[English] 日本語
Yorodumi
- PDB-6gzl: Complex between the dynein light chain DYNLL1/DLC8 and a peptide ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / sialic acid binding / Activation of BIM and translocation to mitochondria / 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 / dynein intermediate chain binding / transmission of nerve impulse / 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 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / myelination / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Mitotic Prometaphase / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / substantia nigra development / EML4 and NUDC in mitotic spindle formation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / 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: 1.953 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 )

+
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