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- PDB-4bl6: Bicaudal-D uses a parallel, homodimeric coiled coil with heteroty... -

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Basic information

Entry
Database: PDB / ID: 4bl6
TitleBicaudal-D uses a parallel, homodimeric coiled coil with heterotypic registry to co-ordinate recruitment of cargos to dynein
ComponentsPROTEIN BICAUDAL D
KeywordsPROTEIN TRANSPORT / CARGO BINDING
Function / homology
Function and homology information


oocyte nucleus migration involved in oocyte dorsal/ventral axis specification / cellular macromolecule localization / microtubule anchoring at microtubule organizing center / germarium-derived egg chamber formation / oocyte microtubule cytoskeleton polarization / germarium-derived oocyte fate determination / positive regulation of synaptic vesicle exocytosis / positive regulation of clathrin-dependent endocytosis / COPI-independent Golgi-to-ER retrograde traffic / protein localization to organelle ...oocyte nucleus migration involved in oocyte dorsal/ventral axis specification / cellular macromolecule localization / microtubule anchoring at microtubule organizing center / germarium-derived egg chamber formation / oocyte microtubule cytoskeleton polarization / germarium-derived oocyte fate determination / positive regulation of synaptic vesicle exocytosis / positive regulation of clathrin-dependent endocytosis / COPI-independent Golgi-to-ER retrograde traffic / protein localization to organelle / oocyte axis specification / RNA transport / clathrin heavy chain binding / intracellular mRNA localization / cytoskeletal anchor activity / dynein complex binding / oogenesis / dynactin binding / regulation of endocytosis / synaptic vesicle endocytosis / mRNA transport / regulation of microtubule cytoskeleton organization / small GTPase binding / presynapse / cytoskeleton / Golgi apparatus / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2470 / Bicaudal-D protein / Microtubule-associated protein Bicaudal-D / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
ARGININE / Protein bicaudal D
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.18 Å
AuthorsLiu, Y. / Salter, H.K. / Holding, A.N. / Johnson, C.M. / Stephens, E. / Lukavsky, P.J. / Walshaw, J. / Bullock, S.L.
CitationJournal: Genes Dev. / Year: 2013
Title: Bicaudal-D Uses a Parallel, Homodimeric Coiled Coil with Heterotypic Registry to Coordinate Recruitment of Cargos to Dynein
Authors: Liu, Y. / Salter, H.K. / Holding, A.N. / Johnson, C.M. / Stephens, E. / Lukavsky, P.J. / Walshaw, J. / Bullock, S.L.
History
DepositionMay 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jul 12, 2017Group: Derived calculations / Category: struct_conn
Item: _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag ..._struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN BICAUDAL D
B: PROTEIN BICAUDAL D
C: PROTEIN BICAUDAL D
D: PROTEIN BICAUDAL D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1995
Polymers45,0244
Non-polymers1751
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-90.5 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.199, 62.199, 190.511
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
PROTEIN BICAUDAL D


Mass: 11256.005 Da / Num. of mol.: 4 / Fragment: CARGO BINDING DOMAIN, RESIDUES 656-745
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Description: FLY CDNA / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P16568
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS PH 8.5, 5 % PEG4000, 10 % GLYCEROL, 30 MM MAGNESIUM CHLORIDE, 30 MM CALCIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98055
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 10, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98055 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.523
11-H-K, K, -L20.477
ReflectionResolution: 2.2→47 Å / Num. obs: 20073 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 34 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 18
Reflection shellResolution: 2.18→2.23 Å / Redundancy: 34.7 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 18 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.18→46.89 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.598 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23518 1746 8 %RANDOM
Rwork0.20367 ---
obs0.2061 20073 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.344 Å2
Baniso -1Baniso -2Baniso -3
1-19.37 Å20 Å20 Å2
2--19.37 Å20 Å2
3----38.75 Å2
Refinement stepCycle: LAST / Resolution: 2.18→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 4 106 2678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222580
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4261.9913464
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7945324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21225124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.40315525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3081525
X-RAY DIFFRACTIONr_chiral_restr0.1690.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021857
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3661.51634
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2122596
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.563946
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.794.5868
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.175→2.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 111 -
Rwork0.192 1492 -
obs--100 %

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