[English] 日本語
Yorodumi
- PDB-6pse: Complex of BICD2 with a Dynein Light Intermediate Chain Peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pse
TitleComplex of BICD2 with a Dynein Light Intermediate Chain Peptide
Components
  • Cytoplasmic dynein 1 light intermediate chain 1
  • Protein bicaudal D homolog 2
KeywordsMOTOR PROTEIN / Effector
Function / homology
Function and homology information


microtubule anchoring at microtubule organizing center / minus-end-directed organelle transport along microtubule / early endosome to recycling endosome transport / positive regulation of mitotic cell cycle spindle assembly checkpoint / dynein heavy chain binding / annulate lamellae / protein localization to Golgi apparatus / regulation of vesicle-mediated transport / cytoskeletal anchor activity / COPI-independent Golgi-to-ER retrograde traffic ...microtubule anchoring at microtubule organizing center / minus-end-directed organelle transport along microtubule / early endosome to recycling endosome transport / positive regulation of mitotic cell cycle spindle assembly checkpoint / dynein heavy chain binding / annulate lamellae / protein localization to Golgi apparatus / regulation of vesicle-mediated transport / cytoskeletal anchor activity / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / dynein light intermediate chain binding / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / centrosome localization / dynein complex binding / microtubule-based movement / dynactin binding / ficolin-1-rich granule membrane / mRNA transport / COPI-mediated anterograde transport / nuclear pore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / regulation of microtubule cytoskeleton organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / secretory granule membrane / RHO GTPases Activate Formins / kinetochore / microtubule cytoskeleton organization / small GTPase binding / spindle pole / Aggrephagy / HCMV Early Events / recycling endosome membrane / Separation of Sister Chromatids / GDP binding / endocytic vesicle membrane / protein transport / nuclear envelope / protein-macromolecule adaptor activity / cytoplasmic vesicle / microtubule / molecular adaptor activity / cell division / centrosome / Neutrophil degranulation / Golgi apparatus / RNA binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Bicaudal-D protein / Microtubule-associated protein Bicaudal-D / Dynein 1 light intermediate chain / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein bicaudal D homolog 2 / Cytoplasmic dynein 1 light intermediate chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.404 Å
AuthorsDominguez, R. / Lee, I.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2020
Title: A tunable LIC1-adaptor interaction modulates dynein activity in a cargo-specific manner.
Authors: Lee, I.G. / Cason, S.E. / Alqassim, S.S. / Holzbaur, E.L.F. / Dominguez, R.
History
DepositionJul 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein bicaudal D homolog 2
B: Protein bicaudal D homolog 2
C: Cytoplasmic dynein 1 light intermediate chain 1


Theoretical massNumber of molelcules
Total (without water)25,8473
Polymers25,8473
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-55 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.773, 61.844, 81.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein bicaudal D homolog 2 / Bic-D 2


Mass: 11585.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BICD2, KIAA0699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TD16
#2: Protein/peptide Cytoplasmic dynein 1 light intermediate chain 1 / LIC1 / Dynein light chain A / DLC-A / Dynein light intermediate chain 1 / cytosolic


Mass: 2676.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y6G9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% v/v 2-propanol, 0.08M Sodium citrate tribasic dehydrate, pH 5.5, 18% w/v polyethylene glycol 4,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 2.4→49.04 Å / Num. obs: 19602 / % possible obs: 94.9 % / Redundancy: 11.2 %
Details: The data were corrected for anisotropy using HKL2000. This treatment eliminated many weak reflections and reduced the number of reflections and completeness of the data used for refinement ...Details: The data were corrected for anisotropy using HKL2000. This treatment eliminated many weak reflections and reduced the number of reflections and completeness of the data used for refinement compared to the number of reflections and completeness reported for data collection.
CC1/2: 0.99 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.033 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.785 / Num. unique obs: 1396 / CC1/2: 0.289 / Rpim(I) all: 0.76

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000v701.c3data reduction
PHENIX1.12_2829phasing
RefinementMethod to determine structure: SAD / Resolution: 2.404→34.08 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 732 5.08 %
Rwork0.1928 13691 -
obs0.1955 14423 69.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.94 Å2 / Biso mean: 49.4651 Å2 / Biso min: 10.67 Å2
Refinement stepCycle: final / Resolution: 2.404→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 0 42 1351
Biso mean---38.09 -
Num. residues----158
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4044-2.590.3304490.236790723
2.59-2.85060.2751010.2475188148
2.8506-3.26280.27951650.2307313079
3.2628-4.10960.25012030.1766389498
4.1096-34.080.21972140.1768387999
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)
13.733-1.13071.70593.86822.78553.94970.1834-0.3812-0.82240.9917-0.27761.03730.6455-1.3657-0.05150.451-0.11260.05880.5060.0630.315141.3130.046137.5706
21.49250.43453.10340.20360.32045.0805-0.25940.18290.0716-0.2618-0.0480.1633-0.43910.30460.18650.3790.0911-0.06680.2572-0.03130.267132.982841.442-1.9556
33.7036-0.00983.6481-0.0005-0.00973.58950.4289-0.59551.86150.06930.0368-0.1604-2.6497-0.5243-0.43920.892-0.02160.27560.9865-0.57060.989244.232250.782846.7108
42.40470.01134.47181.14811.20872.02120.2419-0.09890.0822-0.166-0.27090.25070.6173-0.55330.19910.23240.01640.0440.2234-0.03350.321733.116137.20723.3907
55.74295.3906-5.72485.3298-6.14187.95070.24540.1410.46480.7641-0.16560.26810.13411.4236-0.07321.26660.224-0.0271.0004-0.01540.582226.560937.0716-41.3075
62.3154-1.91-2.92325.2664-0.10735.4062-0.0826-0.22260.81490.1042-0.11330.8574-1.0902-1.57220.3030.69170.359-0.11860.7058-0.15920.677127.600944.87366.4437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 18 )A4 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 80 )A19 - 80
3X-RAY DIFFRACTION3chain 'B' and (resid 14 through 18 )B14 - 18
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 74 )B19 - 74
5X-RAY DIFFRACTION5chain 'B' and (resid 75 through 79 )B75 - 79
6X-RAY DIFFRACTION6chain 'C' and (resid 441 through 452 )C441 - 452

+
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