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- PDB-5wsu: Crystal structure of Myosin VIIa IQ5-SAH in complex with apo-CaM -

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Basic information

Entry
Database: PDB / ID: 5wsu
TitleCrystal structure of Myosin VIIa IQ5-SAH in complex with apo-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 / upper tip-link density / pigment granule transport / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / phagolysosome assembly / stereocilium base / inner ear receptor cell differentiation / equilibrioception / sensory perception of light stimulus ...pigment granule localization / upper tip-link density / pigment granule transport / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / phagolysosome assembly / stereocilium base / inner ear receptor cell differentiation / equilibrioception / sensory perception of light stimulus / mechanoreceptor differentiation / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / sensory organ development / actin filament-based movement / inner ear auditory receptor cell differentiation / : / sensory perception / establishment of protein localization to mitochondrial membrane / stereocilium / cell projection organization / type 3 metabotropic glutamate receptor binding / myosin complex / auditory receptor cell stereocilium organization / CaM pathway / 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 / inner ear morphogenesis / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / spectrin binding / response to corticosterone / microfilament motor activity / cochlea development / lysosome organization / 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 / cytoskeletal motor activity / RHO GTPases activate PAKs / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / microvillus / inner ear development / 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 / regulation of cardiac muscle contraction / photoreceptor outer segment / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / 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 methylation / phosphatidylinositol 3-kinase binding / eNOS activation / phagocytosis / 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
Similarity search - Function
Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / IQ calmodulin-binding motif / FERM central domain ...Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / IQ calmodulin-binding motif / FERM central domain / FERM/acyl-CoA-binding protein superfamily / 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 / 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 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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: 3 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,9334
Polymers59,9334
Non-polymers00
Water00
1
A: Calmodulin
C: Unconventional myosin-VIIa


Theoretical massNumber of molelcules
Total (without water)29,9672
Polymers29,9672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-24 kcal/mol
Surface area13520 Å2
MethodPISA
2
B: Calmodulin
D: Unconventional myosin-VIIa


Theoretical massNumber of molelcules
Total (without water)29,9672
Polymers29,9672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-24 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.930, 80.930, 175.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Calmodulin / CaM


Mass: 17019.646 Da / Num. of mol.: 2 / Fragment: UNP residues 2-149
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 Unconventional myosin-VIIa


Mass: 12946.976 Da / Num. of mol.: 2 / Fragment: UNP residues 834-935
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

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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: 4.79 Å3/Da / Density % sol: 74.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.6
Details: 0.1M sodium citrate tribasic (pH 5.6), 20%(v/v) isopropanol, 20%(w/v) PEG 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2013
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 3→50 Å / Num. obs: 22489 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 9.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 2 / Rsym value: 0.967 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IX7

2ix7


Resolution: 3→47.917 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.36
RfactorNum. reflection% reflection
Rfree0.2901 2002 8.93 %
Rwork0.2237 --
obs0.2308 22430 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→47.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 0 0 3104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063131
X-RAY DIFFRACTIONf_angle_d0.9374255
X-RAY DIFFRACTIONf_dihedral_angle_d16.9821869
X-RAY DIFFRACTIONf_chiral_restr0.048528
X-RAY DIFFRACTIONf_plane_restr0.007559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0007-3.07570.34121430.30621447X-RAY DIFFRACTION91
3.0757-3.15880.41711410.32971454X-RAY DIFFRACTION91
3.1588-3.25170.3581440.30621458X-RAY DIFFRACTION91
3.2517-3.35660.30521450.27541467X-RAY DIFFRACTION91
3.3566-3.47660.39821460.31141459X-RAY DIFFRACTION91
3.4766-3.61570.32781450.2841460X-RAY DIFFRACTION91
3.6157-3.78010.32551450.29861442X-RAY DIFFRACTION91
3.7801-3.97920.29231500.25521453X-RAY DIFFRACTION90
3.9792-4.22830.26241430.21411469X-RAY DIFFRACTION91
4.2283-4.55440.23921360.19531475X-RAY DIFFRACTION92
4.5544-5.01190.27491380.17191473X-RAY DIFFRACTION91
5.0119-5.73540.24791420.21111463X-RAY DIFFRACTION91
5.7354-7.21930.30771460.22551478X-RAY DIFFRACTION91
7.2193-40.46870.25491380.1641406X-RAY DIFFRACTION86
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)
12.776-0.7515-0.85231.93841.00542.65340.1269-0.4466-0.3435-0.4158-0.23710.1442-0.84510.37830.06910.7705-0.14520.04740.2946-0.04210.546115.710172.61387.6071
24.6791.43993.30181.50011.62612.67580.36940.68471.0509-0.3561-0.446-0.5459-1.36750.4977-01.28870.08330.0310.67130.13370.679820.706181.8896-0.7621
30.32910.4285-0.50550.8071-0.11281.71250.16970.41180.2561-0.1996-0.01050.0912-1.143-0.6095-0.04520.78140.2534-0.06720.86530.03390.482311.707774.6189-10.3786
46.398-0.38390.49519.0294-1.33937.6212-0.12240.0773-0.85780.0190.2070.4208-0.49680.15-0.05930.5741-0.0947-0.20180.60410.12610.736717.206464.3567-14.8697
50.4535-0.8563-1.41262.94292.81694.40490.09410.7568-0.18250.1937-0.79680.6177-0.1852-0.68890.0760.43160.0568-0.04521.2089-0.25010.7925.872864.5617-15.5812
60.22790.13-0.20971.0936-1.97523.72540.1858-0.2247-0.16820.36690.34760.6339-0.3208-0.31610.06520.7687-0.054-0.00140.3090.10140.599317.661847.509322.7348
71.8411-0.2006-0.04061.04850.09491.64480.2025-0.5344-0.03830.0537-0.137-0.4947-0.38970.8882-0.10540.1729-0.20650.17491.10020.11990.722935.451157.6229-48.1306
82.0966-0.19920.73711.0237-0.63180.82460.11340.6550.68820.10190.64990.9149-0.27-0.9133-1.05680.98470.4326-0.63761.084-0.27991.710438.009844.5816-38.5461
90.75410.6767-1.12190.6308-1.10262.05760.19920.13080.010.5066-0.1391-0.2203-0.2150.07550.3581.41660.38620.03910.84810.5771.195133.069644.8278-21.1874
107.46276.4050.62957.66132.5493.95350.0597-0.42260.16290.5230.3611-0.26880.7185-0.1377-0.00830.57910.33370.1491.1680.28090.772927.00556.4243-19.6127
113.93241.5138-2.86636.5017-0.71434.3203-0.2551-0.4302-0.14851.1183-0.3807-1.34250.30370.76490.43671.0033-0.0418-0.17660.30660.28330.995232.375562.5977-26.0305
123.17773.5915-3.21074.3481-4.0563.87380.12590.28550.4148-0.09490.22770.21530.0866-0.34130.01220.62940.08780.12820.2190.30360.653522.953858.9559-28.5681
131.85861.2967-0.13623.789-3.0193.3618-0.05450.1336-0.56030.01860.2586-0.30520.87050.05950.09611.4177-0.21290.10490.3594-0.10261.174924.163345.9404-27.3145
140.5716-0.19210.88130.4776-0.29661.73980.22690.0805-0.1745-0.38040.06010.1289-0.13190.58850.10140.182-0.19350.04390.7563-0.02930.67087.635757.967-64.6292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 111 )
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 131 )
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 148 )
6X-RAY DIFFRACTION6chain 'C' and (resid 762 through 851 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 74 )
8X-RAY DIFFRACTION8chain 'B' and (resid 75 through 82 )
9X-RAY DIFFRACTION9chain 'B' and (resid 83 through 98 )
10X-RAY DIFFRACTION10chain 'B' and (resid 99 through 111 )
11X-RAY DIFFRACTION11chain 'B' and (resid 112 through 117 )
12X-RAY DIFFRACTION12chain 'B' and (resid 118 through 126 )
13X-RAY DIFFRACTION13chain 'B' and (resid 127 through 147 )
14X-RAY DIFFRACTION14chain 'D' and (resid 760 through 850 )

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