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- PDB-9y0r: Importin alpha 2 in complex with ATF2 basic region -

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Basic information

Entry
Database: PDB / ID: 9y0r
TitleImportin alpha 2 in complex with ATF2 basic region
Components
  • Cyclic AMP-dependent transcription factor ATF-2
  • Importin subunit alpha-1
KeywordsPROTEIN TRANSPORT / Importin / ATF2 / bZIP / Complex / AP-1
Function / homology
Function and homology information


abducens nucleus development / hypoglossal nucleus development / detection of cell density / H4 histone acetyltransferase complex / growth plate cartilage chondrocyte proliferation / facial nucleus development / growth plate cartilage chondrocyte differentiation / positive regulation of cardiac muscle myoblast proliferation / positive regulation of transforming growth factor beta2 production / cellular response to anisomycin ...abducens nucleus development / hypoglossal nucleus development / detection of cell density / H4 histone acetyltransferase complex / growth plate cartilage chondrocyte proliferation / facial nucleus development / growth plate cartilage chondrocyte differentiation / positive regulation of cardiac muscle myoblast proliferation / positive regulation of transforming growth factor beta2 production / cellular response to anisomycin / cAMP response element binding / leucine zipper domain binding / cAMP response element binding protein binding / histone H2B acetyltransferase activity / positive regulation of mitochondrial membrane permeability involved in apoptotic process / brainstem development / cellular response to leucine starvation / Sensing of DNA Double Strand Breaks / NK T cell differentiation / entry of viral genome into host nucleus through nuclear pore complex via importin / vacuole organization / positive regulation of viral life cycle / histone H4 acetyltransferase activity / neurofilament cytoskeleton organization / apoptotic process involved in development / NGF-stimulated transcription / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / intrinsic apoptotic signaling pathway in response to hypoxia / mitotic intra-S DNA damage checkpoint signaling / nuclear import signal receptor activity / motor neuron apoptotic process / response to osmotic stress / hepatocyte apoptotic process / Activation of the AP-1 family of transcription factors / p38MAPK cascade / outflow tract morphogenesis / white fat cell differentiation / peptidyl-threonine phosphorylation / Response of EIF2AK4 (GCN2) to amino acid deficiency / adipose tissue development / BMP signaling pathway / positive regulation of DNA-binding transcription factor activity / hematopoietic progenitor cell differentiation / histone acetyltransferase activity / cis-regulatory region sequence-specific DNA binding / JNK cascade / transcription initiation-coupled chromatin remodeling / negative regulation of angiogenesis / Regulation of PTEN gene transcription / RNA polymerase II transcription regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of DNA Repair Genes / mRNA transcription by RNA polymerase II / promoter-specific chromatin binding / liver development / Heme signaling / Transcriptional activation of mitochondrial biogenesis / cellular response to virus / lipid metabolic process / RNA polymerase II transcription regulator complex / : / cytoplasmic stress granule / protein import into nucleus / sequence-specific double-stranded DNA binding / site of double-strand break / host cell / HATs acetylate histones / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / Estrogen-dependent gene expression / in utero embryonic development / mitochondrial outer membrane / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / postsynaptic density / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / DNA damage response / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / regulation of DNA-templated transcription / chromatin / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription factor cyclic AMP-dependent, CRE-BP1-type / : / bZIP transcription factor / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. ...Transcription factor cyclic AMP-dependent, CRE-BP1-type / : / bZIP transcription factor / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Cyclic AMP-dependent transcription factor ATF-2 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGhafoori, S.M. / Forwood, J.K.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: Importin alpha 2 in complex with ATF2 basic region
Authors: Ghafoori, S.M. / Forwood, J.K.
History
DepositionAug 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin subunit alpha-1
B: Cyclic AMP-dependent transcription factor ATF-2


Theoretical massNumber of molelcules
Total (without water)58,6952
Polymers58,6952
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint3 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.611, 90.120, 100.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Importin subunit alpha-1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 55268.473 Da / Num. of mol.: 1 / Fragment: UNP residues 70-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide Cyclic AMP-dependent transcription factor ATF-2 / cAMP-dependent transcription factor ATF-2 / Activating transcription factor 2 / Cyclic AMP- ...cAMP-dependent transcription factor ATF-2 / Activating transcription factor 2 / Cyclic AMP-responsive element-binding protein 2 / CREB-2 / cAMP-responsive element-binding protein 2 / HB16 / cAMP response element-binding protein CRE-BP1


Mass: 3427.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15336
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: sodium citrate 0.7 M, 0.1 M HEPES, 10 mM DTT, pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→29.62 Å / Num. obs: 37013 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 33.41 Å2 / Rpim(I) all: 0.071 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.7 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 16439 / Rpim(I) all: 0.799

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.62 Å / SU ML: 0.2364 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6707
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2216 1856 5.03 %
Rwork0.1913 35069 -
obs0.1928 36925 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.56 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 0 226 3564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223414
X-RAY DIFFRACTIONf_angle_d0.50274644
X-RAY DIFFRACTIONf_chiral_restr0.0348555
X-RAY DIFFRACTIONf_plane_restr0.0039592
X-RAY DIFFRACTIONf_dihedral_angle_d3.749455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.29221270.25882653X-RAY DIFFRACTION99.68
2.26-2.330.28091330.24062665X-RAY DIFFRACTION99.82
2.33-2.40.27831370.2342681X-RAY DIFFRACTION99.89
2.4-2.490.28921500.21752646X-RAY DIFFRACTION99.93
2.49-2.590.26051290.20932675X-RAY DIFFRACTION99.93
2.59-2.70.25191360.22452675X-RAY DIFFRACTION99.93
2.7-2.850.22241450.20082684X-RAY DIFFRACTION99.93
2.85-3.020.23111430.19832682X-RAY DIFFRACTION99.93
3.02-3.260.24591500.20642683X-RAY DIFFRACTION99.82
3.26-3.580.21041580.19262682X-RAY DIFFRACTION99.82
3.59-4.10.20411500.16422727X-RAY DIFFRACTION99.83
4.1-5.160.19051460.15412748X-RAY DIFFRACTION99.86
5.16-29.620.1911520.18522868X-RAY DIFFRACTION99.54

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