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- PDB-5d5k: Crystal Structure NLS from human PARP-2 complexed with Importin a... -

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Basic information

Entry
Database: PDB / ID: 5d5k
TitleCrystal Structure NLS from human PARP-2 complexed with Importin alpha delta IBB
Components
  • Importin subunit alpha-1
  • Poly [ADP-ribose] polymerase 2
KeywordsPROTON TRANSPORT / PARP-2 NLS / PARP-2 / poly(ADP-ribose)polymerase-2 / Importin alpha
Function / homology
Function and homology information


response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / Sensing of DNA Double Strand Breaks / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / regulation of transcription by glucose / DNA ADP-ribosylation / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle ...response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / Sensing of DNA Double Strand Breaks / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / regulation of transcription by glucose / DNA ADP-ribosylation / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / poly-ADP-D-ribose modification-dependent protein binding / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / HDR through MMEJ (alt-NHEJ) / hippocampal neuron apoptotic process / NAD+ ADP-ribosyltransferase / nuclear import signal receptor activity / protein auto-ADP-ribosylation / nuclear localization sequence binding / NLS-bearing protein import into nucleus / NAD+-protein-aspartate ADP-ribosyltransferase activity / non-canonical NF-kappaB signal transduction / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / DNA repair-dependent chromatin remodeling / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / POLB-Dependent Long Patch Base Excision Repair / NAD+ poly-ADP-ribosyltransferase activity / nucleosome binding / site of DNA damage / extrinsic apoptotic signaling pathway / positive regulation of type I interferon production / nucleotidyltransferase activity / base-excision repair / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / histone deacetylase binding / Formation of Incision Complex in GG-NER / cytoplasmic stress granule / protein import into nucleus / double-strand break repair / host cell / nuclear membrane / DNA-binding transcription factor binding / damaged DNA binding / postsynaptic density / DNA repair / DNA damage response / chromatin binding / positive regulation of DNA-templated transcription / nucleolus / glutamatergic synapse / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. ...: / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / 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. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Poly(ADP-ribose) polymerase catalytic domain / Leucine-rich Repeat Variant / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Poly [ADP-ribose] polymerase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRiccio, A.A. / Cingolani, G. / Pascal, J.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R0GM1087282 United States
American Cancer SocietyRSG0918301 United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: PARP-2 domain requirements for DNA damage-dependent activation and localization to sites of DNA damage.
Authors: Riccio, A.A. / Cingolani, G. / Pascal, J.M.
History
DepositionAug 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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
C: Importin subunit alpha-1
B: Poly [ADP-ribose] polymerase 2


Theoretical massNumber of molelcules
Total (without water)61,2342
Polymers61,2342
Non-polymers00
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint2 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.640, 89.980, 100.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 50461.285 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 Poly [ADP-ribose] polymerase 2 / hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / NAD(+) ADP-ribosyltransferase 2 ...hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / NAD(+) ADP-ribosyltransferase 2 / ADPRT-2 / Poly[ADP-ribose] synthase 2 / pADPRT-2


Mass: 10773.156 Da / Num. of mol.: 1 / Fragment: unp residues 1-78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP2, ADPRT2, ADPRTL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGN5, NAD+ ADP-ribosyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.6-0.7M sodium citrate, 0.1M sodium citrate buffer pH 5.6, and 7-10mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→45 Å / Num. all: 56617 / Num. obs: 56607 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.059 / Net I/av σ(I): 1.7 / Net I/σ(I): 20.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y2A

1y2a


Resolution: 1.9→42.344 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1705 2873 5.08 %Random selection
Rwork0.1504 ---
obs0.1514 56607 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→42.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 0 324 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013433
X-RAY DIFFRACTIONf_angle_d1.2694674
X-RAY DIFFRACTIONf_dihedral_angle_d13.8491270
X-RAY DIFFRACTIONf_chiral_restr0.074564
X-RAY DIFFRACTIONf_plane_restr0.007597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.93120.28581550.26622471X-RAY DIFFRACTION99
1.9312-1.96450.26911570.2272522X-RAY DIFFRACTION100
1.9645-2.00020.23271220.21012531X-RAY DIFFRACTION100
2.0002-2.03870.20541360.18512512X-RAY DIFFRACTION100
2.0387-2.08030.20081170.17042573X-RAY DIFFRACTION100
2.0803-2.12560.18421360.15892547X-RAY DIFFRACTION100
2.1256-2.1750.15311440.14982510X-RAY DIFFRACTION100
2.175-2.22940.1691370.14392560X-RAY DIFFRACTION100
2.2294-2.28970.17521090.12972564X-RAY DIFFRACTION100
2.2897-2.3570.15141560.12962524X-RAY DIFFRACTION100
2.357-2.43310.16791360.13712548X-RAY DIFFRACTION100
2.4331-2.52010.16421380.13062564X-RAY DIFFRACTION100
2.5201-2.62090.15561310.13432559X-RAY DIFFRACTION100
2.6209-2.74020.14391310.13812569X-RAY DIFFRACTION100
2.7402-2.88460.14961320.14122572X-RAY DIFFRACTION100
2.8846-3.06530.16861480.14342577X-RAY DIFFRACTION100
3.0653-3.30190.16651350.14912559X-RAY DIFFRACTION100
3.3019-3.6340.15241420.14862601X-RAY DIFFRACTION100
3.634-4.15950.14291360.13322596X-RAY DIFFRACTION100
4.1595-5.2390.15691190.1372665X-RAY DIFFRACTION100
5.239-42.35410.2141560.18612610X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4161-0.20310.40493.6533-1.49141.50190.10430.0183-0.1635-0.1141-0.0298-0.05470.2370.1232-0.06860.31220.0085-0.04540.27990.00470.2307-6.8284-2.6133116.3494
21.64711.0551-0.70432.2814-0.56272.07110.11150.10090.23490.0805-0.0201-0.0377-0.05910.0351-0.07770.20770.0166-0.00240.1978-0.00090.2520.596723.5805112.2733
32.31780.2777-0.90642.8173-0.54741.73930.03380.84470.3217-0.52720.17960.4282-0.0051-0.5050.38510.31290.007-0.0550.53640.16860.35267.834537.447582.0369
43.62122.1929-0.80672.7241.67455.88270.05820.33540.2267-0.20880.09210.3341.0186-1.0437-0.24370.5608-0.107-0.02520.69550.24750.7274-3.064132.585491.4959
53.4398-1.94752.97388.4242-3.14596.63980.04860.06880.2051-0.6303-0.0465-0.8498-0.22140.11290.00480.21910.01620.0540.33390.00520.25731.7614.6665109.5644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 73 through 202 )
2X-RAY DIFFRACTION2chain 'C' and (resid 203 through 322 )
3X-RAY DIFFRACTION3chain 'C' and (resid 323 through 496 )
4X-RAY DIFFRACTION4chain 'B' and (resid 18 through 23 )
5X-RAY DIFFRACTION5chain 'B' and (resid 34 through 40 )

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