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- PDB-2h4m: Karyopherin Beta2/Transportin-M9NLS -

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Basic information

Entry
Database: PDB / ID: 2h4m
TitleKaryopherin Beta2/Transportin-M9NLS
Components
  • Heterogeneous nuclear ribonucleoprotein A1
  • Transportin-1
KeywordsPROTEIN TRANSPORT / HEAT Repeat / Nuclear import complex
Function / homology
Function and homology information


cellular response to sodium arsenite / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / SARS-CoV-1-host interactions / import into nucleus / Intraflagellar transport / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus ...cellular response to sodium arsenite / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / SARS-CoV-1-host interactions / import into nucleus / Intraflagellar transport / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / miRNA binding / FGFR2 alternative splicing / nuclear import signal receptor activity / nuclear localization sequence binding / regulation of alternative mRNA splicing, via spliceosome / SARS-CoV-1 modulates host translation machinery / regulation of RNA splicing / negative regulation of telomere maintenance via telomerase / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / cellular response to glucose starvation / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / cilium / mRNA splicing, via spliceosome / small GTPase binding / protein import into nucleus / single-stranded DNA binding / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Importin beta family / hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / HEAT-like repeat / HEAT repeat / HEAT repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain ...Importin beta family / hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / HEAT-like repeat / HEAT repeat / HEAT 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein A1 / Transportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsChook, Y.M. / Cansizoglu, A.E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Rules for nuclear localization sequence recognition by karyopherin beta 2.
Authors: Lee, B.J. / Cansizoglu, A.E. / Louis, T.H. / Zhang, Z. / Chook, Y.M.
History
DepositionMay 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 14, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_auth_seq_num
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transportin-1
B: Transportin-1
C: Heterogeneous nuclear ribonucleoprotein A1
D: Heterogeneous nuclear ribonucleoprotein A1


Theoretical massNumber of molelcules
Total (without water)206,2054
Polymers206,2054
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.013, 154.093, 141.667
Angle α, β, γ (deg.)90.00, 91.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 98024.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNPO1, KPNB2, MIP1, TRN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q92973
#2: Protein/peptide Heterogeneous nuclear ribonucleoprotein A1 / hnRNP A1 / Helix-destabilizing protein / Single-strand RNA-binding protein / hnRNP core protein A1


Mass: 5078.303 Da / Num. of mol.: 2 / Fragment: RESIDUES: 309-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPA1, HNRPA1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P09651
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 40 mM MES pH 6.5, 3M potassium formate and 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. all: 62111 / Num. obs: 59061 / % possible obs: 95.1 %
Reflection shellResolution: 3.05→3.16 Å / % possible all: 0.7479

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-2000data reduction
PHASERphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QBK

1qbk


Resolution: 3.05→50 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.2502 2978 RANDOM
Rwork0.2385 --
all-62111 -
obs-59061 -
Refinement stepCycle: LAST / Resolution: 3.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12740 0 0 0 12740
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.14651
X-RAY DIFFRACTIONc_bond_d0.007744
X-RAY DIFFRACTIONc_dihedral_angle_d21.55765
X-RAY DIFFRACTIONc_improper_angle_d1.45309

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