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- PDB-4lx2: Crystal structure of Myo5a globular tail domain in complex with m... -

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Basic information

Entry
Database: PDB / ID: 4lx2
TitleCrystal structure of Myo5a globular tail domain in complex with melanophilin GTBD
Components
  • Melanophilin
  • Unconventional myosin-Va
KeywordsCONTRACTILE PROTEIN/PROTEIN TRANSPORT / DIL / CONTRACTILE PROTEIN-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


melanosome localization / unconventional myosin complex / post-Golgi vesicle-mediated transport / insulin-responsive compartment / melanosome transport / actin filament-based movement / filopodium tip / melanocyte differentiation / myosin V binding / microtubule plus-end binding ...melanosome localization / unconventional myosin complex / post-Golgi vesicle-mediated transport / insulin-responsive compartment / melanosome transport / actin filament-based movement / filopodium tip / melanocyte differentiation / myosin V binding / microtubule plus-end binding / vesicle transport along actin filament / myosin complex / pigmentation / microtubule organizing center / microfilament motor activity / myosin binding / cortical actin cytoskeleton / Insulin processing / protein targeting / stress fiber / vesicle-mediated transport / ruffle / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / FCGR3A-mediated phagocytosis / intracellular protein transport / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / cellular response to insulin stimulus / melanosome / actin filament binding / actin cytoskeleton / protein-macromolecule adaptor activity / protein transport / actin binding / growth cone / molecular adaptor activity / calmodulin binding / neuron projection / dendrite / perinuclear region of cytoplasm / RNA binding / extracellular exosome / ATP binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Rab effector MyRIP/Melanophilin / Melanophilin, FYVE-related domain / Rab effector MyRIP/melanophilin C-terminus / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain ...Rab effector MyRIP/Melanophilin / Melanophilin, FYVE-related domain / Rab effector MyRIP/melanophilin C-terminus / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Myosin 5a, 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 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Melanophilin / Unconventional myosin-Va
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPylypenko, O. / Attanda, W. / Gauquelin, C. / Houdusse, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis of myosin V Rab GTPase-dependent cargo recognition.
Authors: Pylypenko, O. / Attanda, W. / Gauquelin, C. / Lahmani, M. / Coulibaly, D. / Baron, B. / Hoos, S. / Titus, M.A. / England, P. / Houdusse, A.M.
History
DepositionJul 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Melanophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3593
Polymers48,1212
Non-polymers2381
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-0 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.870, 41.110, 109.580
Angle α, β, γ (deg.)90.00, 115.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 44947.152 Da / Num. of mol.: 1 / Fragment: Dilute domain residues 1464-1855
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO5A, MYH12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y4I1
#2: Protein/peptide Melanophilin / / Exophilin-3 / Leaden protein / Slp homolog lacking C2 domains a / SlaC2-a / Synaptotagmin-like protein 2a


Mass: 3173.514 Da / Num. of mol.: 1 / Fragment: UNP residues 176-201 / Source method: obtained synthetically / Details: synthesized / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q91V27
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG MPD, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.5→37 Å / Num. all: 65228 / Num. obs: 64638 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.12 Å2
Reflection shellResolution: 1.5→1.59 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LX0

4lx0


Resolution: 1.5→35.572 Å / SU ML: 0.4 / σ(F): 2.04 / Phase error: 18.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 3219 5 %random
Rwork0.1643 ---
obs0.1659 64346 99.55 %-
all-65228 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.178 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9941 Å20 Å2-3.316 Å2
2--0.4547 Å20 Å2
3----1.4488 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 10 436 3412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113145
X-RAY DIFFRACTIONf_angle_d1.2794274
X-RAY DIFFRACTIONf_dihedral_angle_d13.2691220
X-RAY DIFFRACTIONf_chiral_restr0.07494
X-RAY DIFFRACTIONf_plane_restr0.006546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52240.30021390.28462638X-RAY DIFFRACTION100
1.5224-1.54620.271390.25562627X-RAY DIFFRACTION100
1.5462-1.57150.29531390.2492636X-RAY DIFFRACTION100
1.5715-1.59860.3041390.24322652X-RAY DIFFRACTION100
1.5986-1.62770.27451390.22842639X-RAY DIFFRACTION100
1.6277-1.6590.24481390.212643X-RAY DIFFRACTION100
1.659-1.69290.26641400.20842655X-RAY DIFFRACTION100
1.6929-1.72970.21451400.19632647X-RAY DIFFRACTION100
1.7297-1.76990.26661380.1892628X-RAY DIFFRACTION100
1.7699-1.81420.22941390.18672644X-RAY DIFFRACTION100
1.8142-1.86320.19121410.16972674X-RAY DIFFRACTION99
1.8632-1.91810.20631380.15992623X-RAY DIFFRACTION99
1.9181-1.980.18461400.15572663X-RAY DIFFRACTION100
1.98-2.05070.1811380.15372630X-RAY DIFFRACTION99
2.0507-2.13280.17891380.15522613X-RAY DIFFRACTION99
2.1328-2.22990.15821400.14912653X-RAY DIFFRACTION99
2.2299-2.34740.18361400.14812671X-RAY DIFFRACTION99
2.3474-2.49450.16851410.14612670X-RAY DIFFRACTION100
2.4945-2.6870.20461400.14992672X-RAY DIFFRACTION100
2.687-2.95730.17451410.15492682X-RAY DIFFRACTION100
2.9573-3.38490.20951420.15192686X-RAY DIFFRACTION99
3.3849-4.26350.17911420.14342696X-RAY DIFFRACTION100
4.2635-35.58180.19221470.18052785X-RAY DIFFRACTION99
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)
10.64310.42250.69790.76090.68612.32150.0267-0.05410.0411-0.0484-0.01540.02980.0357-0.0475-0.01920.06010.02260.00780.09430.01390.11219.4579-20.513-16.7305
21.86161.0333-0.18155.84360.19551.58580.07910.0156-0.1245-0.09060.0161-0.16280.5039-0.0476-0.09990.69390.0419-0.02260.1588-0.00450.32713.7768-46.6486-34.7343
34.8539-5.5377-2.42256.39992.81571.24180.2679-0.0704-0.839-0.04010.1089-0.36431.11760.5291-0.36960.74340.26110.05270.5341-0.11390.815117.536-41.9858-32.6243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1470:1853))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 185:191))
3X-RAY DIFFRACTION3chain 'B' and ((resseq 192:196))

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