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- PDB-2qmr: Karyopherin beta2/transportin -

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Basic information

Entry
Database: PDB / ID: 2qmr
TitleKaryopherin beta2/transportin
ComponentsTransportin-1
KeywordsTRANSPORT PROTEIN / HEAT REPEAT / Cytoplasm / Host-virus interaction / Nucleus / Polymorphism / Protein transport / Transport
Function / homology
Function and homology information


Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / cilium / small GTPase binding / protein import into nucleus / RNA binding / extracellular exosome ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / cilium / small GTPase binding / protein import into nucleus / RNA binding / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Importin beta family / HEAT repeat / HEAT repeat / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...Importin beta family / HEAT repeat / HEAT repeat / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCansizoglu, A.E. / Chook, Y.M.
CitationJournal: Structure / Year: 2007
Title: Conformational heterogeneity of karyopherin beta2 is segmental
Authors: Cansizoglu, A.E. / Chook, Y.M.
History
DepositionJul 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transportin-1
B: Transportin-1
C: Transportin-1
D: Transportin-1


Theoretical massNumber of molelcules
Total (without water)405,6344
Polymers405,6344
Non-polymers00
Water0
1
A: Transportin-1


Theoretical massNumber of molelcules
Total (without water)101,4081
Polymers101,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transportin-1


Theoretical massNumber of molelcules
Total (without water)101,4081
Polymers101,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Transportin-1


Theoretical massNumber of molelcules
Total (without water)101,4081
Polymers101,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Transportin-1


Theoretical massNumber of molelcules
Total (without water)101,4081
Polymers101,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.338, 168.892, 140.958
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22C
13A
23D
14B
24C
15A
25D
16B
26C

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROILEILEAA7 - 1627 - 162
21PROPROILEILEDD7 - 1627 - 162
12GLNGLNASPASPBB30 - 15830 - 158
22GLNGLNASPASPCC30 - 15830 - 158
13ARGARGASNASNAA170 - 557170 - 557
23ARGARGASNASNDD170 - 557170 - 557
14ARGARGASNASNBB170 - 557170 - 557
24ARGARGASNASNCC170 - 557170 - 557
15TYRTYRVALVALAA604 - 890604 - 890
25TYRTYRVALVALDD604 - 890604 - 890
16TYRTYRVALVALBB604 - 890604 - 890
26TYRTYRVALVALCC604 - 890604 - 890

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Transportin-1 / Importin beta-2 / Karyopherin beta-2 / M9 region interaction protein / MIP


Mass: 101408.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNPO1, KPNB2, MIP1, TRN / Plasmid: pGEXTEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92973

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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: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.2 M potassium formate, 0.1 M HEPES pH 7.5 and 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 126673 / Redundancy: 5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 24

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2h4m

2h4m


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.894 / SU B: 19.491 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R: 1.189 / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28575 6073 5 %RANDOM
Rwork0.26059 ---
obs0.26185 114642 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.183 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å23.26 Å2
2--0.61 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25774 0 0 0 25774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02226327
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.97235804
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6953284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.74124.9781139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.944154533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.86915118
X-RAY DIFFRACTIONr_chiral_restr0.0790.24141
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219714
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.213166
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.218400
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2621
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.2181
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5081.516942
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.905226700
X-RAY DIFFRACTIONr_scbond_it0.848310526
X-RAY DIFFRACTIONr_scangle_it1.4584.59104
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1075tight positional0.020.05
21B941tight positional0.020.05
31A2716tight positional0.040.05
41B2696tight positional0.030.05
51A2271tight positional0.030.05
61B2271tight positional0.030.05
12A1075tight thermal5.320.5
22B941tight thermal4.80.5
32A2716tight thermal2.390.5
42B2696tight thermal4.110.5
52A2271tight thermal2.860.5
62B2271tight thermal2.860.5
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 438 -
Rwork0.328 8433 -
obs--100 %

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