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- PDB-3tpm: Crystal structure of MAL RPEL domain in complex with importin-alpha -

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Basic information

Entry
Database: PDB / ID: 3tpm
TitleCrystal structure of MAL RPEL domain in complex with importin-alpha
Components
  • Importin subunit alpha-2
  • MAL
KeywordsPROTEIN TRANSPORT/TRANSCRIPTION / nuclear import / PROTEIN TRANSPORT-TRANSCRIPTION complex
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / protein import into nucleus / cytoplasmic stress granule / host cell / DNA-binding transcription factor binding ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / protein import into nucleus / cytoplasmic stress granule / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / cytosol
Similarity search - Function
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 ...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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHirano, H. / Matsuura, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Sensing actin dynamics: structural basis for G-actin-sensitive nuclear import of MAL
Authors: Hirano, H. / Matsuura, Y.
History
DepositionSep 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 1, 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

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Assembly

Deposited unit
A: Importin subunit alpha-2
B: MAL


Theoretical massNumber of molelcules
Total (without water)59,8572
Polymers59,8572
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint0 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.658, 90.116, 98.853
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Importin subunit alpha-2 / 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: 45799.469 Da / Num. of mol.: 1 / Fragment: ARM-repeat domain, UNP residues 75-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein MAL


Mass: 14057.305 Da / Num. of mol.: 1 / Fragment: RPEL domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mkl1 / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE UNP ENTRY FOR CHAIN B DOES NOT CURRENTLY EXIST.

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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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: 50mM Tris-HCl, 1.4M Li2SO4, pH 7.4, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Apr 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→43.34 Å / Num. obs: 41177 / % possible obs: 99 %
Reflection shellResolution: 2.1→2.21 Å / % possible all: 98

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IAL

1ial


Resolution: 2.1→41 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.007 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2097 5.1 %RANDOM
Rwork0.166 ---
obs0.1681 41135 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.7 Å2 / Biso mean: 48.1449 Å2 / Biso min: 20.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---1.7 Å20 Å2
3---2.52 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 0 279 3618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.023395
X-RAY DIFFRACTIONr_angle_refined_deg2.21.9734616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0455433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.58525.597134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7815602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4441514
X-RAY DIFFRACTIONr_chiral_restr0.1590.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212478
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 145 -
Rwork0.246 2614 -
all-2759 -
obs--97.42 %
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)
15.1711-3.22131.1156.1841-2.52538.72820.066-0.25790.22630.422-0.0459-0.3254-0.23190.0878-0.02020.1452-0.07410.05860.073-0.00090.1488-3.772358.9617-16.7966
22.226-0.0743-0.69244.2217-0.80441.21080.13510.06150.1386-0.03-0.036-0.0171-0.20010.1052-0.09910.0428-0.01260.0230.03540.00370.0166-7.690242.4645-15.5291
35.08680.77-2.47853.0401-0.05384.04920.02360.0424-0.129-0.129-0.0145-0.05590.0026-0.04-0.00910.03270.0191-0.02130.0161-0.0080.0416-1.927125.9455-15.3093
42.2491-0.05290.07893.7103-1.41473.63230.0692-0.0147-0.164-0.1257-0.00640.01990.09430.0022-0.06280.01690.0124-0.02410.0175-0.01370.08963.841616.7563-7.3239
52.05240.15430.54292.2266-0.76952.49080.0372-0.3375-0.12270.18350.04030.37310.0545-0.2838-0.07750.0339-0.00590.00820.10690.04230.15310.89228.400110.8481
63.4479-1.10130.814710.1680.20773.79060.0528-0.3674-0.10340.59530.02420.49740.0373-0.4165-0.07690.2623-0.0190.12530.50750.11270.32634.48065.494524.4955
75.83450.84980.765911.45932.23057.62450.2219-0.3277-0.41220.51990.0634-0.13410.3927-0.122-0.28540.5171-0.00830.00750.58710.13560.347113.92111.33931.9549
83.0612-1.58612.27159.63591.25762.4272-0.2494-0.40010.28930.65530.0030.1711-0.2451-0.41720.24640.65210.01160.17540.92590.11760.56980.94038.115634.438
90.91361.2776-5.86711.7888-8.227839.0585-0.14020.10010.0213-0.04860.07820.04340.7469-1.84450.0620.4759-0.28750.0841.179-0.07190.581-2.505110.76868.7001
108.95543.1581-3.882310.128-3.286812.63560.0191-0.3301-0.4153-0.073-0.4341-1.13090.1881.01080.4150.14440.0057-0.02460.1914-0.0030.17533.209240.6083-9.0828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 107
2X-RAY DIFFRACTION2A108 - 213
3X-RAY DIFFRACTION3A214 - 256
4X-RAY DIFFRACTION4A257 - 329
5X-RAY DIFFRACTION5A330 - 429
6X-RAY DIFFRACTION6A430 - 455
7X-RAY DIFFRACTION7A456 - 472
8X-RAY DIFFRACTION8A473 - 496
9X-RAY DIFFRACTION9B118 - 121
10X-RAY DIFFRACTION10B151 - 160

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