[English] 日本語
Yorodumi
- PDB-4lx0: Crystal structure of Myo5b globular tail domain in complex with a... -

+
Open data


ID or keywords:

Loading...

-
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 early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization / regulation of cilium assembly / exosomal secretion ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization / regulation of cilium assembly / exosomal secretion / amyloid-beta clearance by transcytosis / melanosome 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 / protein localization to cilium / multivesicular body assembly / vesicle transport along actin filament / dynein light intermediate chain binding / establishment of protein localization to membrane / renal water homeostasis / protein localization to cell surface / TBC/RABGAPs / myosin complex / syntaxin binding / microfilament motor activity / endosomal transport / mitotic metaphase chromosome alignment / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / centriolar satellite / mitotic spindle assembly / phagocytic vesicle / transport vesicle / vesicle-mediated transport / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / multivesicular body / small monomeric GTPase / G protein activity / trans-Golgi network membrane / regulation of cytokinesis / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / small GTPase binding / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / neuron projection development / endocytic vesicle membrane / actin filament binding / actin cytoskeleton / protein transport / 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 / cytosol / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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 / Guanosine 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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 651 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more