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- PDB-2qna: Crystal structure of human Importin-beta (127-876) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2qna
TitleCrystal structure of human Importin-beta (127-876) in complex with the IBB-domain of Snurportin1 (1-65)
Components
  • Importin subunit beta-1
  • Snurportin-1SPN1
KeywordsTRANSPORT PROTEIN / Nuclear transport / import of spliceosomal subunits / protein-protein interaction / HEAT-repeat protein / Host-virus interaction / Nucleus / Protein transport / RNA-binding
Function / homology
Function and homology information


RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / establishment of mitotic spindle localization / astral microtubule organization / RNA cap binding / snRNA import into nucleus / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / establishment of mitotic spindle localization / astral microtubule organization / RNA cap binding / snRNA import into nucleus / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / ribosomal protein import into nucleus / importin-alpha family protein binding / NS1 Mediated Effects on Host Pathways / Initiation of Nuclear Envelope (NE) Reformation / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / mitotic metaphase chromosome alignment / mitotic spindle assembly / nuclear pore / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / ISG15 antiviral mechanism / small GTPase binding / cytoplasmic stress granule / protein import into nucleus / specific granule lumen / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nuclear envelope / snRNP Assembly / nuclear membrane / ficolin-1-rich granule lumen / protein domain specific binding / Neutrophil degranulation / enzyme binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain ...Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Importin-alpha, importin-beta-binding domain / IBB domain profile. / HEAT repeat profile. / HEAT, type 2 / 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
Snurportin-1 / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.84 Å
AuthorsWohlwend, D. / Strasser, A. / Dickmanns, A. / Ficner, R.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural basis for RanGTP independent entry of spliceosomal U snRNPs into the nucleus.
Authors: Wohlwend, D. / Strasser, A. / Dickmanns, A. / Ficner, R.
History
DepositionJul 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit beta-1
B: Snurportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4374
Polymers92,2452
Non-polymers1922
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-19.2 kcal/mol
Surface area36220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.220, 79.070, 208.460
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 beta-1 / / Karyopherin subunit beta-1 / Nuclear factor P97 / Importin 90


Mass: 84567.398 Da / Num. of mol.: 1 / Fragment: residues 127-876
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNB1, NTF97 / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q14974
#2: Protein Snurportin-1 / SPN1 / RNA U transporter 1


Mass: 7677.634 Da / Num. of mol.: 1 / Fragment: residues 1-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNUPN, RNUT1, SPN1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: O95149
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.91 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.55
Details: sodium citrate, Ammonium SO4, Ethanol, NaCl, Tris, pH 5.55, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 13, 2007
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.84→3104.26 Å / Num. obs: 25868 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.82 % / Rmerge(I) obs: 0.192 / Net I/σ(I): 9.18
Reflection shellResolution: 2.84→2.92 Å / Redundancy: 4.92 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2.55 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.3.0008refinement
PDB_EXTRACT3data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→15 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.821 / SU B: 34.556 / SU ML: 0.312 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 30.298 / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28247 1304 5.1 %RANDOM
Rwork0.23279 ---
obs0.23526 24343 99.99 %-
all-25868 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2--2.59 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.84→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6030 0 10 50 6090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226128
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8811.9788308
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8875771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02125.607280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.688151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2281531
X-RAY DIFFRACTIONr_chiral_restr0.0570.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024568
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1710.23010
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2840.24319
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0880.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2071.53979
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.37626228
X-RAY DIFFRACTIONr_scbond_it0.27332402
X-RAY DIFFRACTIONr_scangle_it0.4724.52080
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.84→2.911 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 93 -
Rwork0.307 1737 -
obs--100 %
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)
10.40180.2511-0.17940.7817-0.52730.3560.0372-0.0425-0.009-0.0342-0.00170.00560.03820.0935-0.0355-0.02820.0119-0.01440.00130.0001-0.0547-42.3958-0.8452-11.6393
20.4067-0.18290.20991.71721.26061.23120.0183-0.0048-0.02710.0355-0.00170.02930.0025-0.0495-0.0166-0.0866-0.01590.0285-0.04070.0138-0.0429-6.4843-5.5173-43.9141
31.2896-1.73-2.06162.60283.71366.48280.14940.14-0.1922-0.0515-0.0090.242-0.4459-1.3351-0.14040.0122-0.0295-0.03710.00540.02030.0303-15.442-1.7826-41.5629
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA126 - 5641 - 439
2X-RAY DIFFRACTION2AA577 - 881452 - 756
3X-RAY DIFFRACTION3BB37 - 6637 - 66

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