[English] 日本語
Yorodumi
- PDB-7d35: Human LC8 bound to ebola virus VP35(67-76) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d35
TitleHuman LC8 bound to ebola virus VP35(67-76)
Components
  • Dynein light chain 1, cytoplasmic
  • Peptide from Polymerase cofactor VP35
KeywordsUNKNOWN FUNCTION / LC8 / Ebola virus / EBOV / VP35
Function / homology
Function and homology information


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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / motile cilium assembly / Activation of BIM and translocation to mitochondria / ciliary tip ...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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / motile cilium assembly / Activation of BIM and translocation to mitochondria / ciliary tip / Intraflagellar transport / negative regulation of nitric oxide biosynthetic process / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / dynein intermediate chain binding / Macroautophagy / spermatid development / tertiary granule membrane / ficolin-1-rich granule membrane / 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 / Mitotic Prometaphase / substantia nigra development / axon cytoplasm / EML4 and NUDC in mitotic spindle formation / 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 / Aggrephagy / virion component / Separation of Sister Chromatids / HCMV Early Events / Regulation of PLK1 Activity at G2/M Transition / mitotic spindle / site of double-strand break / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / scaffold protein binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / microtubule / host cell cytoplasm / cytoskeleton / cilium / apoptotic process / centrosome / DNA damage response / Neutrophil degranulation / protein-containing complex binding / enzyme binding / mitochondrion / RNA binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / 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 ...Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / 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
Similarity search - Domain/homology
Dynein light chain 1, cytoplasmic / Polymerase cofactor VP35
Similarity search - Component
Biological speciesHomo sapiens (human)
Ebola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsKu, B. / Lim, D.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1C1C1008451 Korea, Republic Of
National Research Foundation (NRF, Korea)2019M3E5D6063955 Korea, Republic Of
Ministry of Science, ICT and Future Planning (MSIP)KRIBB Research Initiative Programs Korea, Republic Of
CitationJournal: J.Microbiol / Year: 2021
Title: Crystal structure of human LC8 bound to a peptide from Ebola virus VP35.
Authors: Lim, D. / Shin, H.C. / Choi, J.S. / Kim, S.J. / Ku, B.
History
DepositionSep 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Peptide from Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)11,7572
Polymers11,7572
Non-polymers00
Water30617
1
A: Dynein light chain 1, cytoplasmic
B: Peptide from Polymerase cofactor VP35

A: Dynein light chain 1, cytoplasmic
B: Peptide from Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)23,5154
Polymers23,5154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5020 Å2
ΔGint-15 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.426, 43.426, 205.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 10577.098 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P63167
#2: Protein/peptide Peptide from Polymerase cofactor VP35 / Ebola VP35 / eVP35


Mass: 1180.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Ebola virus / References: UniProt: Q6V1Q9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200mM ammonium citrate dibasic, 200mM ammonium citrate tribasic (pH 5.5), 30% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 4869 / % possible obs: 95 % / Redundancy: 4.7 % / CC1/2: 0.975 / Rmerge(I) obs: 0.094 / Net I/σ(I): 17.2
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.31 / Num. unique obs: 225 / CC1/2: 0.949

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CMI

1cmi


Resolution: 2.401→30.33 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 28.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2917 487 10.02 %
Rwork0.2276 4373 -
obs0.234 4860 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.3 Å2 / Biso mean: 33.0497 Å2 / Biso min: 12.39 Å2
Refinement stepCycle: final / Resolution: 2.401→30.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 0 0 17 807
Biso mean---32.12 -
Num. residues----96
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007805
X-RAY DIFFRACTIONf_angle_d0.9111080
X-RAY DIFFRACTIONf_chiral_restr0.056116
X-RAY DIFFRACTIONf_plane_restr0.004137
X-RAY DIFFRACTIONf_dihedral_angle_d17.059485
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.401-2.74790.37281530.2943136995
2.7479-3.46130.30581570.2452141496
3.4613-30.330.25681770.1977159098

+
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