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- PDB-4j5l: Structure of the Cargo Binding Domain from Human Myosin Va -

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Basic information

Entry
Database: PDB / ID: 4j5l
TitleStructure of the Cargo Binding Domain from Human Myosin Va
ComponentsUnconventional myosin-Va
KeywordsPROTEIN TRANSPORT / human Myosin Va / C-terminal globular tail / intracellular traffic / vesicles
Function / homology
Function and homology information


vesicle transport along actin filament / insulin-responsive compartment / post-Golgi vesicle-mediated transport / filopodium tip / actin filament-based movement / melanosome transport / myosin complex / Insulin processing / microfilament motor activity / Regulation of MITF-M-dependent genes involved in pigmentation ...vesicle transport along actin filament / insulin-responsive compartment / post-Golgi vesicle-mediated transport / filopodium tip / actin filament-based movement / melanosome transport / myosin complex / Insulin processing / microfilament motor activity / Regulation of MITF-M-dependent genes involved in pigmentation / ruffle / vesicle-mediated transport / actin filament organization / protein localization to plasma membrane / FCGR3A-mediated phagocytosis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / cellular response to insulin stimulus / endocytosis / actin filament binding / melanosome / protein transport / actin cytoskeleton / growth cone / calmodulin binding / neuron projection / ATP hydrolysis activity / RNA binding / extracellular exosome / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
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 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Unconventional myosin-Va
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNascimento, A.F.Z. / Trindade, D.M. / Tonoli, C.C.C. / Assis, L.H.P. / Mahajan, P. / Berridge, G. / Krojer, T. / Vollmar, M. / Burgess-Brown, N. / von Delft, F. / Murakami, M.T.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Insights into Functional Overlapping and Differentiation among Myosin V Motors.
Authors: Nascimento, A.F. / Trindade, D.M. / Tonoli, C.C. / de Giuseppe, P.O. / Assis, L.H. / Honorato, R.V. / de Oliveira, P.S. / Mahajan, P. / Burgess-Brown, N.A. / von Delft, F. / Larson, R.E. / Murakami, M.T.
History
DepositionFeb 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-Va
B: Unconventional myosin-Va
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6704
Polymers93,4782
Non-polymers1922
Water1,65792
1
A: Unconventional myosin-Va


Theoretical massNumber of molelcules
Total (without water)46,7391
Polymers46,7391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Unconventional myosin-Va
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9313
Polymers46,7391
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.799, 79.494, 94.139
Angle α, β, γ (deg.)90.00, 105.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Unconventional myosin-Va / Dilute myosin heavy chain / non-muscle / Myosin heavy chain 12 / Myosin-12 / Myoxin


Mass: 46739.176 Da / Num. of mol.: 2 / Fragment: C-terminal Globular Tail
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYH12, MYO5A / Plasmid: pET28a-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) (Rosetta 2) / References: UniProt: Q9Y4I1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.23 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M bis-tris, 22% PEG 3350, 0.2M ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2011
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.2→39.356 Å / Num. obs: 41574 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.1
Reflection shellResolution: 2.2→2.2506 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 4.1 / % possible all: 83.2

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Processing

Software
NameVersionClassification
NatXraysoftwaredata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.356 Å / SU ML: 0.36 / σ(F): 1.99 / Phase error: 30.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2641 2098 5.05 %
Rwork0.2051 --
obs0.2081 41574 99.46 %
all-23270 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.183 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.7938 Å2-0 Å2-11.3664 Å2
2---6.7624 Å20 Å2
3---0.9686 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5830 0 10 92 5932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025947
X-RAY DIFFRACTIONf_angle_d0.5988022
X-RAY DIFFRACTIONf_dihedral_angle_d14.4562275
X-RAY DIFFRACTIONf_chiral_restr0.044922
X-RAY DIFFRACTIONf_plane_restr0.0031019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25060.41571340.38972460X-RAY DIFFRACTION94
2.2506-2.30680.40891450.32542637X-RAY DIFFRACTION100
2.3068-2.36920.31791440.28542606X-RAY DIFFRACTION100
2.3692-2.43890.32231260.26262630X-RAY DIFFRACTION100
2.4389-2.51760.32551300.24912685X-RAY DIFFRACTION100
2.5176-2.60760.28841330.23972638X-RAY DIFFRACTION100
2.6076-2.7120.31161240.2342637X-RAY DIFFRACTION100
2.712-2.83540.2711370.23582656X-RAY DIFFRACTION100
2.8354-2.98480.26261480.23472611X-RAY DIFFRACTION100
2.9848-3.17170.29511420.2242650X-RAY DIFFRACTION100
3.1717-3.41650.28071670.20942630X-RAY DIFFRACTION100
3.4165-3.76010.24061450.1862636X-RAY DIFFRACTION100
3.7601-4.30360.25561370.1682661X-RAY DIFFRACTION100
4.3036-5.41980.22761340.15932678X-RAY DIFFRACTION100
5.4198-39.36260.21921520.18212661X-RAY DIFFRACTION98
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)
11.8122-1.9987-0.68277.3744-1.12752.211-0.02790.0148-0.08460.1672-0.2846-1.74670.11470.6307-0.98130.82420.2952-0.59070.3284-0.23281.338115.2604-23.654123.1657
23.7341-1.71830.00625.79274.33285.3320.10580.7141-0.67071.47780.02680.01191.660.2178-0.51830.8042-0.0833-0.42330.42110.03511.04042.1665-23.846630.7265
33.07330.17630.55124.30481.40592.57850.49730.0014-0.85980.40330.4711-0.98130.84910.28-0.46630.45290.0834-0.31830.2981-0.12360.80658.6576-17.094127.0703
44.1596-1.2435-1.02299.3654.86037.58150.4453-0.5389-0.80750.9328-0.1350.57280.6582-0.1635-0.11820.5062-0.1439-0.13670.47740.03430.5219-4.3482-11.441133.5526
53.0282-0.4944-0.11975.48861.59032.86730.25410.2051-0.45-0.40270.1431-0.92420.14680.3665-0.41130.26010.01110.01610.3339-0.12710.64558.9596-5.718625.9548
62.9303-0.19050.07570.47670.59360.7460.37380.0821-0.5965-0.61060.4144-2.588-0.73821.1353-0.12320.28350.00830.20380.7388-0.65131.320416.8953-12.266615.7243
71.6845-1.7919-0.73667.01845.05548.53650.09420.0989-0.4281-0.3413-0.54170.5646-0.1463-0.7175-0.05970.2384-0.0641-0.05250.43360.0170.3401-2.31060.333631.2747
86.11641.63230.42048.20823.11593.84580.0623-0.79411.04432.140.54520.00150.6310.6036-0.09870.79310.1279-0.09630.5483-0.03710.3536-1.065918.564954.1278
93.89990.050.79173.66782.52163.71160.0106-0.29950.51671.096-0.4339-0.47110.329-0.5024-0.30950.98520.0718-0.22080.54370.09350.67241.76720.991858.7975
101.2494-0.37210.32315.70443.88113.95540.0458-0.3498-0.23271.32280.5527-1.49990.4386-0.2085-0.49190.62850.1222-0.25080.4346-0.04580.5347.3186.006446.6822
112.9284-2.8114-1.19058.6052.72072.7581-0.0821-0.4996-0.2606-0.13110.328-0.0615-0.05460.3764-0.17820.25680.0097-0.03080.2955-0.02550.3078-0.430216.176240.3674
122.9253-3.7464-1.56138.38633.81243.15080.3033-0.8123-0.0130.31360.6142-1.2936-0.03510.7149-0.29370.4050.0436-0.22090.3639-0.08150.55526.793723.73848.6691
133.9992-2.4346-0.04673.77571.70932.81010.09160.34480.2948-0.39610.2023-1.6741-0.11380.6368-0.47770.3699-0.03980.10570.4617-0.09910.63099.85217.751536.5335
142.1878-1.55970.34818.64042.49123.66870.05240.17490.15550.0206-0.5036-0.2048-0.78720.2672-0.2660.2763-0.03680.04260.30580.01740.30111.048833.568244.4182
152.7590.34620.58033.01843.71684.64970.06970.25820.3905-0.5813-0.0342-0.8653-1.16690.4977-0.24110.5879-0.1264-0.01810.31250.05720.46690.055441.109738.4801
161.78170.33751.05916.08483.7594.1512-0.037-0.30490.3590.4604-0.1417-0.11090.178-0.34220.14470.33340.0139-0.00580.2306-0.01560.2601-7.717536.703948.6346
174.4985-1.2112-0.08457.22241.89728.85920.32510.15320.0895-1.0117-0.31920.056-1.5023-0.66640.23050.64870.0566-0.13010.32820.01950.3389-8.972643.092338.5837
183.8434-1.10350.0212.62472.96923.61380.31820.355-0.5108-1.02810.03351.2079-0.23840.27340.23750.478-0.015-0.09490.3885-0.08470.282-9.241422.075533.7674
191.5842-0.39320.10313.05511.6281.72130.3193-0.3747-0.52960.28750.4441-1.93070.09350.4933-0.64960.30990.004-0.14730.4956-0.22290.81413.3383-7.541428.7425
202.6029-1.6280.80286.17344.35445.53370.78570.3163-0.80740.6439-0.0608-1.95641.01311.1872-0.6381.1730.2189-0.4640.6199-0.03361.19313.0878-26.142929.9594
212.7034-0.1856-0.54026.02450.19174.5183-0.3918-0.36720.70220.0973-0.13611.1166-0.7795-0.56040.32150.51710.1322-0.11210.5751-0.09180.4773-31.993524.738627.671
223.83040.10951.29386.72062.06215.1385-0.0058-0.03010.4362-0.1353-0.31850.6745-0.4261-0.52510.42530.44720.1453-0.06310.3972-0.01210.3353-26.367225.873422.4668
232.40741.24890.86717.58812.32382.5910.1706-0.34540.11420.5555-0.50410.87160.1255-0.29060.21510.30620.04330.02440.3925-0.05180.2197-23.411616.016130.5838
244.55520.02220.41043.5822-0.91943.1629-0.1240.1085-0.27360.8059-0.14882.00410.2357-1.22260.34710.5301-0.1431-0.0210.6064-0.06440.5527-29.20782.875321.052
251.71690.48180.64915.18150.86941.8667-0.19540.27490.2211-0.4880.1345-0.045-0.54540.03340.18460.39710.0409-0.01910.3377-0.00670.1759-20.771618.76716.9251
267.6901-1.4621.22228.1771-0.65595.7258-0.002-0.51830.4681-1.0825-0.371-0.8293-1.19290.44230.00971.0408-0.05490.1220.7020.01420.6531-10.790228.222310.0735
272.32120.60520.51072.70571.34442.5416-0.10480.23360.2251-0.1912-0.0098-0.2783-0.52180.07860.09690.4351-0.0172-0.04150.35230.06130.2265-16.511219.650419.6975
282.5217-1.2112-0.55795.84261.47126.1798-0.15620.3777-0.94880.0227-0.13360.8831.16120.98480.05380.2906-0.0215-0.07640.5134-0.1490.6369-25.4421-14.62638.3044
291.41410.17090.18775.69282.35943.6979-0.08990.026-0.1204-0.6753-0.46171.4981-0.1854-0.81210.30770.39320.0599-0.12730.5617-0.1520.5035-29.5978-2.80586.7574
302.2937-2.27350.83388.60431.13662.82570.16020.0817-0.2789-0.5518-0.00320.48690.19360.1604-0.07440.30410.0009-0.01350.4544-0.07830.2556-16.8377-6.56988.3341
318.5158-1.7827-1.8688.8712-1.0944.48920.3641.1204-1.34340.3395-0.41930.57880.4789-0.1281-0.19390.95830.1796-0.39560.1814-0.43370.956-17.6452-27.08591.428
321.5127-0.95650.58223.5181.72163.030.01620.3328-0.3474-1.56680.29370.64110.07120.36070.01950.74460.1162-0.27610.5616-0.15640.4398-22.3003-8.861-3.3102
337.01640.96781.56127.97340.90458.2083-0.36331.21850.5735-1.41980.0201-0.6294-0.77150.4307-0.32240.4052-0.09460.25070.72730.02080.389-14.1484-0.4823-0.8941
341.0574-0.4697-0.64074.19061.91511.77040.46721.2098-0.4997-0.8528-0.0137-0.39690.46450.6134-0.24460.64990.2476-0.0450.853-0.31650.4752-6.3354-20.4102-2.7905
354.58333.42340.78913.79072.55375.1389-0.39280.4672-0.8698-0.8211-0.1027-0.07151.2848-0.0167-0.77370.82110.2062-0.2430.5287-0.50361.0804-12.5088-30.70711.8006
365.5613-0.66592.21323.64490.5171.87550.2880.8679-1.4029-0.7681-0.09420.02390.90580.4707-0.40831.33790.3989-0.34371.1766-0.5441.3662-10.5649-35.0995-3.6689
370.1231-0.2563-0.25323.85493.11063.53650.41260.7377-0.6495-0.13520.2616-0.11490.94861.2894-0.58240.70730.3032-0.10280.8876-0.36940.8783.1483-23.67652.1551
381.2659-1.33770.2573.48391.8341.9172-0.1110.38650.2037-0.12940.0112-1.5808-0.21340.5978-0.26190.3578-0.0425-0.08060.5241-0.10410.5528-10.7598-7.290514.0672
391.7122-0.6877-0.53.2270.64452.2211-0.01180.4676-0.2027-0.7158-0.20930.7816-0.754-0.5130.34450.5013-0.0232-0.18870.41480.05190.3666-27.549822.920914.1283
402.26840.9499-0.6797.7759-2.14646.5312-0.4054-0.38691.011-0.5076-0.25971.1215-0.4829-1.33030.28260.71480.6879-0.02540.76480.04370.6141-35.349631.12924.2844
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1473:1479)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1480:1493)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 1494:1533)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 1534:1549)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 1550:1579)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 1580:1595)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 1596:1623)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 1624:1634)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 1635:1657)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 1658:1680)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 1681:1709)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 1710:1732)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 1733:1745)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 1746:1758)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 1759:1774)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 1775:1793)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 1794:1811)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 1812:1824)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 1825:1847)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 1848:1855)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 1472:1496)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 1497:1527)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 1528:1546)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 1547:1554)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 1555:1573)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 1574:1580)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 1581:1616)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 1617:1635)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 1636:1680)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 1681:1707)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 1708:1713)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 1714:1735)
33X-RAY DIFFRACTION33(CHAIN B AND RESID 1736:1742)
34X-RAY DIFFRACTION34(CHAIN B AND RESID 1743:1783)
35X-RAY DIFFRACTION35(CHAIN B AND RESID 1784:1788)
36X-RAY DIFFRACTION36(CHAIN B AND RESID 1793:1797)
37X-RAY DIFFRACTION37(CHAIN B AND RESID 1798:1816)
38X-RAY DIFFRACTION38(CHAIN B AND RESID 1817:1827)
39X-RAY DIFFRACTION39(CHAIN B AND RESID 1828:1849)
40X-RAY DIFFRACTION40(CHAIN B AND RESID 1850:1855)

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