus / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of protein autophosphorylation / RHO GTPases activate PAKs / phosphatidylinositol-3,4,5-trisphosphate binding / cytoskeletal motor activity / brush border / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / actin filament bundle assembly / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / adenylate cyclase binding / Regulation of MECP2 expression and activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / activation of adenylate cyclase activity / Protein methylation / presynaptic cytosol / Activation of AMPK downstream of NMDARs / phosphatidylinositol 3-kinase binding / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of nitric-oxide synthase activity / eNOS activation / titin binding / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / voltage-gated potassium channel complex / regulation of calcium-mediated signaling / phosphatidylinositol-4,5-bisphosphate binding / calcium channel complex / substantia nigra development / FCERI mediated Ca+2 mobilization / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / nitric-oxide synthase regulator activity / calyx of Held / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / adenylate cyclase activator activity
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4820 / 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. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4820 / 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. / 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 / : / 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 / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-3 / Unconventional myosin-Ib
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShuman, H. / Zwolak, A. / Dominguez, R. / Ostap, E.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: A vertebrate myosin-I structure reveals unique insights into myosin mechanochemical tuning.
Authors: Shuman, H. / Greenberg, M.J. / Zwolak, A. / Lin, T. / Sindelar, C.V. / Dominguez, R. / Ostap, E.M.
History
DepositionJun 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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-Ib
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8793
Polymers102,8552
Non-polymers241
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-34 kcal/mol
Surface area40820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.184, 45.090, 115.547
Angle α, β, γ (deg.)90.00, 117.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Unconventional myosin-Ib / Myosin I alpha / MMI-alpha / MMIa / Myosin heavy chain myr 1


Mass: 86002.008 Da / Num. of mol.: 1 / Fragment: UNP residues 1-728
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Myo1a, Myo1b, Myr1 / Plasmid: pLT11 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q05096
#2: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM, CALM1, CALM2, CALM3, CALML2, calmodulin, CAM, CAM1, CAM2, CAM3, CAMB, CAMC, CAMIII
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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 3350, 100 mM LiOOCCH3, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2012 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 52157 / % possible obs: 99 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.4 Å / % possible all: 87.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: dev_1314)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1oe9

1oe9


Resolution: 2.3→39.209 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 2381 5.06 %
Rwork0.1893 --
obs0.1924 47074 99.68 %
all-57157 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→39.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7133 0 1 459 7593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087324
X-RAY DIFFRACTIONf_angle_d1.0819883
X-RAY DIFFRACTIONf_dihedral_angle_d16.0732805
X-RAY DIFFRACTIONf_chiral_restr0.0731077
X-RAY DIFFRACTIONf_plane_restr0.0051295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.34820.32311250.23592506X-RAY DIFFRACTION95
2.3482-2.39920.33771240.23072612X-RAY DIFFRACTION100
2.3992-2.4550.25711600.21882595X-RAY DIFFRACTION100
2.455-2.51640.2511300.21362618X-RAY DIFFRACTION100
2.5164-2.58440.28791270.21242603X-RAY DIFFRACTION100
2.5844-2.66050.26951280.1992661X-RAY DIFFRACTION100
2.6605-2.74630.26911250.20192591X-RAY DIFFRACTION100
2.7463-2.84440.21671270.20812662X-RAY DIFFRACTION100
2.8444-2.95830.27241590.21452590X-RAY DIFFRACTION100
2.9583-3.09290.32221480.20972600X-RAY DIFFRACTION100
3.0929-3.25590.24931510.20292644X-RAY DIFFRACTION100
3.2559-3.45970.26621390.20022643X-RAY DIFFRACTION100
3.4597-3.72670.25571530.1822623X-RAY DIFFRACTION100
3.7267-4.10140.24481570.17142641X-RAY DIFFRACTION100
4.1014-4.6940.22271310.15362646X-RAY DIFFRACTION100
4.694-5.91070.2161450.1762677X-RAY DIFFRACTION100
5.9107-39.21420.20171520.17172781X-RAY DIFFRACTION100

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