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- PDB-5wsv: Crystal structure of Myosin VIIa IQ5 in complex with Ca2+-CaM -

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Basic information

Entry
Database: PDB / ID: 5wsv
TitleCrystal structure of Myosin VIIa IQ5 in complex with Ca2+-CaM
Components
  • Calmodulin
  • Unconventional myosin-VIIa
KeywordsMOTOR PROTEIN/CALCIUM BINDING PROTEIN / Molecular motor / Calcium signaling / Protein complex / Calmodulin / MOTOR PROTEIN-CALCIUM BINDING PROTEIN complex
Function / homology
Function and homology information


pigment granule localization / pigment granule transport / upper tip-link density / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / stereocilium base / inner ear receptor cell differentiation / phagolysosome assembly / equilibrioception / sensory perception of light stimulus ...pigment granule localization / pigment granule transport / upper tip-link density / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / stereocilium base / inner ear receptor cell differentiation / phagolysosome assembly / equilibrioception / sensory perception of light stimulus / mechanoreceptor differentiation / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / actin filament-based movement / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / : / positive regulation of protein autophosphorylation / negative regulation of peptidyl-threonine phosphorylation / sensory perception / cell projection organization / stereocilium / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / auditory receptor cell stereocilium organization / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of peptidyl-threonine phosphorylation / 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 / lysosome organization / inner ear morphogenesis / 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 / Activation of RAC1 downstream of NMDARs / response to corticosterone / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / spectrin binding / 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 / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / microvillus / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / inner ear development / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / adenylate cyclase binding / Regulation of MECP2 expression and activity / cochlea development / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / photoreceptor outer segment / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / phagocytosis / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cellular response to interferon-beta / activation of adenylate cyclase activity / Protein methylation / calcium channel inhibitor activity / presynaptic cytosol / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / positive regulation of nitric-oxide synthase activity / titin binding
Similarity search - Function
Myosin VII N-terminal beta barrel domain / Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / Myosin-X FERM PH domain-like / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. ...Myosin VII N-terminal beta barrel domain / Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / Myosin-X FERM PH domain-like / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / RA like domain / IRS-type PTB domain / PTB domain (IRS-1 type) / IQ calmodulin-binding motif / FERM central domain / FERM/acyl-CoA-binding protein superfamily / 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. / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / : / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / SH3-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-3 / Unconventional myosin-VIIa
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsLi, J. / Chen, Y. / Deng, Y. / Lu, Q. / Zhang, M.
CitationJournal: Structure / Year: 2017
Title: Ca(2+)-Induced Rigidity Change of the Myosin VIIa IQ Motif-Single alpha Helix Lever Arm Extension
Authors: Li, J. / Chen, Y. / Deng, Y. / Unarta, I.C. / Lu, Q. / Huang, X. / Zhang, M.
History
DepositionDec 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Unconventional myosin-VIIa
C: Calmodulin
D: Unconventional myosin-VIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,82715
Polymers45,2194
Non-polymers60911
Water21612
1
A: Calmodulin
B: Unconventional myosin-VIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7706
Polymers22,6092
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-48 kcal/mol
Surface area8290 Å2
MethodPISA
2
C: Calmodulin
D: Unconventional myosin-VIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0589
Polymers22,6092
Non-polymers4497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-120 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.683, 89.755, 45.724
Angle α, β, γ (deg.)90.000, 106.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin / CaM


Mass: 16950.584 Da / Num. of mol.: 2 / Fragment: UNP residues 1-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Unconventional myosin-VIIa


Mass: 5658.692 Da / Num. of mol.: 2 / Fragment: UNP residues 828-870
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo7a, Myo7 / Production host: Escherichia coli (E. coli) / References: UniProt: P97479
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1.69 Å3/Da / Density % sol: 27.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M Bis-Tris (pH 6.5), 25%(w/v) PEG 3,500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2014
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 12459 / % possible obs: 97.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 23
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.36 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G43

3g43


Resolution: 2.33→44.88 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.897 / SU B: 25.713 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.643 / ESU R Free: 0.289
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 598 4.8 %RANDOM
Rwork0.2281 ---
obs0.2298 11840 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.27 Å2 / Biso mean: 45.433 Å2 / Biso min: 23.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å2-0.21 Å2
2--1.04 Å20 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 2.33→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 23 12 2500
Biso mean--63.41 36.69 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192517
X-RAY DIFFRACTIONr_bond_other_d0.0020.022216
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9433419
X-RAY DIFFRACTIONr_angle_other_deg0.98235040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9925339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09325.714112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99115370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.768159
X-RAY DIFFRACTIONr_chiral_restr0.0710.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022965
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02554
X-RAY DIFFRACTIONr_mcbond_it1.5153.3321362
X-RAY DIFFRACTIONr_mcbond_other1.5153.331361
X-RAY DIFFRACTIONr_mcangle_it2.5064.9871696
LS refinement shellResolution: 2.329→2.389 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 29 -
Rwork0.315 769 -
all-798 -
obs--85.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.73830.15010.23140.3693-0.45861.2183-0.021-0.08610.1091-0.08040.0691-0.09560.125-0.1539-0.04810.0405-0.01790.00920.0324-0.04460.227441.3881-75.168350.0792
21.23110.07560.90060.09070.16730.80940.0967-0.14450.10560.0271-0.1227-0.00690.1167-0.23330.0260.0695-0.01830.00150.1471-0.01430.18237.1482-73.018652.5876
30.6681-0.52140.58280.77510.40052.51310.06310.12710.097-0.0212-0.1598-0.05270.1059-0.02220.09670.0582-0.02050.02430.05240.02610.142127.839-76.702428.0984
41.2804-1.27670.9992.9689-1.1730.9590.2314-0.1676-0.0527-0.2284-0.1909-0.0270.0548-0.1365-0.04040.14040.0055-0.01610.11320.00660.103624.5869-79.180328.799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 144
2X-RAY DIFFRACTION2B826 - 854
3X-RAY DIFFRACTION3C5 - 146
4X-RAY DIFFRACTION4D828 - 856

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