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- PDB-4kp3: Crystal Structure of MyoVa-GTD in Complex with Two Cargos -

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Basic information

Entry
Database: PDB / ID: 4kp3
TitleCrystal Structure of MyoVa-GTD in Complex with Two Cargos
Components
  • Melanophilin
  • RILP-like protein 2
  • Unconventional myosin-Va
KeywordsMOTOR PROTEIN/PROTEIN TRANSPORT / Helix bundle / MOTOR PROTEIN-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


protein transport from ciliary membrane to plasma membrane / actomyosin, myosin complex part / establishment of endoplasmic reticulum localization to postsynapse / regulation of postsynaptic cytosolic calcium ion concentration / axo-dendritic protein transport / positive regulation of cellular response to insulin stimulus / melanosome localization / endoplasmic reticulum localization / locomotion involved in locomotory behavior / melanin metabolic process ...protein transport from ciliary membrane to plasma membrane / actomyosin, myosin complex part / establishment of endoplasmic reticulum localization to postsynapse / regulation of postsynaptic cytosolic calcium ion concentration / axo-dendritic protein transport / positive regulation of cellular response to insulin stimulus / melanosome localization / endoplasmic reticulum localization / locomotion involved in locomotory behavior / melanin metabolic process / vesicle transport along actin filament / negative regulation of dopamine secretion / insulin-responsive compartment / unconventional myosin complex / post-Golgi vesicle-mediated transport / secretory granule localization / developmental pigmentation / reactive gliosis / Regulation of MITF-M-dependent genes involved in pigmentation / Regulation of actin dynamics for phagocytic cup formation / filopodium tip / melanin biosynthetic process / hair follicle maturation / regulation of exocytosis / melanocyte differentiation / actin filament-based movement / actomyosin / myosin V binding / epithelial cell morphogenesis / melanosome transport / microtubule plus-end binding / postsynaptic actin cytoskeleton / ATP-dependent protein binding / positive regulation of vascular associated smooth muscle cell migration / myosin complex / odontogenesis / long-chain fatty acid biosynthetic process / syntaxin-1 binding / negative regulation of synaptic transmission, glutamatergic / insulin secretion / intermediate filament / cortical actin cytoskeleton / microfilament motor activity / myosin binding / exocytosis / pigmentation / smooth endoplasmic reticulum / dopamine metabolic process / cytoskeletal motor activity / microtubule organizing center / intracellular membrane-bounded organelle / photoreceptor outer segment / protein targeting / vesicle-mediated transport / ruffle / stress fiber / myelination / visual perception / secretory granule / actin filament organization / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / SNARE binding / macroautophagy / intracellular protein transport / synapse organization / recycling endosome / Schaffer collateral - CA1 synapse / small GTPase binding / endocytosis / cellular response to insulin stimulus / disordered domain specific binding / calcium-dependent protein binding / actin filament binding / synaptic vesicle / melanosome / actin cytoskeleton / actin binding / protein-containing complex assembly / molecular adaptor activity / chemical synaptic transmission / protein-macromolecule adaptor activity / calmodulin binding / protein dimerization activity / postsynapse / cilium / ribonucleoprotein complex / axon / neuronal cell body / calcium ion binding / centrosome / dendrite / protein kinase binding / protein-containing complex binding / perinuclear region of cytoplasm / glutamatergic synapse / Golgi apparatus / ATP hydrolysis activity / zinc ion binding / ATP binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1770 / Rab effector MyRIP/Melanophilin / Melanophilin, FYVE-related domain / : / Rab effector MyRIP/melanophilin C-terminus / Rab interacting lysosomal protein, dimerization domain / : / Rab interacting lysosomal protein / RH1 domain / RH2 domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1770 / Rab effector MyRIP/Melanophilin / Melanophilin, FYVE-related domain / : / Rab effector MyRIP/melanophilin C-terminus / Rab interacting lysosomal protein, dimerization domain / : / Rab interacting lysosomal protein / RH1 domain / RH2 domain / RILP homology 1 domain / RH1 domain profile. / RH2 domain profile. / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Myosin 5a, cargo-binding domain / : / Unconventional myosin-Va 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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Melanophilin / Unconventional myosin-Va / RILP-like protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.405 Å
AuthorsWei, Z. / Liu, X. / Yu, C. / Zhang, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis of cargo recognitions for class V myosins
Authors: Wei, Z. / Liu, X. / Yu, C. / Zhang, M.
History
DepositionMay 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unconventional myosin-Va
C: RILP-like protein 2
E: Melanophilin
B: Unconventional myosin-Va
D: RILP-like protein 2
F: Melanophilin


Theoretical massNumber of molelcules
Total (without water)125,1936
Polymers125,1936
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10380 Å2
ΔGint-68 kcal/mol
Surface area41720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.850, 107.933, 83.510
Angle α, β, γ (deg.)90.000, 96.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Unconventional myosin-Va / Dilute myosin heavy chain / non-muscle


Mass: 46106.254 Da / Num. of mol.: 2
Fragment: Globular Tail Domain (GTD), UNP residues 1469-1853
Mutation: C1674S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo5a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99104
#2: Protein RILP-like protein 2 / RILPL2 / Rab-interacting lysosomal-like protein 2


Mass: 11607.970 Da / Num. of mol.: 2 / Fragment: Rilp Homology (RH1), UNP residues 1-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rilpl2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99LE1
#3: Protein/peptide Melanophilin / Exophilin-3 / Leaden protein / Slp homolog lacking C2 domains a / SlaC2-a / Synaptotagmin-like protein 2a


Mass: 4882.339 Da / Num. of mol.: 2
Fragment: Globular Tail Binding Domain (GTBD), UNP residues 170-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mlph / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91V27
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12-16%(w/v) PEG3350, 2-4% tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorDate: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 54968 / Num. obs: 54968 / % possible obs: 98.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 48.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WB8

3wb8


Resolution: 2.405→38.694 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.7917 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 2795 5.09 %
Rwork0.192 --
obs0.1945 54917 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.07 Å2 / Biso mean: 53.4859 Å2 / Biso min: 17.22 Å2
Refinement stepCycle: LAST / Resolution: 2.405→38.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7286 0 0 57 7343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047410
X-RAY DIFFRACTIONf_angle_d0.7699990
X-RAY DIFFRACTIONf_chiral_restr0.0571157
X-RAY DIFFRACTIONf_plane_restr0.0031279
X-RAY DIFFRACTIONf_dihedral_angle_d14.5662851
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4048-2.44630.33171210.27752328244989
2.4463-2.49080.31861460.2762636278299
2.4908-2.53870.32211510.26362609276099
2.5387-2.59050.31681380.25132646278499
2.5905-2.64680.31291560.245326302786100
2.6468-2.70830.3171400.23142648278899
2.7083-2.7760.2841410.21922614275599
2.776-2.85110.27511340.22192641277599
2.8511-2.93490.31391430.21882640278399
2.9349-3.02960.27161390.22892625276499
3.0296-3.13790.28621260.21652631275799
3.1379-3.26350.31411440.23692638278299
3.2635-3.41190.25781470.22352624277199
3.4119-3.59170.2991390.21072629276899
3.5917-3.81650.2181550.19122579273498
3.8165-4.11090.22151580.17082603276198
4.1109-4.5240.21071200.15052629274997
4.524-5.17730.18831290.15792608273797
5.1773-6.51780.23251360.19692581271796
6.5178-38.69940.16491320.14352583271594
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)
11.6748-0.19690.61052.1032-0.60561.91040.02730.1862-0.2041-0.4042-0.023-0.12560.14910.1748-0.00590.2765-0.01150.05980.217-0.01260.2818-0.52-5.337-1.783
21.1545-0.26660.55151.07490.48781.8708-0.0660.0327-0.05330.03170.13560.00480.05570.0423-0.02550.2375-0.0042-0.01620.22180.04560.2899-1.1573-2.012612.7228
31.42710.63280.47571.0120.44561.4914-0.27640.19920.87480.0761-0.055-0.0714-0.4997-0.2220.04750.49780.0839-0.14510.1248-0.06120.6287-1.314320.434419.7153
41.14340.0589-0.02660.84280.31621.9338-0.125-0.75770.52410.0368-0.06780.1892-0.4411-0.42970.0370.4130.1361-0.0740.5194-0.2880.50680.600418.633337.9982
51.5643-1.61790.33312.6914-0.21491.6632-0.4774-0.98320.58980.10720.4132-0.3546-0.151-0.5217-0.01310.58270.134-0.09140.8836-0.31250.67627.969325.962554.6147
60.87380.27130.08560.91680.17180.2950.0496-0.18030.08110.1098-0.021-0.08750.2129-0.1254-0.0460.27960.0122-0.01930.2127-0.01090.291-1.73411.163316.11
70.0835-0.04730.59860.0218-0.29755.331-0.0906-0.6174-0.38411.20020.0410.160.1962-0.1718-0.17030.6754-0.031-0.10830.5405-0.00020.5583-16.314522.84095.6616
81.58750.421-0.56521.5942-0.66551.66050.2035-0.5381-0.16830.2998-0.2454-0.15810.00450.05850.01750.3335-0.003-0.06050.38660.0260.3661-14.351615.84111.9669
90.96511.622-1.52493.7386-3.03392.91970.1048-0.046-0.0194-0.0388-0.1354-0.0954-0.12020.18640.01710.34640.04280.03120.27070.0350.3155-6.901122.8713-15.1883
101.22-0.155-0.44253.9486-0.34540.88440.25060.0403-0.1764-0.22940.0498-0.42320.42280.15950.37450.480.1078-0.1202-0.4646-0.0620.78712.4361-22.11177.3219
118.0478-4.34611.03442.8731-0.01216.01480.18850.1940.1410.3664-0.7058-0.9609-0.80810.76960.03090.6001-0.02010.06170.49230.09090.789714.1864-11.33447.1621
123.36040.1010.69072.00360.6282.3482-0.0666-0.19230.60410.129-0.02930.2503-0.2383-0.6758-0.00230.28640.1044-0.01010.4986-0.02420.3712-43.418826.3461-5.9627
130.7441.19190.82811.09681.31692.1673-0.05610.358-0.0948-0.11550.2343-0.1465-0.01590.1348-0.04630.35140.0187-0.03530.75720.0120.3712-42.4149.0732-31.9214
141.19410.7231.16220.94181.08641.32320.04480.1031-0.1441-0.07-0.02310.08370.04280.5651-0.03330.44160.0098-0.03820.5587-0.02750.3337-54.5527-5.248-46.4526
151.02070.11110.56990.15690.53570.59940.0302-0.1417-0.0364-0.0642-0.09970.0830.0577-0.5128-0.05030.4504-0.0392-0.02040.6002-0.04880.2819-47.781315.5743-18.6122
162.0388-1.61841.46442.46540.57263.74090.18890.2643-0.2533-0.4972-0.0412-0.15330.4814-0.70590.00140.51150.0352-0.02670.4284-0.04260.3463-15.907611.8453-17.8097
172.15371.0175-0.99493.0576-1.8524.03350.01570.24820.1935-0.33340.33120.71520.4848-0.6688-0.04870.3405-0.0161-0.0790.35280.01350.4091-27.230911.9633-9.5152
182.74451.719-2.52842.0119-1.93333.3601-0.05220.11520.1935-0.33150.11320.06210.0886-0.13510.01370.33060.03980.03640.2340.02080.3302-13.254826.8309-17.1974
192.26380.0386-0.73242.9454-0.91130.570.2517-0.44510.60230.4482-0.27670.4581-0.1591-0.0194-0.06870.51440.17070.13630.9505-0.20440.8932-59.88731.4561-1.5599
207.5112-1.8914.61588.7627-2.92793.2123-0.19890.54180.0065-0.43010.049-0.60820.2161-0.1420.04681.25340.3089-0.00610.79260.07391.0305-54.833936.1747-16.03
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1470 : 1544 )
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 1545 : 1627 )
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 1628 : 1679 )
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 1680 : 1783 )
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 1784 : 1807 )
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 1808 : 1853 )
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 14 : 20 )
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 21 : 48 )
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 49 : 94 )
10X-RAY DIFFRACTION10CHAIN E AND (RESSEQ 184 : 192 )
11X-RAY DIFFRACTION11CHAIN E AND (RESSEQ 193 : 197 )
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 1470 : 1593 )
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 1594 : 1731 )
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 1732 : 1805 )
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 1806 : 1853 )
16X-RAY DIFFRACTION16CHAIN D AND (RESSEQ 14 : 27 )
17X-RAY DIFFRACTION17CHAIN D AND (RESSEQ 28 : 48 )
18X-RAY DIFFRACTION18CHAIN D AND (RESSEQ 49 : 95 )
19X-RAY DIFFRACTION19CHAIN F AND (RESSEQ 184 : 192 )
20X-RAY DIFFRACTION20CHAIN F AND (RESSEQ 193 : 197 )

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