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- PDB-4d07: DYNLL2 dynein light chain binds to an extended, unstructured line... -

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Basic information

Entry
Database: PDB / ID: 4d07
TitleDYNLL2 dynein light chain binds to an extended, unstructured linear motif of myosin 5a tail
Components
  • DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
  • MYOSIN VA VARIANT
KeywordsMOTOR PROTEIN / INSTRINSICALLY DISORDERED DOMAIN / HUB PROTEIN
Function / homology
Function and homology information


myosin V complex / Activation of BMF and translocation to mitochondria / 9+0 non-motile cilium / vesicle transport along actin filament / post-Golgi vesicle-mediated transport / insulin-responsive compartment / melanosome transport / ciliary tip / filopodium tip / actin filament-based movement ...myosin V complex / Activation of BMF and translocation to mitochondria / 9+0 non-motile cilium / vesicle transport along actin filament / post-Golgi vesicle-mediated transport / insulin-responsive compartment / melanosome transport / ciliary tip / filopodium tip / actin filament-based movement / Intraflagellar transport / COPI-independent Golgi-to-ER retrograde traffic / myosin complex / cytoplasmic dynein complex / dynein intermediate chain binding / Macroautophagy / microfilament motor activity / Insulin processing / Regulation of MITF-M-dependent genes involved in pigmentation / cytoskeletal motor activity / microtubule-based process / COPI-mediated anterograde transport / vesicle-mediated transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / ruffle / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / actin filament organization / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / RHO GTPases Activate Formins / small GTPase binding / Regulation of actin dynamics for phagocytic cup formation / cellular response to insulin stimulus / HCMV Early Events / Aggrephagy / actin filament binding / Separation of Sister Chromatids / melanosome / protein transport / actin cytoskeleton / actin binding / growth cone / microtubule / cytoskeleton / postsynapse / calmodulin binding / neuron projection / cilium / centrosome / glutamatergic synapse / ATP hydrolysis activity / RNA binding / extracellular exosome / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Myosin 5a, cargo-binding domain / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / Class V myosin, motor domain ...Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Myosin 5a, cargo-binding domain / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / 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. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Myosin Va variant / Dynein light chain 2, cytoplasmic / Unconventional myosin-Va
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBodor, A. / Radnai, L. / Hetenyi, C. / Rapali, P. / Lang, A. / Kover, K.E. / Perczel, A. / Wahlgren, W.Y. / Katona, G. / Nyitray, L.
CitationJournal: Biochemistry / Year: 2014
Title: Dynll2 Dynein Light Chain Binds to an Extended Linear Motif of Myosin 5A Tail that Has Structural Plasticity.
Authors: Bodor, A. / Radnai, L. / Hetenyi, C. / Rapali, P. / Lang, A. / Kover, K.E. / Perczel, A. / Wahlgren, W.Y. / Katona, G. / Nyitray, L.
History
DepositionApr 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
B: MYOSIN VA VARIANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9475
Polymers13,6692
Non-polymers2773
Water1,78399
1
A: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
B: MYOSIN VA VARIANT
hetero molecules

A: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
B: MYOSIN VA VARIANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,89310
Polymers27,3394
Non-polymers5546
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_774-y+2,-x+2,-z-1/61
Buried area6140 Å2
ΔGint-62.8 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.160, 45.160, 204.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2051-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein DYNEIN LIGHT CHAIN 2, CYTOPLASMIC / 8 KDA DYNEIN LIGHT CHAIN B / DLC8B / DYNEIN LIGHT CHAIN LC8-TYPE 2 / DYNLL2


Mass: 10647.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q96FJ2
#2: Protein/peptide MYOSIN VA VARIANT / MYO5A


Mass: 3022.365 Da / Num. of mol.: 1 / Fragment: RESIDUES 856-878 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q59FF5, UniProt: Q9Y4I1*PLUS

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Non-polymers , 4 types, 102 molecules

#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.51 Å3/Da / Density % sol: 51.03 % / Description: NONE
Crystal growDetails: 2.5UL PROTEIN PLUS 1UL RESERVOIR SOLUTION OF 1.8 M (NH4)2SO4, 0.02 M COCL2, 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.85→19.76 Å / Num. obs: 11478 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 22 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 30.18
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 20 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 6.09 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CMI

1cmi


Resolution: 1.85→204.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.97 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 544 4.8 %RANDOM
Rwork0.19303 ---
obs0.19492 10853 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.851 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.37 Å20 Å2
2--0.75 Å20 Å2
3----2.42 Å2
Refinement stepCycle: LAST / Resolution: 1.85→204.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms841 0 14 99 954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019918
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9411250
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5485121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.12625.68244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28915169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg0.183151
X-RAY DIFFRACTIONr_chiral_restr0.0860.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02696
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0461.898438
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8052.807549
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2772.116479
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 34 -
Rwork0.251 788 -
obs--99.64 %

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