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- PDB-4j5m: Structure of the Cargo Binding Domain from Human Myosin Vb -

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Basic information

Entry
Database: PDB / ID: 4j5m
TitleStructure of the Cargo Binding Domain from Human Myosin Vb
ComponentsUnconventional myosin-Vb
KeywordsPROTEIN TRANSPORT / intracellular traffic / organelles / vesicles / human myosin Vb
Function / homology
Function and homology information


apical cortex / vesicle transport along actin filament / renal water homeostasis / myosin complex / endosomal transport / microfilament motor activity / vesicle-mediated transport / actin filament organization / cytoplasmic vesicle membrane / small GTPase binding ...apical cortex / vesicle transport along actin filament / renal water homeostasis / myosin complex / endosomal transport / microfilament motor activity / vesicle-mediated transport / actin filament organization / cytoplasmic vesicle membrane / small GTPase binding / Vasopressin regulates renal water homeostasis via Aquaporins / actin filament binding / protein transport / actin cytoskeleton / vesicle / calmodulin binding / protein-containing complex / extracellular exosome / ATP binding / membrane / cytoplasm
Similarity search - Function
Myosin 5b, 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 5b, 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 head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NITRATE ION / Unconventional myosin-Vb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsNascimento, A.F.Z. / Trindade, D.M. / Mahajan, P. / Berridge, G. / Krojer, T. / Vollmar, M. / Tonoli, C.C.C. / Assis, L.H.P. / 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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-Vb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6343
Polymers45,5101
Non-polymers1242
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.093, 78.200, 151.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2194-

HOH

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Components

#1: Protein Unconventional myosin-Vb


Mass: 45510.414 Da / Num. of mol.: 1 / Fragment: C-terminal Globular Tail
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1119, MYO5B / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) (Rosetta 2) / References: UniProt: Q9ULV0
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2M sodium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2012
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 25401 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.57
Reflection shellResolution: 2.07→2.1108 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.2 / % possible all: 97.3

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Processing

Software
NameVersionClassification
GDAdata acquisition softwaredata collection
Rosettamodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→49.006 Å / SU ML: 0.24 / σ(F): 1.19 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 -5.09 %
Rwork0.1894 --
obs0.1915 25401 97.09 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.88 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.6466 Å2-0 Å2-0 Å2
2---3.915 Å2-0 Å2
3---0.2684 Å2
Refinement stepCycle: LAST / Resolution: 2.07→49.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 8 206 3148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073029
X-RAY DIFFRACTIONf_angle_d0.9924102
X-RAY DIFFRACTIONf_dihedral_angle_d15.8861153
X-RAY DIFFRACTIONf_chiral_restr0.065476
X-RAY DIFFRACTIONf_plane_restr0.004526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.11080.33571430.28642239X-RAY DIFFRACTION82
2.1108-2.15670.27661250.26322505X-RAY DIFFRACTION93
2.1567-2.20690.30711370.25132650X-RAY DIFFRACTION99
2.2069-2.26210.27541580.2232722X-RAY DIFFRACTION99
2.2621-2.32330.23691380.2172638X-RAY DIFFRACTION99
2.3233-2.39160.26211130.21252720X-RAY DIFFRACTION99
2.3916-2.46880.24381500.2152672X-RAY DIFFRACTION98
2.4688-2.5570.2241540.19552615X-RAY DIFFRACTION98
2.557-2.65940.24211240.19772703X-RAY DIFFRACTION99
2.6594-2.78040.26891660.1912652X-RAY DIFFRACTION99
2.7804-2.9270.24431590.18892664X-RAY DIFFRACTION99
2.927-3.11040.24021510.18912657X-RAY DIFFRACTION98
3.1104-3.35050.16951310.18492691X-RAY DIFFRACTION98
3.3505-3.68760.22231400.17842663X-RAY DIFFRACTION98
3.6876-4.22090.20441490.15252616X-RAY DIFFRACTION98
4.2209-5.31690.21311390.15172678X-RAY DIFFRACTION98
5.3169-49.01990.21831250.18962664X-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)
13.5216-1.47960.98535.3446-2.6774.4053-0.0186-0.4761-0.28361.05740.33210.5738-0.4855-0.1556-0.18480.386-0.00510.11490.26630.03650.167328.911616.818277.3568
20.77421.2884-0.4095.4299-2.27131.50440.0375-0.095-0.10130.15920.05520.08580.0195-0.0551-0.04570.1208-0.02470.00710.1750.0050.110134.566320.794662.6156
30.43530.5982-0.3213.1316-1.59212.56210.0868-0.07840.05360.603-0.1213-0.1488-0.48760.040.00570.1269-0.0321-0.00570.1427-0.03390.11743.290547.927753.8443
41.94231.5277-1.49943.8482-2.41273.65060.1198-0.01360.05650.1881-0.0741-0.2123-0.318-0.0276-0.02290.09550.00380.04160.1654-0.01230.198751.525154.680638.9543
54.27221.6961-2.14281.1620.31673.8907-1.06330.4048-1.1141-0.72780.4636-0.72431.1718-0.35330.37340.414-0.12720.17290.273-0.08410.399750.67949.958326.1114
61.24730.7127-0.41014.3998-4.48415.3785-0.2377-0.0263-0.10450.3834-0.0894-0.5912-0.35380.20560.32440.2152-0.0043-0.02490.1232-0.02770.136842.295129.47353.5832
76.7278-4.42661.34135.5998-2.57193.0127-0.4432-1.21850.27061.49640.48430.1857-0.91610.1372-0.00610.6073-0.00210.15630.4636-0.03640.22531.356718.238380.6893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1459:1499)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 1500:1622)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 1623:1725)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 1726:1790)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 1791:1810)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 1811:1830)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 1831:1848)

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