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- PDB-2v66: Crystal Structure of the coiled-coil domain of Ndel1 (a.a. 58 to ... -

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Basic information

Entry
Database: PDB / ID: 2v66
TitleCrystal Structure of the coiled-coil domain of Ndel1 (a.a. 58 to 169) C
ComponentsNUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1
KeywordsSTRUCTURAL PROTEIN / DEVELOPMENTAL PROTEIN / STRUCTURAL PROTEIN PHOSPHORYLATION / TRANSPORT / MICROTUBULE / NEUROGENESIS / CYTOSKELETON / DIFFERENTIATION
Function / homology
Function and homology information


neurofilament cytoskeleton / cerebral cortex radially oriented cell migration / establishment of chromosome localization / central nervous system neuron axonogenesis / radial glia-guided pyramidal neuron migration / vesicle transport along microtubule / neurofilament cytoskeleton organization / lysosome localization / axon hillock / microtubule nucleation ...neurofilament cytoskeleton / cerebral cortex radially oriented cell migration / establishment of chromosome localization / central nervous system neuron axonogenesis / radial glia-guided pyramidal neuron migration / vesicle transport along microtubule / neurofilament cytoskeleton organization / lysosome localization / axon hillock / microtubule nucleation / positive regulation of ruffle assembly / mitotic centrosome separation / retrograde axonal transport / kinesin complex / centrosome localization / neuron projection extension / inner cell mass cell proliferation / regulation of intracellular protein transport / regulation of neuron projection development / beta-tubulin binding / cell leading edge / establishment of mitotic spindle orientation / alpha-tubulin binding / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / axon cytoplasm / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of GTPase activity / Resolution of Sister Chromatid Cohesion / chromosome segregation / RHO GTPases Activate Formins / kinetochore / spindle / Separation of Sister Chromatids / synaptic vesicle / insulin receptor signaling pathway / cell migration / microtubule binding / microtubule / centrosome / identical protein binding / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1080 / NUDE domain / NUDE family / NUDE protein, C-terminal conserved region / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
: / Nuclear distribution protein nudE-like 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsTarricone, C. / Perrina, F. / Musacchio, A.
CitationJournal: Structure / Year: 2007
Title: The Structure of the Coiled-Coil Domain of Ndel1 and the Basis of its Interaction with Lis1, the Causal Protein of Miller-Dieker Lissencephaly.
Authors: Derewenda, U. / Tarricone, C. / Choi, W.C. / Cooper, D.R. / Lukasik, S. / Perrina, F. / Tripathy, A. / Kim, M.H. / Cafiso, D.S. / Musacchio, A. / Derewenda, Z.S.
History
DepositionJul 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: NUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1
C: NUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1
D: NUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1
E: NUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0676
Polymers52,6664
Non-polymers4012
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21010 Å2
ΔGint-175.5 kcal/mol
Surface area31710 Å2
MethodPQS
Unit cell
Length a, b, c (Å)46.431, 73.221, 69.026
Angle α, β, γ (deg.)90.00, 105.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1 / NDEL1 / PROTEIN NUDEL / MITOSIN-ASSOCIATED PROTEIN 1


Mass: 13166.511 Da / Num. of mol.: 4 / Fragment: COILED COIL, LIS1 BINDING, RESIDUES 58-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9GZM8
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.11 Å3/Da / Density % sol: 41.32 % / Description: NONE
Crystal growpH: 6.8
Details: 4% PEG 8000, 50 MM SODIUM PHOSPHATE PH 6.8, 100 MM NACL. PROTEIN CONCENTRATION 20 MG/ML. CRYOBUFFER = RESERVOIR PLUS 17% PEG 400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→49.3 Å / Num. obs: 300363 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 11.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 12 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.1→18 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.876 / SU B: 14.284 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1074 4.1 %RANDOM
Rwork0.233 ---
obs0.236 24984 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.26 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å20 Å2-2.25 Å2
2--2.86 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3700 0 2 123 3825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223728
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.9685000
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7315440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38625.593236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.63115760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6271536
X-RAY DIFFRACTIONr_chiral_restr0.1350.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022844
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2480.21777
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22577
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.340.2101
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2791.52341
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83623548
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.48631590
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3354.51452
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.344 90
Rwork0.233 1794
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)
111.7525-1.51376.94190.2504-0.92644.11920.1331-0.219-0.1078-0.0215-0.04110.00830.1288-0.1414-0.092-0.04080.03330.0458-0.0102-0.00610.0073-18.6731.76562.433
214.0578-2.82829.3490.569-1.88096.2175-0.0940.17660.21880.0062-0.0436-0.0581-0.04850.1520.13760.00570.03630.0193-0.00660.0260.0081-14.73132.64459.192
317.4883-2.52689.54690.4949-1.45565.2767-0.35380.26790.26660.04650.13130.0407-0.25790.09740.22260.0018-0.00650.01820.0017-0.00580.0073-64.34842.87434.333
49.0595-1.61896.06130.4356-1.20624.159-0.0526-0.75080.1913-0.03230.11660.05670.0429-0.5046-0.06390.00670.03370.0437-0.010.00940.0161-64.2239.24831.017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E58 - 168
2X-RAY DIFFRACTION2B58 - 168
3X-RAY DIFFRACTION3C58 - 168
4X-RAY DIFFRACTION4D58 - 168

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