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

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Basic information

Entry
Database: PDB / ID: 5xbk
TitleCrystal structure of human Importin4
Components
  • Importin-4
  • histone H3
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 / structural constituent of chromatin / nucleosome / protein heterodimerization activity / chromatin / protein-containing complex ...nuclear import signal receptor activity / nuclear localization sequence binding / protein localization to nucleus / small GTPase binding / protein import into nucleus / structural constituent of chromatin / nucleosome / protein heterodimerization activity / chromatin / protein-containing complex / DNA binding / nucleoplasm / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Histone H3.2 / Importin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.223 Å
AuthorsSong, J.J. / Yoon, J.
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 20, 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
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Importin-4
A: Importin-4
B: Importin-4
C: Importin-4
E: histone H3


Theoretical massNumber of molelcules
Total (without water)181,2915
Polymers181,2915
Non-polymers00
Water0
1
D: Importin-4


Theoretical massNumber of molelcules
Total (without water)44,8351
Polymers44,8351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Importin-4


Theoretical massNumber of molelcules
Total (without water)44,8351
Polymers44,8351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Importin-4
E: histone H3


Theoretical massNumber of molelcules
Total (without water)46,7852
Polymers46,7852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Importin-4


Theoretical massNumber of molelcules
Total (without water)44,8351
Polymers44,8351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.021, 108.536, 124.860
Angle α, β, γ (deg.)90.00, 103.41, 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: 44835.434 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)
References: UniProt: Q8TEX9
#2: Protein/peptide histone H3 /


Mass: 1949.286 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P84233*PLUS

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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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Sodium tartrate, PEG3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: CCD / Date: Sep 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 26893 / % possible obs: 99.2 % / Redundancy: 7.3 % / Biso Wilson estimate: 90.87 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 shellResolution: 3.2→3.36 Å / Mean I/σ(I) obs: 2.34 / Rsym value: 0.85 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XAH

5xah


Resolution: 3.223→49.977 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2809 2672 9.94 %
Rwork0.218 --
obs0.2246 26872 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.223→49.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11165 0 0 0 11165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411370
X-RAY DIFFRACTIONf_angle_d0.67215432
X-RAY DIFFRACTIONf_dihedral_angle_d16.3974191
X-RAY DIFFRACTIONf_chiral_restr0.0381834
X-RAY DIFFRACTIONf_plane_restr0.0042001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2231-3.28170.37411100.32351010X-RAY DIFFRACTION77
3.2817-3.34480.34981310.30281269X-RAY DIFFRACTION100
3.3448-3.4130.37791310.28041325X-RAY DIFFRACTION100
3.413-3.48720.32681480.2551277X-RAY DIFFRACTION100
3.4872-3.56830.34141410.24761286X-RAY DIFFRACTION100
3.5683-3.65760.27421200.24511294X-RAY DIFFRACTION100
3.6576-3.75640.31841450.24291308X-RAY DIFFRACTION100
3.7564-3.86690.28371530.23031285X-RAY DIFFRACTION100
3.8669-3.99170.311390.23061289X-RAY DIFFRACTION100
3.9917-4.13430.29551400.23211292X-RAY DIFFRACTION100
4.1343-4.29970.29461450.20981297X-RAY DIFFRACTION100
4.2997-4.49530.28761710.19691257X-RAY DIFFRACTION100
4.4953-4.73210.27211430.20031299X-RAY DIFFRACTION100
4.7321-5.02830.23111430.18441316X-RAY DIFFRACTION100
5.0283-5.41620.28881670.21151277X-RAY DIFFRACTION100
5.4162-5.96040.31381280.24311305X-RAY DIFFRACTION100
5.9604-6.8210.3271240.23761317X-RAY DIFFRACTION100
6.821-8.58670.23721440.19521276X-RAY DIFFRACTION97
8.5867-49.98320.23831490.18681221X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: -2.1702 Å / Origin y: -9.8608 Å / Origin z: -29.957 Å
111213212223313233
T0.7656 Å20.0449 Å2-0.0203 Å2-0.8207 Å20.0246 Å2--0.6987 Å2
L0.1931 °20.0203 °20.0116 °2-0.3459 °2-0.0062 °2--0.045 °2
S-0.0346 Å °0.0746 Å °-0.0051 Å °-0.0314 Å °0.0622 Å °0.0099 Å °-0.0492 Å °-0.0057 Å °-0.0221 Å °
Refinement TLS groupSelection details: all

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