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- PDB-4ytd: Crystal structure of the C-terminal Coiled Coil of mouse Bicaudal D1 -

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Basic information

Entry
Database: PDB / ID: 4ytd
TitleCrystal structure of the C-terminal Coiled Coil of mouse Bicaudal D1
ComponentsProtein bicaudal D homolog 1
KeywordsTRANSPORT PROTEIN / Retrograde transport / Cytoplasmic dynein / Bicaudal D1 / Coiled Coil / CARGO BINDING
Function / homology
Function and homology information


negative regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / microtubule anchoring at microtubule organizing center / proteinase activated receptor binding / COPI-independent Golgi-to-ER retrograde traffic / protein localization to organelle / cytoskeletal anchor activity / dynein intermediate chain binding / dynein complex binding / dynactin binding / regulation of microtubule cytoskeleton organization ...negative regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / microtubule anchoring at microtubule organizing center / proteinase activated receptor binding / COPI-independent Golgi-to-ER retrograde traffic / protein localization to organelle / cytoskeletal anchor activity / dynein intermediate chain binding / dynein complex binding / dynactin binding / regulation of microtubule cytoskeleton organization / stress granule assembly / positive regulation of receptor-mediated endocytosis / Golgi apparatus / cytosol
Similarity search - Function
Bicaudal-D protein / Microtubule-associated protein Bicaudal-D
Similarity search - Domain/homology
PHOSPHATE ION / Protein bicaudal D homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsTerawaki, S. / Yoshikane, A. / Higuchi, Y. / Wakamatsu, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology23121527 Japan
Ministry of Education, Culture, Sports, Science and Technology25121705 Japan
Ministry of Education, Culture, Sports, Science and Technology22770112 Japan
Ministry of Education, Culture, Sports, Science and Technology25840017 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Structural basis for cargo binding and autoinhibition of Bicaudal-D1 by a parallel coiled-coil with homotypic registry
Authors: Terawaki, S.I. / Yoshikane, A. / Higuchi, Y. / Wakamatsu, K.
History
DepositionMar 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Nov 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein bicaudal D homolog 1
B: Protein bicaudal D homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3096
Polymers23,9302
Non-polymers3804
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-68 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.029, 36.825, 104.303
Angle α, β, γ (deg.)90.00, 99.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1118-

HOH

21B-1075-

HOH

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Components

#1: Protein Protein bicaudal D homolog 1 / Bic-D 1 / Bicaudal D1


Mass: 11964.788 Da / Num. of mol.: 2 / Fragment: UNP residues 711-808
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bicd1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BR07
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 48% MPD, 0.1 M Tris-HCL, 0.2 M ammonium phosphate, 10 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 35669 / % possible obs: 99.6 % / Redundancy: 7.2 % / Net I/σ(I): 44.6
Reflection shellResolution: 1.5→1.53 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→31.113 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.1 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2062 1928 5.6 %
Rwork0.1747 --
obs0.1765 34426 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→31.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 20 252 1851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131763
X-RAY DIFFRACTIONf_angle_d1.3082397
X-RAY DIFFRACTIONf_dihedral_angle_d14.201743
X-RAY DIFFRACTIONf_chiral_restr0.057274
X-RAY DIFFRACTIONf_plane_restr0.006312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4987-1.51690.22061380.19772156X-RAY DIFFRACTION89
1.5169-1.53610.24671310.18652138X-RAY DIFFRACTION93
1.5361-1.55640.28381230.17922292X-RAY DIFFRACTION97
1.5564-1.57770.21081190.17692348X-RAY DIFFRACTION98
1.5777-1.60020.21251540.17082305X-RAY DIFFRACTION99
1.6002-1.62410.22361320.16232232X-RAY DIFFRACTION100
1.6241-1.64950.19991430.1642461X-RAY DIFFRACTION100
1.6495-1.67650.22081370.16462320X-RAY DIFFRACTION100
1.6765-1.70540.22631580.16542268X-RAY DIFFRACTION100
1.7054-1.73640.20621250.16412458X-RAY DIFFRACTION100
1.7364-1.76980.27731400.15192246X-RAY DIFFRACTION100
1.7698-1.8060.2341430.15532319X-RAY DIFFRACTION100
1.806-1.84520.20681310.15962460X-RAY DIFFRACTION100
1.8452-1.88810.23681400.15022228X-RAY DIFFRACTION100
1.8881-1.93530.21721590.15132444X-RAY DIFFRACTION100
1.9353-1.98770.15331180.15312228X-RAY DIFFRACTION100
1.9877-2.04610.22881580.15372449X-RAY DIFFRACTION100
2.0461-2.11220.21741190.15642249X-RAY DIFFRACTION100
2.1122-2.18760.23051370.14852418X-RAY DIFFRACTION100
2.1876-2.27520.16411620.14312276X-RAY DIFFRACTION100
2.2752-2.37870.14151150.14852367X-RAY DIFFRACTION100
2.3787-2.50410.16341470.15622370X-RAY DIFFRACTION100
2.5041-2.66090.18281280.16462360X-RAY DIFFRACTION100
2.6609-2.86620.17821380.17662348X-RAY DIFFRACTION100
2.8662-3.15440.18371300.18362359X-RAY DIFFRACTION100
3.1544-3.61030.21611440.18752294X-RAY DIFFRACTION100
3.6103-4.54630.21681450.17392344X-RAY DIFFRACTION100
4.5463-31.120.25631410.25872260X-RAY DIFFRACTION96

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