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- PDB-4lwz: Crystal structure of Myo5b globular tail domain in complex with i... -

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Basic information

Entry
Database: PDB / ID: 4lwz
TitleCrystal structure of Myo5b globular tail domain in complex with inactive Rab11a
Components
  • Ras-related protein Rab-11A
  • Unconventional myosin-Vb
KeywordsPROTEIN TRANSPORT / DIL
Function / homology
Function and homology information


regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / regulation of cilium assembly / exosomal secretion / melanosome transport / amyloid-beta clearance by transcytosis / protein transmembrane transport / astral microtubule organization / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / apical cortex / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / Golgi to plasma membrane protein transport / vesicle transport along actin filament / multivesicular body assembly / dynein light intermediate chain binding / protein localization to cilium / establishment of protein localization to membrane / renal water homeostasis / protein localization to cell surface / myosin complex / TBC/RABGAPs / syntaxin binding / endosomal transport / mitotic metaphase chromosome alignment / microfilament motor activity / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / centriolar satellite / mitotic spindle assembly / vesicle-mediated transport / transport vesicle / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / phagocytic vesicle / multivesicular body / small monomeric GTPase / G protein activity / trans-Golgi network membrane / regulation of cytokinesis / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament organization / cytoplasmic vesicle membrane / trans-Golgi network / recycling endosome / small GTPase binding / spindle pole / Vasopressin regulates renal water homeostasis via Aquaporins / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / actin filament binding / protein transport / actin cytoskeleton / cytoplasmic vesicle / microtubule binding / vesicle / calmodulin binding / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / Golgi apparatus / protein-containing complex / extracellular exosome / ATP binding / membrane / cytoplasm / cytosol
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 / small GTPase Rab1 family profile. / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. ...Myosin 5b, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / small GTPase Rab1 family profile. / 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 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Kinesin motor domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-11A / Unconventional myosin-Vb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 1.2Dec 25, 2013Group: Derived calculations
Revision 1.3Jan 15, 2014Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Ras-related protein Rab-11A
B: Unconventional myosin-Vb
C: Ras-related protein Rab-11A
D: Unconventional myosin-Vb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,3618
Polymers138,4264
Non-polymers9354
Water2,252125
1
A: Ras-related protein Rab-11A
B: Unconventional myosin-Vb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6804
Polymers69,2132
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ras-related protein Rab-11A
D: Unconventional myosin-Vb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6804
Polymers69,2132
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.680, 143.140, 162.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ras-related protein Rab-11A / Rab-11 / YL8


Mass: 19972.469 Da / Num. of mol.: 2 / Fragment: Dilute domain residues 1456-1848
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491
#2: Protein Unconventional myosin-Vb


Mass: 49240.441 Da / Num. of mol.: 2 / Fragment: UNP residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO5B, KIAA1119 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULV0
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 17% peg, 100 mM NaCl, 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: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2011
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.55→39 Å / Num. all: 52363 / Num. obs: 52120 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 66.83 Å2
Reflection shellResolution: 2.55→2.62 Å / % possible all: 99.7

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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 / Resolution: 2.55→24.968 Å / SU ML: 0.83 / σ(F): 1.99 / Phase error: 35.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2953 2606 5 %random
Rwork0.231 ---
obs0.2342 52109 99.67 %-
all-52109 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.901 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-20.1086 Å2-0 Å2-0 Å2
2---6.4345 Å20 Å2
3----13.6741 Å2
Refinement stepCycle: LAST / Resolution: 2.55→24.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7947 0 58 125 8130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088142
X-RAY DIFFRACTIONf_angle_d1.00311051
X-RAY DIFFRACTIONf_dihedral_angle_d15.8952919
X-RAY DIFFRACTIONf_chiral_restr0.0511302
X-RAY DIFFRACTIONf_plane_restr0.0041404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.59630.3671350.2832568X-RAY DIFFRACTION100
2.5963-2.64620.39251330.29062535X-RAY DIFFRACTION100
2.6462-2.70020.37241370.28992599X-RAY DIFFRACTION99
2.7002-2.75880.37751340.29222539X-RAY DIFFRACTION100
2.7588-2.82290.4131370.3032600X-RAY DIFFRACTION100
2.8229-2.89340.4121340.28992558X-RAY DIFFRACTION100
2.8934-2.97150.36011360.26412588X-RAY DIFFRACTION100
2.9715-3.05880.3841350.25052563X-RAY DIFFRACTION100
3.0588-3.15730.35221360.26242577X-RAY DIFFRACTION100
3.1573-3.26990.34641360.25752590X-RAY DIFFRACTION100
3.2699-3.40060.31561380.26152606X-RAY DIFFRACTION100
3.4006-3.55490.32961360.26132602X-RAY DIFFRACTION100
3.5549-3.74180.34221370.25712595X-RAY DIFFRACTION100
3.7418-3.97530.3111370.2332612X-RAY DIFFRACTION100
3.9753-4.28080.24571380.2072622X-RAY DIFFRACTION100
4.2808-4.7090.25041380.18582615X-RAY DIFFRACTION100
4.709-5.38450.23791400.19912652X-RAY DIFFRACTION100
5.3845-6.76150.30911420.24432705X-RAY DIFFRACTION100
6.7615-24.96930.24531470.20442777X-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)
15.3279-3.79830.05554.6505-0.46122.3110.188-0.5018-0.5053-0.15740.18890.71560.5313-0.5662-0.39150.6305-0.24810.01070.58960.04390.468627.9925-15.091440.2489
21.71050.4616-1.3811.257-0.53578.8080.05280.26270.2766-0.18460.1059-0.0088-0.8164-0.3418-0.17960.41390.0092-0.05490.2944-0.01160.487423.935121.89940.1416
32.2398-0.13450.64153.4435-2.21458.1557-0.1152-0.29140.07490.36170.0298-0.00520.0914-0.45550.10340.4304-0.0366-0.00840.3973-0.07330.47523.996610.018930.9869
47.2266-0.01622.3523.64633.88397.4686-0.2438-1.06530.66340.93660.209-0.3782-0.16080.6294-0.00431.1964-0.119-0.36290.7781-0.14370.631434.837715.237951.3478
51.6744-0.6584-1.80161.9453-1.20554.7101-0.20650.30320.24270.02290.02610.3797-0.422-0.32410.04980.6072-0.08470.00530.3737-0.01120.574225.130718.28045.1611
60.5788-0.08330.55281.32490.32621.18630.4359-0.0268-0.5814-1.06260.1480.43481.3087-0.37250.43541.4828-0.2834-0.56310.45640.0290.040625.8849-12.31381.0026
72.2832-0.82531.26133.14520.03963.86290.4683-0.0986-0.0363-0.5556-0.4122-0.23330.79020.5583-0.0440.65620.05590.12720.55140.09970.418460.3688-32.040844.7217
80.2096-0.0056-0.02280.46560.5220.59360.38310.3778-0.294-0.7352-0.34020.22991.18620.0935-0.15951.66870.2499-0.0060.4422-0.00940.490347.0397-32.733816.5298
90.43240.105-0.47020.0551-0.19962.56780.38220.4207-0.0256-0.5004-0.2215-0.04730.0498-0.28120.08851.70530.522-0.07240.78160.00260.449943.6323-25.05436.0345
101.4723-0.2523-1.00213.81010.66752.81360.02520.3978-0.1162-1.1214-0.434-0.3631-0.13490.01430.2431.17990.43630.46430.69230.260.726252.6001-22.5775-12.4296
112.3912-1.2478-0.34311.49830.22660.05280.32210.0427-0.2316-0.7528-0.5345-0.31160.6982-0.23160.21290.7274-0.06660.08140.5340.05330.454654.6425-30.200640.9657
120.1851.12020.35896.92072.91064.81320.5166-0.2920.3629-0.08650.07510.1659-0.2925-0.1816-0.52340.6046-0.2380.12220.74490.03950.440939.2065-10.627637.6277
134.4079-6.2501-4.69949.36886.77765.1115-0.16650.223-0.5288-0.25290.0542-0.24150.74680.2980.08461.27370.0539-0.07430.5364-0.12360.574434.7494-5.4623.235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 7:173))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 1457:1627))
3X-RAY DIFFRACTION3chain 'B' and ((resseq 1651:1753))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 1754:1806))
5X-RAY DIFFRACTION5chain 'B' and ((resseq 1807:1848))
6X-RAY DIFFRACTION6chain 'C' and ((resseq 10:172))
7X-RAY DIFFRACTION7chain 'D' and ((resseq 1454:1609))
8X-RAY DIFFRACTION8chain 'D' and ((resseq 1610:1696))
9X-RAY DIFFRACTION9chain 'D' and ((resseq 1702:1749))
10X-RAY DIFFRACTION10chain 'D' and ((resseq 1752:1803))
11X-RAY DIFFRACTION11chain 'D' and ((resseq 1813:1848))
12X-RAY DIFFRACTION12chain 'A' and ((resseq 201:202))
13X-RAY DIFFRACTION13chain 'C' and ((resseq 201:202))

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