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- PDB-4i0o: Nucleoporin ELYS (aa1-494), Mus musculus -

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Basic information

Entry
Database: PDB / ID: 4i0o
TitleNucleoporin ELYS (aa1-494), Mus musculus
ComponentsProtein ELYS
KeywordsSTRUCTURAL PROTEIN / beta propeller / nuclear pore complex / WD40 repeat / mRNA transport
Function / homology
Function and homology information


Postmitotic nuclear pore complex (NPC) reformation / kinetochore => GO:0000776 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / nuclear pore complex assembly / Separation of Sister Chromatids / nuclear pore outer ring ...Postmitotic nuclear pore complex (NPC) reformation / kinetochore => GO:0000776 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / nuclear pore complex assembly / Separation of Sister Chromatids / nuclear pore outer ring / hemopoiesis / mRNA transport / regulation of cytokinesis / nuclear matrix / protein transport / nuclear membrane / cell cycle / DNA-binding transcription factor activity / cell division / chromatin / regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
ELYS-like domain / ELYS, beta-propeller domain / Nuclear pore complex assembly / beta-propeller of ELYS nucleoporin
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsBilokapic, S. / Schwartz, T.U.
CitationJournal: Structure / Year: 2013
Title: Structural and Functional Studies of the 252 kDa Nucleoporin ELYS Reveal Distinct Roles for Its Three Tethered Domains.
Authors: Bilokapic, S. / Schwartz, T.U.
History
DepositionNov 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein ELYS


Theoretical massNumber of molelcules
Total (without water)55,0271
Polymers55,0271
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.598, 78.117, 58.849
Angle α, β, γ (deg.)90.00, 106.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein ELYS / Embryonic large molecule derived from yolk sac / Protein MEL-28 / Putative AT-hook-containing ...Embryonic large molecule derived from yolk sac / Protein MEL-28 / Putative AT-hook-containing transcription factor 1


Mass: 55027.129 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ahctf1, Elys / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q8CJF7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 41.58 %
Crystal growTemperature: 292 K / Method: under oil / pH: 6.5
Details: Bis-Tris/HCl, PEG 3350, ammonium acetate, Octyl-beta-D-glucopyranoside, pH 6.5, under oil, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2008
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 69665 / % possible obs: 98.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.084 / Χ2: 1.04 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.932.70.71433870.848197
1.93-1.972.80.57134890.876198
1.97-2.012.90.4534840.865198.3
2.01-2.052.90.37334470.926198.8
2.05-2.092.90.32735050.97198.8
2.09-2.1430.28234631.083198.7
2.14-2.1930.25834711.058198.6
2.19-2.2530.21234561.087198.9
2.25-2.3230.20134921.126198.9
2.32-2.3930.18135001.177199.1
2.39-2.4830.15334971.14199.3
2.48-2.5830.13434901.123199.4
2.58-2.730.11435261.111199.2
2.7-2.8430.09234721.084199.6
2.84-3.0230.08435071.13199.4
3.02-3.2530.07135211.073199.7
3.25-3.5830.06934761.087199.4
3.58-4.092.90.06335501.172199.7
4.09-5.162.90.05134971.113199.2
5.16-502.90.04634350.673197.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8_1063refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→26.525 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8498 / SU ML: 0.23 / σ(F): 1.89 / Phase error: 22.72 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2145 3501 5.03 %
Rwork0.1802 --
obs0.182 69605 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.11 Å2 / Biso mean: 35.3717 Å2 / Biso min: 11.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 0 169 3764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123712
X-RAY DIFFRACTIONf_angle_d1.4295060
X-RAY DIFFRACTIONf_chiral_restr0.095584
X-RAY DIFFRACTIONf_plane_restr0.006653
X-RAY DIFFRACTIONf_dihedral_angle_d14.0071346
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9003-1.92630.37331090.30982326243587
1.9263-1.95380.32181480.25852629277797
1.9538-1.9830.25861590.24712596275599
1.983-2.01390.28821520.23072666281898
2.0139-2.0470.25291260.21892659278599
2.047-2.08220.28551370.19962628276599
2.0822-2.12010.25381210.22668278998
2.1201-2.16080.26641470.20312636278399
2.1608-2.20490.24161160.20072669278599
2.2049-2.25280.24021410.20032644278599
2.2528-2.30520.29381000.19292693279399
2.3052-2.36280.22321310.19872694282599
2.3628-2.42670.24021550.196326912846100
2.4267-2.4980.22471210.18662656277799
2.498-2.57860.22221580.18882676283499
2.5786-2.67070.22341470.18672643279099
2.6707-2.77750.23291610.18662691285299
2.7775-2.90380.2541460.18692622276899
2.9038-3.05660.1791400.183526712811100
3.0566-3.24780.22172020.18526122814100
3.2478-3.49810.19391360.17326832819100
3.4981-3.84920.19561370.16826512788100
3.8492-4.4040.17251230.14592720284399
4.404-5.54020.1751420.14332659280199
5.5402-26.52720.18961460.17222621276798
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)
13.0567-0.3412-0.90936.2797-2.20243.4068-0.0068-0.03350.13150.102-0.1166-0.2885-0.14740.43620.10630.1597-0.03570.01590.3612-0.1120.246447.8877-2.958.4705
23.3911-1.7461-0.70752.5268-0.35932.61540.1350.51270.2194-0.32720.1168-0.3657-0.46740.2187-0.16020.2392-0.08090.06050.2633-0.01090.210838.271710.12846.1218
32.26150.3836-0.01032.45280.11181.88570.01980.37030.3992-0.17110.04020.0793-0.4099-0.0899-0.03750.24770.00470.01160.15970.06760.214623.293114.187912.8916
43.592-0.65080.04752.876-0.14982.8124-0.06080.13530.02840.11190.00870.1927-0.1345-0.04740.03370.1669-0.0368-0.00370.12970.01390.13425.4695-5.908224.4898
53.02470.2948-1.85781.5703-0.29822.0744-0.2989-0.2254-0.5640.02250.0746-0.23010.40080.41610.1490.22620.0247-0.0110.26660.0010.27537.6658-18.173120.6869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 58 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 131 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 248 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 249 through 387 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 388 through 493 )A0

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