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- PDB-6gzj: Complex between the dynein light chain DYNLL1/DLC8 and the specif... -

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Basic information

Entry
Database: PDB / ID: 6gzj
TitleComplex between the dynein light chain DYNLL1/DLC8 and the specific domain of large myelin-associated glycoprotein L-MAG
Components
  • Dynein light chain 1, cytoplasmic
  • Myelin-associated glycoprotein
KeywordsPROTEIN BINDING / complex / heterotetramer / cell adhesion / cytoplasmic domain
Function / homology
Function and homology information


mesaxon / Axonal growth inhibition (RHOA activation) / Basigin interactions / nitric-oxide synthase inhibitor activity / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / negative regulation of phosphorylation / intraciliary retrograde transport / myelin sheath adaxonal region / ganglioside GT1b binding ...mesaxon / Axonal growth inhibition (RHOA activation) / Basigin interactions / nitric-oxide synthase inhibitor activity / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / negative regulation of phosphorylation / intraciliary retrograde transport / myelin sheath adaxonal region / ganglioside GT1b binding / central nervous system myelination / Activation of BIM and translocation to mitochondria / sialic acid binding / motile cilium assembly / central nervous system myelin formation / : / negative regulation of axon extension / ciliary tip / Intraflagellar transport / positive regulation of astrocyte differentiation / positive regulation of myelination / paranode region of axon / Schmidt-Lanterman incisure / negative regulation of nitric oxide biosynthetic process / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / axon regeneration / cytoplasmic dynein complex / Macroautophagy / negative regulation of neuron differentiation / transmission of nerve impulse / dynein intermediate chain binding / tertiary granule membrane / ficolin-1-rich granule membrane / spermatid development / enzyme inhibitor activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / COPI-mediated anterograde transport / myelination / axon cytoplasm / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / substantia nigra development / Mitotic Prometaphase / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / EML4 and NUDC in mitotic spindle formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / cellular response to mechanical stimulus / RHO GTPases Activate Formins / kinetochore / HCMV Early Events / Aggrephagy / mitotic spindle / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / myelin sheath / negative regulation of neuron projection development / site of double-strand break / carbohydrate binding / scaffold protein binding / negative regulation of neuron apoptotic process / microtubule / cytoskeleton / cell adhesion / cilium / membrane raft / signaling receptor binding / apoptotic process / DNA damage response / Neutrophil degranulation / centrosome / protein kinase binding / protein-containing complex binding / enzyme binding / protein homodimerization activity / mitochondrion / identical protein 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. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / CD80-like, immunoglobulin C2-set ...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. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Myelin-associated glycoprotein / Dynein light chain 1, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.977 Å
AuthorsMyllykoski, M. / Kursula, P.
CitationJournal: J. Neurochem. / Year: 2018
Title: High-affinity heterotetramer formation between the large myelin-associated glycoprotein and the dynein light chain DYNLL1.
Authors: Myllykoski, M. / Eichel, M.A. / Jung, R.B. / Kelm, S. / Werner, H.B. / Kursula, P.
History
DepositionJul 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynein light chain 1, cytoplasmic
B: Myelin-associated glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6963
Polymers16,6612
Non-polymers351
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-13 kcal/mol
Surface area5730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.050, 44.050, 204.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Dynein light chain 1, cytoplasmic / 8 kDa dynein light chain / DLC8 / Dynein light chain LC8-type 1 / Protein inhibitor of neuronal ...8 kDa dynein light chain / DLC8 / Dynein light chain LC8-type 1 / Protein inhibitor of neuronal nitric oxide synthase / PIN


Mass: 10468.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLL1, DLC1, DNCL1, DNCLC1, HDLC1 / Plasmid: pJExpress401 / Production host: Escherichia coli (E. coli) / References: UniProt: P63167
#2: Protein Myelin-associated glycoprotein / Siglec-4a


Mass: 6191.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P20917
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 1.72 Å3/Da / Density % sol: 28.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M lithium sulfate, and 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07175 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07175 Å / Relative weight: 1
ReflectionResolution: 1.977→50 Å / Num. obs: 7535 / % possible obs: 82.8 % / Redundancy: 17.6 % / Biso Wilson estimate: 44.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.11 / Net I/σ(I): 17
Reflection shellResolution: 1.977→2.03 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 62 / CC1/2: 0.902 / Rrim(I) all: 0.854 / % possible all: 9.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZKE

3zke


Resolution: 1.977→38.148 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.19
Details: Refinement was carried out with a set of data that has been anisotropically truncated, due to the strong anisotropy of the crystals. Hydrogen atoms were added to their riding positions.
RfactorNum. reflection% reflection
Rfree0.2289 346 4.61 %
Rwork0.1915 --
obs0.1931 7511 83.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.977→38.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms800 0 1 15 816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013817
X-RAY DIFFRACTIONf_angle_d1.1351098
X-RAY DIFFRACTIONf_dihedral_angle_d15.206489
X-RAY DIFFRACTIONf_chiral_restr0.069118
X-RAY DIFFRACTIONf_plane_restr0.006138
LS refinement shellResolution: 1.9774→2.4912 Å
RfactorNum. reflection% reflection
Rfree0.2746 117 -
Rwork0.2449 2740 -
obs--66 %
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)
11.43631.19470.00242.62210.53371.4360.21180.0141-0.09730.05920.2061-0.1245-0.46420.20120.49240.8363-0.2943-0.22220.26560.06340.5406-10.915220.5423-7.5058
21.9969-2.03161.07644.407-1.28360.59860.1101-0.25740.28661.15880.1938-0.0801-0.652-0.04460.19471.0008-0.08120.050.1317-0.03080.2905-15.915616.31090.0164
33.50020.87310.15230.22810.14132.5870.1305-0.4070.11950.93290.12590.4716-0.3356-0.7326-0.21410.54880.05860.1520.26580.06350.2295-22.493510.748-5.909
43.08050.59240.0962.8132-0.22483.55240.03630.15960.66550.82960.345-0.0025-1.1429-0.1571-0.06430.5095-0.03750.0440.10880.02920.2387-16.624416.8067-13.1359
53.8829-4.6589-2.75458.08812.18628.8912-0.02510.56721.53620.08750.0615-0.7314-1.696-0.2047-0.12080.579-0.0580.03760.40990.15890.5087-15.592320.3217-19.4034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 31 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 89 )
5X-RAY DIFFRACTION5chain 'B' and (resid 606 through 615 )

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