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- PDB-5xah: Crystal structure of human Importin4 -

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Basic information

Entry
Database: PDB / ID: 5xah
TitleCrystal structure of human Importin4
ComponentsImportin-4
KeywordsPROTEIN TRANSPORT / Histone / Chromatin / Assembly
Function / homology
Function and homology information


nuclear import signal receptor activity / nuclear localization sequence binding / protein localization to nucleus / small GTPase binding / protein import into nucleus / chromatin / protein-containing complex / membrane / nucleus / cytoplasm
Similarity search - Function
Importin beta family / TOG domain / TOG / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 ...Importin beta family / TOG domain / TOG / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.004 Å
AuthorsSong, J.J. / Yoon, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF)2016R1A2B3006293,2016K1A1A2912057 Korea, Republic Of
Citation
Journal: J. Mol. Biol. / Year: 2018
Title: Integrative Structural Investigation on the Architecture of Human Importin4_Histone H3/H4_Asf1a Complex and Its Histone H3 Tail Binding
Authors: Yoon, J. / Kim, S.J. / An, S. / Cho, S. / Leitner, A. / Jung, T. / Aebersold, R. / Hebert, H. / Cho, U.S. / Song, J.J.
#1: Journal: To Be Published
Title: Structural insights into the Architecture of human Importin4_Histone H3/H4_Asfla complex and its histone H3 tail binding
Authors: Yoon, J. / Song, J.J.
History
DepositionMar 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin-4
B: Importin-4
C: Importin-4
D: Importin-4


Theoretical massNumber of molelcules
Total (without water)180,4674
Polymers180,4674
Non-polymers00
Water0
1
A: Importin-4


Theoretical massNumber of molelcules
Total (without water)45,1171
Polymers45,1171
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Importin-4


Theoretical massNumber of molelcules
Total (without water)45,1171
Polymers45,1171
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Importin-4


Theoretical massNumber of molelcules
Total (without water)45,1171
Polymers45,1171
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Importin-4


Theoretical massNumber of molelcules
Total (without water)45,1171
Polymers45,1171
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.920, 110.769, 126.820
Angle α, β, γ (deg.)90.00, 106.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Importin-4 / / Imp4 / Importin-4b / Imp4b / Ran-binding protein 4 / RanBP4


Mass: 45116.801 Da / Num. of mol.: 4 / Fragment: UNP residues 668-1081
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IPO4, IMP4B, RANBP4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8TEX9

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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: 2.41 Å3/Da / Density % sol: 48.87 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 291 K / Method: evaporation / Details: Sodium Tartrate, PEG3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.980001 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980001 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 33901 / % possible obs: 99.2 % / Redundancy: 7.3 % / Biso Wilson estimate: 76.14 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.041 / Rrim(I) all: 0.11 / Χ2: 3.232 / Net I/σ(I): 12.9 / Num. measured all: 247205
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.056.60.59916620.7980.2530.6521.32797.5
3.05-3.1170.5216470.8650.2120.5631.36996.6
3.11-3.1770.45816550.8710.1870.4951.3998.6
3.17-3.2370.39716800.8990.1620.431.56498
3.23-3.37.10.33916470.9220.1380.3671.49398.6
3.3-3.3870.26717040.9550.1090.2891.54598.6
3.38-3.467.10.22216530.9710.0890.241.85398.2
3.46-3.567.10.18517100.9760.0750.21.81899.2
3.56-3.667.20.15216670.9880.0610.1642.13998.5
3.66-3.787.20.12917120.9910.0520.142.11399.8
3.78-3.917.40.12216790.9910.0490.1322.62299.9
3.91-4.077.50.11117240.9930.0440.1192.388100
4.07-4.267.60.09617020.9950.0370.1032.675100
4.26-4.487.60.08717010.9950.0340.0933.061100
4.48-4.767.60.08417190.9950.0320.093.422100
4.76-5.137.60.08416960.9960.0320.093.808100
5.13-5.647.60.09617260.9950.0370.1034.267100
5.64-6.467.60.10117310.9950.0390.1095.33100
6.46-8.137.60.07717250.9980.030.0837.021100
8.13-507.20.0717610.9950.0280.07611.84899.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-20002000data scaling
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
HKL-2000data scaling
HKL-2000data scaling
HKLdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.004→46.623 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.39 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2803 6550 9.9 %
Rwork0.2257 --
obs0.2311 33887 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.004→46.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11259 0 0 0 11259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311473
X-RAY DIFFRACTIONf_angle_d0.73915583
X-RAY DIFFRACTIONf_dihedral_angle_d2.9727041
X-RAY DIFFRACTIONf_chiral_restr0.041848
X-RAY DIFFRACTIONf_plane_restr0.0052024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0044-3.03850.42061770.3881442X-RAY DIFFRACTION72
3.0385-3.07420.37722200.35582023X-RAY DIFFRACTION96
3.0742-3.11170.36432000.33281908X-RAY DIFFRACTION97
3.1117-3.15110.43591980.31891994X-RAY DIFFRACTION98
3.1511-3.19260.38552440.34191965X-RAY DIFFRACTION98
3.1926-3.23630.37052230.30861936X-RAY DIFFRACTION96
3.2363-3.28250.38982230.29682042X-RAY DIFFRACTION98
3.2825-3.33150.32782010.29681968X-RAY DIFFRACTION98
3.3315-3.38350.3782120.29581999X-RAY DIFFRACTION98
3.3835-3.4390.3662340.26541947X-RAY DIFFRACTION97
3.439-3.49830.32531920.26691998X-RAY DIFFRACTION99
3.4983-3.56190.32142090.28162052X-RAY DIFFRACTION98
3.5619-3.63030.29371910.24642008X-RAY DIFFRACTION98
3.6303-3.70440.28772690.25191932X-RAY DIFFRACTION100
3.7044-3.78490.30731990.23082065X-RAY DIFFRACTION99
3.7849-3.87290.28992370.22941995X-RAY DIFFRACTION99
3.8729-3.96970.27182130.21932014X-RAY DIFFRACTION100
3.9697-4.0770.27762230.2162050X-RAY DIFFRACTION100
4.077-4.19690.27532280.21231983X-RAY DIFFRACTION100
4.1969-4.33230.23552160.2062061X-RAY DIFFRACTION100
4.3323-4.4870.25152380.20551993X-RAY DIFFRACTION100
4.487-4.66650.27752340.21432041X-RAY DIFFRACTION100
4.6665-4.87870.28432440.20592004X-RAY DIFFRACTION100
4.8787-5.13560.2882220.21642016X-RAY DIFFRACTION100
5.1356-5.45690.27272530.23692016X-RAY DIFFRACTION100
5.4569-5.87740.31732080.23652063X-RAY DIFFRACTION100
5.8774-6.46750.31932100.2412020X-RAY DIFFRACTION100
6.4675-7.40020.24442300.19842010X-RAY DIFFRACTION100
7.4002-9.31130.19372100.14412051X-RAY DIFFRACTION100
9.3113-46.62860.1961920.17622028X-RAY DIFFRACTION99

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