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- PDB-4l8t: Structure of the Cargo Binding Domain from Human Myosin Vc -

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Basic information

Entry
Database: PDB / ID: 4l8t
TitleStructure of the Cargo Binding Domain from Human Myosin Vc
ComponentsUnconventional myosin-Vc
KeywordsPROTEIN TRANSPORT / C-terminal globular tail / vesicles / intracellular traffic
Function / homology
Function and homology information


myosin complex / microfilament motor activity / actin filament organization / actin filament binding / actin cytoskeleton / calmodulin binding / extracellular exosome / ATP binding / membrane / cytoplasm
Similarity search - Function
Myosin 5c, cargo-binding 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. ...Myosin 5c, cargo-binding 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 head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Unconventional myosin-Vc
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsNascimento, A.F.Z. / Tonoli, C.C.C. / Trindade, D.M. / Assis, L.H.P. / Mahajan, P. / Berridge, G. / Krojer, T. / 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
DepositionJun 17, 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 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Unconventional myosin-Vc


Theoretical massNumber of molelcules
Total (without water)51,5151
Polymers51,5151
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.399, 116.399, 114.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Unconventional myosin-Vc


Mass: 51515.258 Da / Num. of mol.: 1 / Fragment: Cargo Binding Domain (UNP residues 1319-1742)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO5C / Plasmid: pNIC28-Bsa4-BR1-D10 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q9NQX4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 0.1M CAPS, 2M NH4SO4, 0.2M Li2SO4, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 1, 2013
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.95→90 Å / Num. all: 17192 / Num. obs: 17097 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.55 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.49

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Processing

Software
NameVersionClassification
NatXraydata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→47.068 Å / SU ML: 0.54 / σ(F): 2 / Phase error: 33.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2742 865 5.07 %Random
Rwork0.2221 ---
obs0.2247 17073 99.35 %-
all-17194 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→47.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 0 7 2957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043006
X-RAY DIFFRACTIONf_angle_d0.7544058
X-RAY DIFFRACTIONf_dihedral_angle_d16.6171147
X-RAY DIFFRACTIONf_chiral_restr0.053460
X-RAY DIFFRACTIONf_plane_restr0.003516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.13460.4371650.36952616X-RAY DIFFRACTION99
3.1346-3.37650.38941380.31532658X-RAY DIFFRACTION100
3.3765-3.71620.32521170.25182710X-RAY DIFFRACTION100
3.7162-4.25360.26881710.19522656X-RAY DIFFRACTION100
4.2536-5.35790.22291400.18792717X-RAY DIFFRACTION99
5.3579-47.07420.24381340.20312851X-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)
16.88044.52961.00923.125-0.56416.5401-0.34531.1363-1.2162-1.40960.4197-2.11410.54821.1846-0.13261.06130.26110.17821.9808-0.32121.330749.1547-47.5038-4.767
29.64171.24542.4122.69592.22282.15842.53320.9372-0.6304-2.0619-0.6461-3.20641.3039-2.1956-1.42221.27970.4821-0.13771.24640.06971.440742.3385-56.27379.5
34.82622.9766-4.36082.5232-3.19044.4472-1.371-1.1456-0.72290.5021.8237-0.86570.6204-4.5118-1.09591.1452-0.11980.05461.84870.23551.067141.2108-48.510212.5058
45.92664.8499-3.8035.0777-0.85397.6139-0.87542.07880.7186-1.26761.7762-0.2347-0.4262-0.0927-0.86291.15250.10240.03221.98230.01331.165843.8852-41.0998-7.602
55.22215.6881-5.33276.1261-5.74045.5339-0.60110.1209-1.650.2039-0.1621-2.86581.6922-0.70310.8061.57840.1767-0.07862.0403-0.1981.369132.0249-57.5024-1.2965
67.51465.79610.67774.38960.3342.3162-0.18080.67090.8609-0.41290.13780.4101-0.5828-0.4626-0.02841.01120.12460.15951.45740.02190.912633.6877-38.0541.2598
74.08963.32782.28185.38054.70494.28592.5106-0.29120.8442.20682.0817-0.0519-2.6536-0.6889-3.86312.1443-0.34930.33741.910.09391.435241.6151-28.67183.3416
82.3075-2.2572-0.50437.5332.78211.76012.28560.8990.0482-0.8313-0.9043-1.345-0.1417-0.7693-0.99272.27360.268-0.1532.29040.07341.77834.9412-35.4852-10.5579
96.20122.7802-2.41883.9878-3.19392.871-0.18032.00570.2998-0.74851.10060.54480.8745-1.1038-0.76131.23620.08730.06851.5096-0.17140.902122.3404-53.43561.0385
103.8038-3.2218-3.1835.0783.68473.32610.2686-1.64450.09410.2019-0.609-0.33251.2567-0.07570.49741.52990.094-0.17782.2948-0.05771.36856.5897-65.709420.8779
118.25686.0775-3.49074.9961-4.37567.019-0.37882.1872-0.7260.77481.3414-1.49460.7998-1.6668-0.9011.16470.1984-0.24512.0645-0.00371.380118.6023-60.434119.1971
128.34972.11372.65442.7742-0.95762.5915-0.0859-0.16540.0905-0.15940.1827-0.1131-0.3686-0.587-0.22171.3674-0.0312-0.00661.8495-0.05780.763315.998-52.498811.1209
135.06612.4649-1.85047.3957-3.12962.93650.7767-2.6638-0.82150.2709-0.2454-0.26520.2502-1.1487-0.5141.5446-0.2017-0.03692.30580.1451.0014.572-57.242121.9204
143.83813.00242.54643.07871.94878.9640.0974-0.40641.20690.7242-0.16460.7424-1.22740.2525-0.09991.66410.18380.07041.89330.02951.134110.0943-46.26716.9881
159.76265.9601-6.50449.1545-0.24877.01862.2759-1.69450.92961.6654-0.45740.6215-1.0258-0.2534-1.29271.54850.34730.05512.60540.25921.0754-10.9168-52.68219.682
164.7109-3.7398-5.51463.26284.05768.78980.0204-1.16660.6880.7153-0.19230.5615-0.42980.19710.52821.16710.1622-0.10892.1317-0.02281.1474-9.9705-48.150912.9605
174.9553-2.3107-6.72033.4831.13482.0098-1.1095-0.82510.76320.94931.7706-0.32011.7645-1.0001-1.05051.5913-0.044-0.21372.31160.15791.5895-12.3717-62.619219.4971
186.9903-2.84984.15353.6944-1.83239.7656-0.4636-0.50830.4106-0.63182.50421.66941.6149-0.798-1.46261.4017-0.204-0.10592.40480.03030.9581-16.7287-50.46328.117
199.77835.60891.70824.09961.34712.02510.4047-0.0240.69370.5258-0.38390.11740.2123-1.0447-0.04121.28520.10570.02632.1764-0.01891.120613.7517-47.92043.0846
208.54742.0813-1.13778.3418-4.24057.51430.2503-0.4321-0.40380.7540.1059-0.9052-0.01180.998-0.16511.2859-0.0265-0.00641.4436-0.09961.296150.0458-44.3844.3443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1359:1381)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1382:1387)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 1388:1394)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 1395:1422)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 1423:1442)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 1443:1466)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 1467:1478)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 1479:1486)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 1487:1509)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 1510:1523)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 1545:1559)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 1560:1593)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 1594:1619)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 1620:1635)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 1636:1648)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 1649:1667)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 1668:1683)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 1684:1700)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 1701:1721)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 1722:1742)

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