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- PDB-4lx0: Crystal structure of Myo5b globular tail domain in complex with a... -

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Basic information

Entry
Database: PDB / ID: 4lx0
TitleCrystal structure of Myo5b globular tail domain in complex with active Rab11a
Components
  • Ras-related protein Rab-11A
  • Unconventional myosin-Vb
KeywordsPROTEIN TRANSPORT/CONTRACTILE PROTEIN / DIL / PROTEIN TRANSPORT-CONTRACTILE PROTEIN complex
Function / homology
Function and homology information


: / regulation of protein localization to centrosome / synaptic vesicle endosomal processing / : / regulation of endocytic recycling / establishment of protein localization to organelle / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / establishment of vesicle localization / regulation of cilium assembly ...: / regulation of protein localization to centrosome / synaptic vesicle endosomal processing / : / regulation of endocytic recycling / establishment of protein localization to organelle / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / establishment of vesicle localization / regulation of cilium assembly / regulation of protein transport / amyloid-beta clearance by transcytosis / neurotransmitter receptor transport, endosome to postsynaptic membrane / exosomal secretion / apical cortex / vesicle-mediated transport in synapse / presynaptic endosome / VxPx cargo-targeting to cilium / plasma membrane to endosome transport / regulation of vesicle-mediated transport / protein transmembrane transport / astral microtubule organization / RAB geranylgeranylation / myosin V binding / multivesicular body assembly / protein localization to cilium / melanosome transport / Golgi to plasma membrane protein transport / establishment of protein localization to membrane / myosin complex / TBC/RABGAPs / protein localization to cell surface / syntaxin binding / dynein light intermediate chain binding / endosomal transport / mitotic metaphase chromosome alignment / microfilament motor activity / exocytosis / cleavage furrow / positive regulation of epithelial cell migration / mitotic spindle assembly / positive regulation of G2/M transition of mitotic cell cycle / renal water homeostasis / transport vesicle / phagocytic vesicle / multivesicular body / vesicle-mediated transport / Anchoring of the basal body to the plasma membrane / cytoplasmic vesicle membrane / trans-Golgi network membrane / actin filament organization / regulation of cytokinesis / small monomeric GTPase / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / centriole / recycling endosome / regulation of long-term neuronal synaptic plasticity / Schaffer collateral - CA1 synapse / recycling endosome membrane / small GTPase binding / endocytosis / spindle pole / neuron projection development / actin filament binding / endocytic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / protein transport / synaptic vesicle membrane / actin cytoskeleton / G protein activity / cytoplasmic vesicle / microtubule binding / vesicle / calmodulin binding / Golgi membrane / GTPase activity / centrosome / GTP binding / glutamatergic synapse / Golgi apparatus / protein-containing complex / extracellular exosome / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
Myosin 5b, 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 5b, cargo-binding domain / : / : / Unconventional myosin-Va domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Small GTPase Rab domain profile. / 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 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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
BERYLLIUM TRIFLUORIDE ION / 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: 2.19 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_sheet / 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_sheet.number_strands / _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)139,58511
Polymers138,4264
Non-polymers1,1597
Water11,728651
1
A: Ras-related protein Rab-11A
B: Unconventional myosin-Vb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8396
Polymers69,2132
Non-polymers6264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-29 kcal/mol
Surface area25240 Å2
MethodPISA
2
C: Ras-related protein Rab-11A
D: Unconventional myosin-Vb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7465
Polymers69,2132
Non-polymers5343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-28 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.100, 125.920, 157.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#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

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Non-polymers , 5 types, 658 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#5: 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
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 3.41 Å3/Da / Density % sol: 63.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 % peg, 90 mM NaF, 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: Dec 5, 2011
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: 2.14→31.5 Å / Num. all: 98382 / Num. obs: 98156 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 51.82 Å2
Reflection shellResolution: 2.14→2.32 Å / % possible all: 99

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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: 2.19→31.5 Å / SU ML: 0.68 / σ(F): 1.99 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 4887 5 %random
Rwork0.1811 ---
obs0.1829 97752 99.9 %-
all-97752 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.633 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-18.3845 Å2-0 Å2-0 Å2
2---0.8623 Å20 Å2
3----17.5222 Å2
Refinement stepCycle: LAST / Resolution: 2.19→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8608 0 72 651 9331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138836
X-RAY DIFFRACTIONf_angle_d1.32811997
X-RAY DIFFRACTIONf_dihedral_angle_d15.3953207
X-RAY DIFFRACTIONf_chiral_restr0.0891413
X-RAY DIFFRACTIONf_plane_restr0.0061523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.21490.36281610.29473066X-RAY DIFFRACTION100
2.2149-2.24090.31631590.273006X-RAY DIFFRACTION100
2.2409-2.26830.29471600.27563069X-RAY DIFFRACTION100
2.2683-2.2970.32321610.26163068X-RAY DIFFRACTION100
2.297-2.32720.30021630.25663091X-RAY DIFFRACTION100
2.3272-2.35910.32121590.26453026X-RAY DIFFRACTION100
2.3591-2.39270.2851620.24323075X-RAY DIFFRACTION100
2.3927-2.42840.25751620.23073088X-RAY DIFFRACTION100
2.4284-2.46640.26181600.22333040X-RAY DIFFRACTION100
2.4664-2.50680.27711620.21533080X-RAY DIFFRACTION100
2.5068-2.550.24511620.20983063X-RAY DIFFRACTION100
2.55-2.59640.28371610.20563071X-RAY DIFFRACTION100
2.5964-2.64630.26721610.1973052X-RAY DIFFRACTION100
2.6463-2.70030.2271610.19163065X-RAY DIFFRACTION100
2.7003-2.75890.26121640.18923112X-RAY DIFFRACTION100
2.7589-2.82310.23091630.18713089X-RAY DIFFRACTION100
2.8231-2.89360.22981610.18293073X-RAY DIFFRACTION100
2.8936-2.97180.2241640.1833106X-RAY DIFFRACTION100
2.9718-3.05920.21941620.17933080X-RAY DIFFRACTION100
3.0592-3.15780.24551630.18173089X-RAY DIFFRACTION100
3.1578-3.27060.20631620.17723092X-RAY DIFFRACTION100
3.2706-3.40140.21791640.18033103X-RAY DIFFRACTION100
3.4014-3.5560.2041630.18313093X-RAY DIFFRACTION100
3.556-3.74320.23141650.18763136X-RAY DIFFRACTION100
3.7432-3.97730.20831630.16713098X-RAY DIFFRACTION100
3.9773-4.28370.18511650.1493142X-RAY DIFFRACTION100
4.2837-4.71350.16771650.13873125X-RAY DIFFRACTION100
4.7135-5.39260.1711650.1543154X-RAY DIFFRACTION100
5.3926-6.7830.23751690.2023211X-RAY DIFFRACTION100
6.783-31.52320.20641750.17823302X-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)
13.9337-3.25391.21263.0557-1.57741.2855-0.4628-0.4658-0.82670.01620.38110.13410.3719-0.85940.00831.6644-0.184-0.8551.0336-0.05681.9306-15.6547-24.0386-92.294
29.7113-2.71144.76344.4873-2.02949.14750.1223-0.0398-0.6666-0.79470.17450.54090.38691.0503-0.35041.5128-0.1695-0.10460.9610.13580.64362.2673-25.7954-78.0831
31.96180.3457-0.39370.9808-0.18085.442-0.07480.36740.0264-0.22530.13190.17050.3623-0.7399-0.03990.2624-0.08940.00580.27420.05780.36399.6173-26.5379-28.913
43.36141.70870.25434.4166-0.04143.3370.04620.06-0.27280.1867-0.02720.00590.29040.04840.00110.20550.07370.02090.27260.03770.304741.9347-22.2926-8.8353
54.45090.79610.97691.78030.14250.21480.23940.53980.7730.05670.04690.4485-0.07890.1262-0.28440.36240.0163-0.04470.39220.06140.541136.1848-12.0332-11.2881
63.2096-2.79692.04256.4710.09262.1675-1.18220.547-0.2048-1.0525-0.9121-1.42281.39311.16731.99661.289-0.33640.51621.54090.11151.142660.274622.552835.3816
76.72081.74716.33265.1557-0.84818.0865-0.732-0.5781-0.691-0.721-0.652-0.5521-0.62830.18831.31220.72950.0156-0.06221.6947-0.41760.97358.275815.79928.4169
81.15330.39630.39391.6113-0.29436.70910.15370.04470.05740.2205-0.0277-0.0717-0.50210.5294-0.11340.2983-0.00820.11120.28950.09010.430853.38635.3932-26.299
95.6621.0464-1.22943.2361-0.44792.579-0.45330.1078-1.0557-0.8495-0.1542-1.3130.84750.6530.42010.68870.10050.29640.46830.1710.773538.6024-23.4738-48.551
103.99071.1534-5.28180.3403-1.54597.06330.4162-0.23320.99080.01290.07530.4769-0.5678-0.4749-0.55870.41860.05920.06120.56720.00150.561731.0673-15.1777-45.9023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1447:1452 )B1447 - 1452
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1455:1467 )B1455 - 1467
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1468:1848 )B1468 - 1848
4X-RAY DIFFRACTION4( CHAIN A AND RESID 7:177 )A7 - 177
5X-RAY DIFFRACTION5( CHAIN A AND RESID 201:203 )A201 - 203
6X-RAY DIFFRACTION6( CHAIN D AND RESID 1443:1448 )D1443 - 1448
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1454:1462 )D1454 - 1462
8X-RAY DIFFRACTION8( CHAIN D AND RESID 1463:1848 )D1463 - 1848
9X-RAY DIFFRACTION9( CHAIN C AND RESID 7:177 )C7 - 177
10X-RAY DIFFRACTION10( CHAIN C AND RESID 201:203 )C201 - 203

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