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- PDB-5j3v: Crystal structure of human Karyopherin-beta2 bound to the histone... -

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Basic information

Entry
Database: PDB / ID: 5j3v
TitleCrystal structure of human Karyopherin-beta2 bound to the histone H3 tail
Components
  • Histone H3
  • Transportin-1,Transportin-1
KeywordsTRANSPORT PROTEIN / Karyopherin / Importin / Transporting / Histone
Function / homology
Function and homology information


Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / small GTPase binding / cilium / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / protein import into nucleus / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Importin beta family / HEAT repeat / HEAT repeat / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...Importin beta family / HEAT repeat / HEAT repeat / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 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 / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Histone H3.1 / Transportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsSoniat, M. / Chook, Y.M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM069909 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01 GM98256-01 United States
Welch FoundationI-1532 United States
Leukemia & Lymphoma Society United States
The University of Texas Southwestern Endowed Scholars Program United States
CitationJournal: Structure / Year: 2016
Title: Karyopherin-beta 2 Recognition of a PY-NLS Variant that Lacks the Proline-Tyrosine Motif.
Authors: Soniat, M. / Chook, Y.M.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Structure summary / Category: pdbx_audit_support / struct
Item: _pdbx_audit_support.funding_organization / _struct.pdbx_descriptor
Revision 1.4Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Transportin-1,Transportin-1
C: Histone H3
B: Transportin-1,Transportin-1
D: Histone H3


Theoretical massNumber of molelcules
Total (without water)197,1104
Polymers197,1104
Non-polymers00
Water00
1
A: Transportin-1,Transportin-1
C: Histone H3


Theoretical massNumber of molelcules
Total (without water)98,5552
Polymers98,5552
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transportin-1,Transportin-1
D: Histone H3


Theoretical massNumber of molelcules
Total (without water)98,5552
Polymers98,5552
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.296, 154.185, 192.661
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Transportin-1,Transportin-1 / Importin beta-2 / Karyopherin beta-2 / M9 region interaction protein / MIP


Mass: 96766.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNPO1, KPNB2, MIP1, TRN / Production host: Escherichia coli (E. coli) / References: UniProt: Q92973
#2: Protein/peptide Histone H3


Mass: 1788.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P68431*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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 200 mM NaF, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 43618 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 13.2
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMR

2qmr


Resolution: 3.05→37.797 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 27
RfactorNum. reflection% reflection
Rfree0.2559 1990 4.99 %
Rwork0.2131 --
obs0.2153 39895 92.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.94 Å2 / Biso mean: 56.5453 Å2 / Biso min: 6.59 Å2
Refinement stepCycle: final / Resolution: 3.05→37.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13357 0 0 0 13357
Num. residues----1682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213633
X-RAY DIFFRACTIONf_angle_d0.71718501
X-RAY DIFFRACTIONf_chiral_restr0.0232131
X-RAY DIFFRACTIONf_plane_restr0.0042375
X-RAY DIFFRACTIONf_dihedral_angle_d10.8735130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.05-3.12630.3404510.29691032108335
3.1263-3.21070.32631060.28582116222274
3.2107-3.30520.351470.27312743289096
3.3052-3.41180.33031530.26192852300599
3.4118-3.53360.31191520.254528633015100
3.5336-3.6750.29081490.220529103059100
3.675-3.84210.27241500.219128923042100
3.8421-4.04440.23421510.204128863037100
4.0444-4.29750.22151540.191929113065100
4.2975-4.62880.25591510.184729033054100
4.6288-5.09360.23941560.189129163072100
5.0936-5.82830.24241590.214629163075100
5.8283-7.33430.2761540.230229673121100
7.3343-37.80010.1831570.17752998315598

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