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- PDB-6ofp: Structure of the C-terminal cargo binding domain of human Bicaudal D2 -

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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 / protein localization to organelle / annulate lamellae / protein localization to Golgi apparatus / cytoskeletal anchor activity / COPI-independent Golgi-to-ER retrograde traffic / dynein light intermediate chain binding / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / centrosome localization ...microtubule anchoring at microtubule organizing center / minus-end-directed organelle transport along microtubule / protein localization to organelle / annulate lamellae / protein localization to Golgi apparatus / cytoskeletal anchor activity / COPI-independent Golgi-to-ER retrograde traffic / dynein light intermediate chain binding / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / centrosome localization / dynein complex binding / microtubule-based movement / dynactin binding / mRNA transport / nuclear pore / regulation of microtubule cytoskeleton organization / small GTPase binding / protein transport / nuclear envelope / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 2.34 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

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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

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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

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