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- PDB-4jlq: Crystal structure of human Karyopherin-beta2 bound to the PY-NLS ... -

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Basic information

Entry
Database: PDB / ID: 4jlq
TitleCrystal structure of human Karyopherin-beta2 bound to the PY-NLS of Saccharomyces cerevisiae NAB2
Components
  • Nuclear polyadenylated RNA-binding protein NAB2
  • Transportin-1
KeywordsTRANSPORT PROTEIN / HEAT REPEATS / KARYOPHERIN / NUCLEAR IMPORT / PROTEINTRANSPORT / IMPORTIN / TRANSPORTIN / NLS / NAB2 / Structural genomics / NUCLEOCYTOPLASMIC TRANSPORT: A TARGET FOR CELLULAR CONTROL (NPCXSTALS) / New York Structural Genomics Research Consortium (NYSGRC) / PSI-Biology / NPCXstals
Function / homology
Function and homology information


spliceosome-depend formation of circular RNA / ribonuclease P RNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / 7S RNA binding / poly(A) binding / nuclear localization sequence binding / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity ...spliceosome-depend formation of circular RNA / ribonuclease P RNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / 7S RNA binding / poly(A) binding / nuclear localization sequence binding / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / positive regulation of transcription by RNA polymerase III / poly(A)+ mRNA export from nucleus / regulation of mRNA stability / small GTPase binding / protein import into nucleus / 5S rRNA binding / tRNA binding / cilium / mRNA binding / nucleolus / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear abundant poly(A) RNA-binding protein Nab2, N-terminal / Nuclear polyadenylated RNA-binding 2 protein, CCCH zinc finger 1 / Nab2/ZC3H14, N-terminal domain superfamily / : / : / Nuclear abundant poly(A) RNA-bind protein 2 (Nab2) / Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1 / RNA-binding, Nab2-type zinc finger / Nab2-type CCCH zinc finger 4 / Nuclear polyadenylated RNA-binding protein Nab2/ZC3H14 ...Nuclear abundant poly(A) RNA-binding protein Nab2, N-terminal / Nuclear polyadenylated RNA-binding 2 protein, CCCH zinc finger 1 / Nab2/ZC3H14, N-terminal domain superfamily / : / : / Nuclear abundant poly(A) RNA-bind protein 2 (Nab2) / Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1 / RNA-binding, Nab2-type zinc finger / Nab2-type CCCH zinc finger 4 / Nuclear polyadenylated RNA-binding protein Nab2/ZC3H14 / RNA-binding, Nab2-type zinc finger / Importin beta family / HEAT-like repeat / HEAT repeat / HEAT repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Nuclear polyadenylated RNA-binding protein NAB2 / Transportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsSampathkumar, P. / Gizzi, A. / Rout, M.P. / Chook, Y.M. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals)
CitationJournal: J.Struct.Funct.Genom. / Year: 2013
Title: Crystal structure of human Karyopherin beta 2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2.
Authors: Soniat, M. / Sampathkumar, P. / Collett, G. / Gizzi, A.S. / Banu, R.N. / Bhosle, R.C. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / ...Authors: Soniat, M. / Sampathkumar, P. / Collett, G. / Gizzi, A.S. / Banu, R.N. / Bhosle, R.C. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Love, J.D. / Matikainen, B. / Seidel, R.D. / Toro, R. / Rajesh Kumar, P. / Bonanno, J.B. / Chook, Y.M. / Almo, S.C.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionApr 3, 2013ID: 4H1K
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 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
B: Nuclear polyadenylated RNA-binding protein NAB2


Theoretical massNumber of molelcules
Total (without water)100,7902
Polymers100,7902
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-6 kcal/mol
Surface area37360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.234, 172.383, 68.443
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a 1:1 complex of HsKapBeta2 and ScNAB2-PY-NLS

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Components

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


Mass: 96766.773 Da / Num. of mol.: 1 / Fragment: UNP residues 9-331 and 375-898
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNB2, MIP1, TNPO1, TRN / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q92973
#2: Protein/peptide Nuclear polyadenylated RNA-binding protein NAB2


Mass: 4023.457 Da / Num. of mol.: 1 / Fragment: UNP residues 205-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: NAB2, YGL122C / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: P32505
Sequence detailsTHE AUTHORS STATE THAT RESIDUES 337 TO 367 WERE REPLACED WITH GGSGGSG

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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: 3.88 Å3/Da / Density % sol: 68.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: CRYSTALLIZATION CONDITIONS: PROTEIN (20 MM HEPES, PH 7.3, 110 MM POTASSIUM ACETATE, 2MM MAGNESIUM ACETATE, 20% GLYCEROL, 2MM DTT); RESERVOIR (MCSG3 #95: 0.7 M SODIUM CITRATE TRIBASIC, 100MM ...Details: CRYSTALLIZATION CONDITIONS: PROTEIN (20 MM HEPES, PH 7.3, 110 MM POTASSIUM ACETATE, 2MM MAGNESIUM ACETATE, 20% GLYCEROL, 2MM DTT); RESERVOIR (MCSG3 #95: 0.7 M SODIUM CITRATE TRIBASIC, 100MM BIS-TRISPROPANTE pH 7.0); CRYOPROTECTION (20% GLYCEROL), temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2011 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 30914 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rsym value: 0.123 / Net I/σ(I): 16.6
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.18 / Num. unique all: 1536 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0025refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QMR and 4FDD

2qmr

4fdd


Resolution: 3.05→47.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.868 / SU ML: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.007 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1538 5 %RANDOM
Rwork0.1841 ---
obs0.1867 30636 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 195.84 Å2 / Biso mean: 104.7336 Å2 / Biso min: 61.18 Å2
Baniso -1Baniso -2Baniso -3
1--2.82 Å20 Å20 Å2
2--2.89 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 3.05→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6733 0 0 0 6733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196877
X-RAY DIFFRACTIONr_bond_other_d0.0010.026683
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9769344
X-RAY DIFFRACTIONr_angle_other_deg0.847315401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5825844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.32725.146309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1631532
X-RAY DIFFRACTIONr_chiral_restr0.0790.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217706
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021506
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 127 -
Rwork0.318 2097 -
all-2224 -
obs--99.96 %

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