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- PDB-2v71: Coiled-coil region of NudEL -

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Basic information

Entry
Database: PDB / ID: 2v71
TitleCoiled-coil region of NudEL
ComponentsNUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1
KeywordsNUCLEAR PROTEIN / DEVELOPMENTAL PROTEIN / NEUROGENESIS / CYTOSKELETON / LIS1 BINDING / DIFFERENTIATION / PHOSPHORYLATION / TRANSPORT / MICROTUBULE / MICROTUBULE ASSOCIATED MIGRATION
Function / homology
Function and homology information


: / neurofilament cytoskeleton / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / cerebral cortex radially oriented cell migration / Separation of Sister Chromatids / kinetochore => GO:0000776 ...: / neurofilament cytoskeleton / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / cerebral cortex radially oriented cell migration / Separation of Sister Chromatids / kinetochore => GO:0000776 / establishment of chromosome localization / central nervous system neuron axonogenesis / oligopeptidase activity / central region of growth cone / nuclear membrane disassembly / vesicle transport along microtubule / microtubule nucleation / neurofilament cytoskeleton organization / lysosome localization / axon hillock / retrograde axonal transport / activation of GTPase activity / positive regulation of ruffle assembly / mitotic centrosome separation / microtubule associated complex / microtubule organizing center / centrosome localization / inner cell mass cell proliferation / kinesin complex / neuron projection extension / beta-tubulin binding / regulation of neuron projection development / positive regulation of axon regeneration / regulation of intracellular protein transport / cell leading edge / establishment of mitotic spindle orientation / alpha-tubulin binding / positive regulation of axon extension / axon cytoplasm / chromosome segregation / neuron migration / spindle / microtubule cytoskeleton organization / kinetochore / positive regulation of GTPase activity / neuron projection development / cell migration / synaptic vesicle / insulin receptor signaling pathway / nuclear envelope / cell body / microtubule binding / microtubule / axon / centrosome / protein-containing complex binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Nuclear distribution protein nudE-like 1 / NUDE domain / NUDE family / NUDE protein, C-terminal conserved region
Similarity search - Domain/homology
Nuclear distribution protein nudE-like 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.24 Å
AuthorsDerewenda, U. / Cooper, D.R. / Kim, M.H. / Derewenda, Z.S.
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 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1
B: NUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1


Theoretical massNumber of molelcules
Total (without water)45,3492
Polymers45,3492
Non-polymers00
Water0
1
A: NUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1
B: NUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1

A: NUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1
B: NUCLEAR DISTRIBUTION PROTEIN NUDE-LIKE 1


Theoretical massNumber of molelcules
Total (without water)90,6994
Polymers90,6994
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area23830 Å2
ΔGint-203.6 kcal/mol
Surface area52080 Å2
MethodPQS
Unit cell
Length a, b, c (Å)89.872, 44.975, 124.377
Angle α, β, γ (deg.)90.00, 97.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 22674.662 Da / Num. of mol.: 2 / Fragment: COILED-COIL DOMAIN, RESIDUES 8-193 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PHIS PARALLEL 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q78PB6
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 24 TO MSE ENGINEERED RESIDUE IN CHAIN A, VAL 134 TO MSE ...ENGINEERED RESIDUE IN CHAIN A, LEU 24 TO MSE ENGINEERED RESIDUE IN CHAIN A, VAL 134 TO MSE ENGINEERED RESIDUE IN CHAIN B, LEU 24 TO MSE ENGINEERED RESIDUE IN CHAIN B, VAL 134 TO MSE
Sequence detailsMETHIONINES INTRODUCED FOR PHASING PURPOSES

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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: 5.65 Å3/Da / Density % sol: 56.5 % / Description: NONE
Crystal growpH: 6
Details: 18-22% TERT-BUTANOL, 100 MM SODIUM CITRATE PH 6.0, 10 MM COCL2, AND 10 MM SPERMINE. BEFORE FREEZING, TERT-BUTANOL WAS SLOWLY EXCHANGED FOR 30% MPD

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODEENRAF-NONIUS FR59111.5418
SYNCHROTRONAPS 22-ID20.97928, 0.97945, 0.97175
Detector
TypeIDDetectorDateDetails
RIGAKU IMAGE PLATE1IMAGE PLATEDec 15, 2005MIRRORS
2IMAGE PLATE
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.979281
30.979451
40.971751
ReflectionResolution: 2.25→50 Å / Num. obs: 23115 / % possible obs: 96.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.8
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.34 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.24→123.09 Å / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1172 5.1 %RANDOM
Rwork0.253 ---
obs0.255 21863 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.69 Å2
Refinement stepCycle: LAST / Resolution: 2.24→123.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 0 0 2671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222699
X-RAY DIFFRACTIONr_bond_other_d0.0010.021887
X-RAY DIFFRACTIONr_angle_refined_deg2.3671.9683616
X-RAY DIFFRACTIONr_angle_other_deg1.46334594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.195318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93825.714168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87715548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.551522
X-RAY DIFFRACTIONr_chiral_restr0.0860.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02522
X-RAY DIFFRACTIONr_nbd_refined0.2230.2582
X-RAY DIFFRACTIONr_nbd_other0.1430.21648
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21290
X-RAY DIFFRACTIONr_nbtor_other0.0880.21515
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.24→2.3 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.384 76
Rwork0.345 1458
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)
121.02646.8393-14.3293.3155-1.438519.2842-0.2617-0.0239-0.24540.5505-0.17930.34760.6064-0.22680.441-0.25830.0169-0.0755-0.3238-0.0209-0.2149-59.379425.761199.0257
221.8198-5.0071-20.92984.12445.027723.0088-0.4989-1.1664-0.60460.22760.35490.08290.5870.92670.1439-0.28970.0386-0.1405-0.3462-0.0033-0.1568-41.374920.7114183.578
345.25761.6421-43.85962.12471.047753.01760.1424-0.4731-0.5858-0.3174-0.3031-0.4997-1.2151.06110.1607-0.1772-0.05080.0257-0.2377-0.0395-0.1396-22.079918.4341163.8174
413.1693-1.979-23.71120.6184.296844.37060.64890.66570.44840.1982-0.26240.2976-1.5229-1.4995-0.38650.31860.06250.19820.5762-0.05030.0695.144617.3396116.6056
517.6916-2.0835-27.60610.62762.891746.8449-0.59810.744-0.6220.1305-0.14040.04491.694-1.27930.7384-0.0742-0.1081-0.0378-0.2409-0.0769-0.124836.16557.242154.0785
664.21591.7761-51.005719.86251.804469.9993-1.4201-0.0781-1.1755-2.42260.3118-2.43591.34951.19181.10830.18830.03190.03850.1563-0.05180.214660.11716.259925.1958
77.9319-4.7055-7.27189.90976.78478.94320.0418-0.4533-0.03990.4632-0.04720.00760.21830.18070.0054-0.35580.012-0.153-0.2916-0.0724-0.2371-54.743433.464200.8782
815.3383-7.9957-25.1677.753815.238651.43681.01181.29010.4714-0.4192-0.80020.038-1.5123-2.2281-0.2116-0.210.093-0.0782-0.29130.0095-0.1743-44.088526.1773176.5086
936.0493-10.0338-36.33034.13589.015637.5085-0.22420.9098-0.6723-0.6155-0.3541-0.0347-0.2437-0.40730.57830.2022-0.19570.16540.3755-0.24460.0073-13.769414.5779141.7386
1012.05452.5329-18.86821.4548-4.703331.0992-0.1066-1.2044-0.26030.3921-0.25620.1413-0.17141.04460.3628-0.0848-0.0768-0.00250.0264-0.0311-0.193127.816816.073693.1158
113.94480.7663-17.93982.1511-6.212285.29980.3192-0.74510.2365-0.0693-0.0444-0.3543-1.44483.2908-0.2748-0.1787-0.0792-0.0426-0.0501-0.0582-0.17346.543621.581349.678
128.1321-2.6622-14.08379.39750.29669.60981.27650.78430.5261-1.0594-0.0846-0.4745-4.33940.5781-1.19190.2722-0.03830.18440.1921-0.00050.100551.827422.891424.9153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 23
2X-RAY DIFFRACTION2A24 - 42
3X-RAY DIFFRACTION3A43 - 60
4X-RAY DIFFRACTION4A61 - 116
5X-RAY DIFFRACTION5A117 - 154
6X-RAY DIFFRACTION6A155 - 167
7X-RAY DIFFRACTION7B8 - 23
8X-RAY DIFFRACTION8B24 - 45
9X-RAY DIFFRACTION9B46 - 85
10X-RAY DIFFRACTION10B86 - 133
11X-RAY DIFFRACTION11B134 - 149
12X-RAY DIFFRACTION12B150 - 167

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