[English] 日本語
Yorodumi
- PDB-6ofp: Structure of the C-terminal cargo binding domain of human Bicaudal D2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ofp
TitleStructure of the C-terminal cargo binding domain of human Bicaudal D2
ComponentsProtein bicaudal D homolog 2
KeywordsMOTOR PROTEIN / Bicaudal D2 / dynein / dynein adaptor / coiled-coil / registry shift / spinal muscular atrophy / cytoskeletal motor
Function / homology
Function and homology information


microtubule anchoring at microtubule organizing center / minus-end-directed organelle transport along microtubule / annulate lamellae / protein localization to Golgi apparatus / cytoskeletal anchor activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-independent Golgi-to-ER retrograde traffic / dynein light intermediate chain binding / centrosome localization / microtubule-based movement ...microtubule anchoring at microtubule organizing center / minus-end-directed organelle transport along microtubule / annulate lamellae / protein localization to Golgi apparatus / cytoskeletal anchor activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-independent Golgi-to-ER retrograde traffic / dynein light intermediate chain binding / centrosome localization / microtubule-based movement / dynein complex binding / dynactin binding / mRNA transport / nuclear pore / regulation of microtubule cytoskeleton organization / small GTPase binding / nuclear envelope / protein transport / cytoplasmic vesicle / centrosome / Golgi apparatus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Bicaudal-D protein / Microtubule-associated protein Bicaudal-D
Similarity search - Domain/homology
Protein bicaudal D homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsNoell, C.R. / Debler, E.W. / Cui, H. / Solmaz, S.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM128119-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
CitationJournal: J Phys Chem Lett / Year: 2019
Title: Role of Coiled-Coil Registry Shifts in the Activation of Human Bicaudal D2 for Dynein Recruitment upon Cargo Binding.
Authors: Noell, C.R. / Loh, J.Y. / Debler, E.W. / Loftus, K.M. / Cui, H. / Russ, B.B. / Zhang, K. / Goyal, P. / Solmaz, S.R.
History
DepositionMar 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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: Protein bicaudal D homolog 2
B: Protein bicaudal D homolog 2


Theoretical massNumber of molelcules
Total (without water)21,8752
Polymers21,8752
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Multi-angle light scattering data supporting the assembly are published in: Noell, C.R., Loftus, K.M., Cui, H., Grewer, C.T., Kizer, M., Debler, E.W., and Solmaz, S.R. ...Evidence: light scattering, Multi-angle light scattering data supporting the assembly are published in: Noell, C.R., Loftus, K.M., Cui, H., Grewer, C.T., Kizer, M., Debler, E.W., and Solmaz, S.R. (2018). A quantitative model for BicD2/cargo interactions. Biochemistry 57, 6538-6550
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-57 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.694, 36.958, 78.706
Angle α, β, γ (deg.)90.00, 107.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-111-

HOH

-
Components

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


Mass: 10937.579 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) / Strain (production host): Rosetta 2 BL21(DE3)pLysS / References: UniProt: Q8TD16
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.05
Details: 0.1 M Tris, pH 8.05, 26% tert-Butanol, 40 mM CaCl2, 60 mM 1,6-Hexanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 13628 / % possible obs: 98 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.5 Å2 / Rsym value: 0.07 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.02 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 542 / Rsym value: 0.34 / % possible all: 85

-
Processing

Software
NameVersionClassification
PHENIXdev_1819refinement
XDSdata reduction
XSCALEdata scaling
PHENIXdev_1819phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YTD

4ytd


Resolution: 2.006→37.551 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.02
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 1313 10.01 %Random
Rwork0.2258 ---
obs0.2288 13113 94.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45 Å2
Refinement stepCycle: LAST / Resolution: 2.006→37.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 0 0 52 1522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031478
X-RAY DIFFRACTIONf_angle_d0.6671973
X-RAY DIFFRACTIONf_dihedral_angle_d14.835589
X-RAY DIFFRACTIONf_chiral_restr0.027231
X-RAY DIFFRACTIONf_plane_restr0.003252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0055-2.08580.36791170.29351061X-RAY DIFFRACTION78
2.0858-2.18070.33261370.26241236X-RAY DIFFRACTION90
2.1807-2.29570.28151490.22751306X-RAY DIFFRACTION95
2.2957-2.43950.24981470.22451326X-RAY DIFFRACTION97
2.4395-2.62780.28421490.22591333X-RAY DIFFRACTION98
2.6278-2.89210.29481500.22261361X-RAY DIFFRACTION99
2.8921-3.31040.23271530.2271365X-RAY DIFFRACTION99
3.3104-4.16990.21881560.19271404X-RAY DIFFRACTION100
4.1699-37.55760.25321550.24191408X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 35.9796 Å / Origin y: -6.1347 Å / Origin z: 55.2714 Å
111213212223313233
T0.282 Å20.0043 Å2-0.0155 Å2-0.2835 Å2-0.0035 Å2--0.2909 Å2
L0.0084 °20.017 °20.0248 °2-0.0218 °20.0251 °2--0.091 °2
S0.0392 Å °0.1321 Å °-0.0496 Å °-0.0029 Å °-0.0135 Å °-0.0089 Å °0.0043 Å °0.0801 Å °-0 Å °
Refinement TLS groupSelection details: all

+
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