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- PDB-6gzl: Complex between the dynein light chain DYNLL1/DLC8 and a peptide ... -

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Basic information

Entry
Database: PDB / ID: 6gzl
TitleComplex between the dynein light chain DYNLL1/DLC8 and a peptide from the large myelin-associated glycoprotein L-MAG
Components
  • Dynein light chain 1, cytoplasmic
  • PRO-THR-LYS-ASP-SER-TYR-THR-LEU-THR-GLU-GLU-LEU
KeywordsPROTEIN BINDING / complex / heterotetramer / cell adhesion / cytoplasmic domain
Function / homology
Function and homology information


mesaxon / Axonal growth inhibition (RHOA activation) / Basigin interactions / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / intraciliary retrograde transport / ganglioside GT1b binding / motile cilium assembly / Activation of BIM and translocation to mitochondria / sialic acid binding ...mesaxon / Axonal growth inhibition (RHOA activation) / Basigin interactions / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / intraciliary retrograde transport / ganglioside GT1b binding / motile cilium assembly / Activation of BIM and translocation to mitochondria / sialic acid binding / negative regulation of phosphorylation / central nervous system myelination / central nervous system myelin formation / positive regulation of myelination / myelin sheath adaxonal region / cell-cell adhesion via plasma-membrane adhesion molecules / negative regulation of axon extension / ciliary tip / Intraflagellar transport / paranode region of axon / Schmidt-Lanterman incisure / positive regulation of astrocyte differentiation / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / axon regeneration / dynein intermediate chain binding / Macroautophagy / transmission of nerve impulse / enzyme inhibitor activity / tertiary granule membrane / ficolin-1-rich granule membrane / negative regulation of neuron differentiation / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / substantia nigra development / EML4 and NUDC in mitotic spindle formation / myelination / 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 / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / RHO GTPases Activate Formins / kinetochore / HCMV Early Events / cellular response to mechanical stimulus / Aggrephagy / mitotic spindle / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / myelin sheath / site of double-strand break / negative regulation of neuron projection development / carbohydrate binding / negative regulation of neuron apoptotic process / microtubule / cytoskeleton / cell adhesion / cilium / membrane raft / signaling receptor binding / apoptotic process / centrosome / DNA damage response / Neutrophil degranulation / protein kinase binding / protein homodimerization activity / mitochondrion / 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: 1.953 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

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Assembly

Deposited unit
A: Dynein light chain 1, cytoplasmic
B: PRO-THR-LYS-ASP-SER-TYR-THR-LEU-THR-GLU-GLU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5523
Polymers12,5162
Non-polymers351
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-17 kcal/mol
Surface area5760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.730, 43.730, 205.390
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/peptide PRO-THR-LYS-ASP-SER-TYR-THR-LEU-THR-GLU-GLU-LEU


Mass: 2047.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P20917*PLUS
#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.: 39 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
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: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 6139 / % possible obs: 65.7 % / Redundancy: 13 % / Biso Wilson estimate: 26.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.213 / Rrim(I) all: 0.222 / Net I/σ(I): 13.34
Reflection shellResolution: 1.95→2 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.812 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 26 / CC1/2: 0.469 / Rrim(I) all: 1.901 / % possible all: 3.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZKE

3zke


Resolution: 1.953→37.871 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.28
Details: Refinement was carried out against anisotropically truncated data. Hydrogen atoms were added at their riding positions.
RfactorNum. reflection% reflection
Rfree0.2511 290 4.79 %
Rwork0.2122 --
obs0.214 6052 65.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.953→37.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms811 0 1 39 851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008857
X-RAY DIFFRACTIONf_angle_d0.9451157
X-RAY DIFFRACTIONf_dihedral_angle_d18.831516
X-RAY DIFFRACTIONf_chiral_restr0.053123
X-RAY DIFFRACTIONf_plane_restr0.004149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9535-2.46110.295570.24361220X-RAY DIFFRACTION29
2.4611-37.87840.24532330.20764542X-RAY DIFFRACTION100
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)
10.27560.18650.00661.16580.2690.2830.0726-0.1111-0.19590.60320.01740.04030.5035-0.0275-0.01990.4995-0.0208-0.01030.1263-0.00040.134117.2395-14.1599-3.4329
20.62530.7060.72291.81470.71871.71190.07040.0031-0.17770.39810.0514-0.06890.48720.12810.03230.2391-0.0069-0.03660.0872-0.0350.066917.9728-16.0984-12.509
30.4851.21760.30573.38610.89754.07370.01430.3393-0.7638-0.1078-0.11910.58730.39160.01450.07950.2217-0.0263-0.0070.1118-0.03590.1512.7538-18.2961-19.2199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 89 )
3X-RAY DIFFRACTION3chain 'B' and (resid 606 through 617 )

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