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- PDB-4pvz: Structure of yeast importin a bound to the membrane protein Nucle... -

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Basic information

Entry
Database: PDB / ID: 4pvz
TitleStructure of yeast importin a bound to the membrane protein Nuclear Localization Signal sequence of INM protein Heh2
Components
  • Importin subunit alpha
  • Inner nuclear membrane protein HEH2
KeywordsPROTEIN BINDING / ARMADILLO repeated structure / nuclear import adapter / importin beta / NLS-cargos
Function / homology
Function and homology information


nuclear membrane organization / proteasome localization / import into nucleus / NLS-dependent protein nuclear import complex / protein targeting to membrane / nuclear inner membrane / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nuclear periphery ...nuclear membrane organization / proteasome localization / import into nucleus / NLS-dependent protein nuclear import complex / protein targeting to membrane / nuclear inner membrane / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nuclear periphery / protein import into nucleus / disordered domain specific binding / nuclear envelope / chromatin binding / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Heh2/Src1-like / HeH/LEM domain / HeH/LEM domain / MAN1, winged-helix domain / Man1/Src1, C-terminal / Man1-Src1p-C-terminal domain / LEM/LEM-like domain superfamily / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily ...Heh2/Src1-like / HeH/LEM domain / HeH/LEM domain / MAN1, winged-helix domain / Man1/Src1, C-terminal / Man1-Src1p-C-terminal domain / LEM/LEM-like domain superfamily / 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 / Inner nuclear membrane protein HEH2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLokareddy, R.K. / Hapsari, A.R. / van Rheenen, M. / Bhardwaj, A. / Veenhoff, L.M. / Cingolani, C.
CitationJournal: Structure / Year: 2015
Title: Distinctive Properties of the Nuclear Localization Signals of Inner Nuclear Membrane Proteins Heh1 and Heh2.
Authors: Lokareddy, R.K. / Hapsari, R.A. / van Rheenen, M. / Pumroy, R.A. / Bhardwaj, A. / Steen, A. / Veenhoff, L.M. / Cingolani, G.
History
DepositionMar 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha
B: Importin subunit alpha
C: Inner nuclear membrane protein HEH2
D: Inner nuclear membrane protein HEH2


Theoretical massNumber of molelcules
Total (without water)103,5504
Polymers103,5504
Non-polymers00
Water4,990277
1
A: Importin subunit alpha
C: Inner nuclear membrane protein HEH2


Theoretical massNumber of molelcules
Total (without water)51,7752
Polymers51,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint2 kcal/mol
Surface area19830 Å2
MethodPISA
2
B: Importin subunit alpha
D: Inner nuclear membrane protein HEH2


Theoretical massNumber of molelcules
Total (without water)51,7752
Polymers51,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint8 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.470, 105.320, 224.990
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 / Karyopherin subunit alpha / Karyopherin-60 / Serine-rich RNA polymerase I suppressor protein


Mass: 46790.484 Da / Num. of mol.: 2 / Fragment: unp residues 88-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: KAP60, N1606, SRP1, YNL189W / Production host: Escherichia coli (E. coli) / References: UniProt: Q02821
#2: Protein/peptide Inner nuclear membrane protein HEH2 / Helix-extension-helix domain-containing protein 2


Mass: 4984.759 Da / Num. of mol.: 2 / Fragment: unp residues 100-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: D8035.2, HEH2, YDR458C / Production host: Escherichia coli (E. coli) / References: UniProt: Q03281
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM ammonium acetate, 20% PEG 8000, 100 mM BisTris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X6A10.97
SYNCHROTRONNSLS X29A21.07
Detector
TypeIDDetectorDate
ADSC QUANTUM 270r1CCDJun 21, 2012
ADSC QUANTUM 315r2CCDSep 20, 2012
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.071
ReflectionResolution: 2.5→50 Å / Num. all: 40670 / Num. obs: 40670 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 35.2 Å2 / Rsym value: 0.088 / Net I/σ(I): 22.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.522 / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EE5

1ee5


Resolution: 2.5→30.545 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 2020 5 %
Rwork0.1907 --
obs0.1925 40406 96.85 %
all-40670 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→30.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7002 0 0 277 7279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067108
X-RAY DIFFRACTIONf_angle_d0.9819639
X-RAY DIFFRACTIONf_dihedral_angle_d15.222709
X-RAY DIFFRACTIONf_chiral_restr0.0411134
X-RAY DIFFRACTIONf_plane_restr0.0051246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.31591280.27392689X-RAY DIFFRACTION97
2.5625-2.63170.3291570.26572671X-RAY DIFFRACTION96
2.6317-2.70910.28951470.25322674X-RAY DIFFRACTION97
2.7091-2.79650.2911270.23452626X-RAY DIFFRACTION95
2.7965-2.89640.31611350.23812708X-RAY DIFFRACTION96
2.8964-3.01230.25961540.22752641X-RAY DIFFRACTION95
3.0123-3.14920.23731510.22242620X-RAY DIFFRACTION93
3.1492-3.31510.25881230.21322632X-RAY DIFFRACTION93
3.3151-3.52250.24591290.2062747X-RAY DIFFRACTION97
3.5225-3.7940.22751620.18172783X-RAY DIFFRACTION99
3.794-4.1750.18781530.15812821X-RAY DIFFRACTION100
4.175-4.77710.17271490.14832848X-RAY DIFFRACTION100
4.7771-6.01110.20931500.17112899X-RAY DIFFRACTION100
6.0111-30.54770.16161550.14573027X-RAY DIFFRACTION99
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)
12.7588-0.38441.23431.7958-1.3544.78510.1236-0.0411-0.43430.09550.11240.07251.0284-0.1981-0.19870.66-0.0157-0.04120.34930.020.2794-10.1692-0.285110.0721
20.6124-0.00730.80631.55650.14784.3237-0.0549-0.0624-0.0450.04430.0154-0.06190.16110.20880.01770.10880.01470.01290.2028-0.00670.2518-11.923914.010273.4854
34.4636-0.31461.38023.3551.1644.00770.0720.3544-0.1734-0.8922-0.040.98620.3126-0.62640.07540.4564-0.03-0.18320.4372-0.09350.5229-28.924110.812950.7752
44.77840.7229-0.08152.7735-1.32094.32850.04670.39580.22-0.4256-0.07840.4212-0.5115-0.32020.07020.39530.094-0.07910.268-0.00790.3376-30.6508-4.450723.6698
52.7479-0.47920.17673.3516-1.00732.4907-0.04610.0180.0321-0.0737-0.0586-0.1243-0.17540.17470.10050.1396-0.0201-0.01970.1971-0.00260.2151-18.9341-16.194834.8245
61.6649-0.24320.81271.84760.70623.6335-0.12650.04010.26340.15420.0555-0.2036-0.18660.38720.04520.1397-0.0207-0.01780.22910.00730.3393-0.9218-16.033255.418
72.37560.3587-0.07173.7621-0.24243.8877-0.0652-1.0557-0.54631.77950.1769-0.05830.61470.2455-0.14631.23470.2015-0.0780.64710.08420.4454-1.6062-19.941684.395
84.2345-2.62432.59484.6899-2.13965.33530.275-0.6021-0.2866-0.17810.05870.62270.297-0.6408-0.33730.24550.046-0.01140.2944-0.0120.3543-24.721214.3872.8939
92.22342.07270.42832.612-1.27514.16290.33580.238-0.4981-0.00950.67440.28571.358-0.3287-1.14231.6144-0.32870.06521.16090.1421.3126-18.5406-1.133876.9282
103.23070.38171.22491.6331-1.14425.7795-0.16011.330.2376-1.0728-0.1661-0.10741.1030.80970.34961.09630.0012-0.05710.775-0.05010.5547-7.3074-3.341695.1336
117.9846-0.85670.88958.5519-0.90438.8937-0.1047-0.163-0.3610.50960.15841.7154-0.0233-1.6918-0.08310.42760.0198-0.01080.53990.03640.5052-9.1951-23.086764.2679
123.0019-1.0010.62933.6826-4.07774.7234-0.45470.10350.8121.236-0.3852-1.2485-1.69311.22260.87170.5782-0.1614-0.15120.3692-0.01150.4786-19.6982-4.157240.2356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 88 through 251 )
2X-RAY DIFFRACTION2chain 'A' and (resid 252 through 441 )
3X-RAY DIFFRACTION3chain 'A' and (resid 442 through 509 )
4X-RAY DIFFRACTION4chain 'B' and (resid 88 through 158 )
5X-RAY DIFFRACTION5chain 'B' and (resid 159 through 251 )
6X-RAY DIFFRACTION6chain 'B' and (resid 252 through 396 )
7X-RAY DIFFRACTION7chain 'B' and (resid 397 through 509 )
8X-RAY DIFFRACTION8chain 'C' and (resid 97 through 106 )
9X-RAY DIFFRACTION9chain 'C' and (resid 107 through 118 )
10X-RAY DIFFRACTION10chain 'C' and (resid 119 through 131 )
11X-RAY DIFFRACTION11chain 'D' and (resid 100 through 108 )
12X-RAY DIFFRACTION12chain 'D' and (resid 109 through 131 )

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