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- PDB-3w3z: Crystal structure of Kap121p bound to RanGTP -

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Basic information

Entry
Database: PDB / ID: 3w3z
TitleCrystal structure of Kap121p bound to RanGTP
Components
  • GTP-binding nuclear protein Ran
  • Importin subunit beta-3
KeywordsPROTEIN TRANSPORT/NUCLEAR PROTEIN / HEAT repeat / nuclear import / PROTEIN TRANSPORT-NUCLEAR PROTEIN complex
Function / homology
Function and homology information


regulation of protein desumoylation / pre-miRNA binding / RISC complex binding / pre-miRNA export from nucleus / snRNA import into nucleus / nuclear export signal receptor activity / nuclear localization sequence binding / RISC complex / GTP metabolic process / nuclear import signal receptor activity ...regulation of protein desumoylation / pre-miRNA binding / RISC complex binding / pre-miRNA export from nucleus / snRNA import into nucleus / nuclear export signal receptor activity / nuclear localization sequence binding / RISC complex / GTP metabolic process / nuclear import signal receptor activity / regulation of mitotic nuclear division / mitotic sister chromatid segregation / ribosomal subunit export from nucleus / mRNA export from nucleus / protein export from nucleus / positive regulation of protein export from nucleus / protein import into nucleus / nuclear envelope / melanosome / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cell division / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
Importin repeat / Importin repeat 6 / Importin repeat 4 / Importin repeat / Importin repeat / Importin repeat 6 / Importin beta family / HEAT-like repeat / small GTPase Ran family profile. / Ran GTPase ...Importin repeat / Importin repeat 6 / Importin repeat 4 / Importin repeat / Importin repeat / Importin repeat 6 / Importin beta family / HEAT-like repeat / small GTPase Ran family profile. / Ran GTPase / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Importin subunit beta-3 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Canis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsKobayashi, J. / Matsuura, Y.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural basis for cell-cycle-dependent nuclear import mediated by the karyopherin Kap121p.
Authors: Kobayashi, J. / Matsuura, Y.
History
DepositionDec 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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-3
B: GTP-binding nuclear protein Ran
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,0624
Polymers142,5152
Non-polymers5472
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-22 kcal/mol
Surface area50510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.750, 97.750, 289.981
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Importin subunit beta-3 / Karyopherin subunit beta-3 / Karyopherin-121 / Protein secretion enhancer 1


Mass: 122304.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PSE1, KAP121, YMR308C, YM9952.10C / Production host: Escherichia coli (E. coli) / References: UniProt: P32337
#2: Protein GTP-binding nuclear protein Ran / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 20210.416 Da / Num. of mol.: 1 / Fragment: UNP residues 1-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: RAN / Production host: Escherichia coli (E. coli) / References: UniProt: P62825
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 0.2M CaCl2, 10% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97897 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 14, 2010
RadiationMonochromator: rotated inclined double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 2.7→48.77 Å / Num. all: 45236 / Num. obs: 45100 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.79 Å / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→46.36 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.889 / SU B: 32.352 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 0.869 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29778 2223 4.9 %RANDOM
Rwork0.26056 ---
all0.2624 45236 --
obs0.2624 42804 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.485 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å22.08 Å20 Å2
2--2.08 Å20 Å2
3----6.76 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9109 0 33 4 9146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0199310
X-RAY DIFFRACTIONr_bond_other_d0.0020.028960
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.98112672
X-RAY DIFFRACTIONr_angle_other_deg0.887320554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70551169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89424.973376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.433151488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4361535
X-RAY DIFFRACTIONr_chiral_restr0.0830.21522
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022016
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 145 -
Rwork0.349 3142 -
obs--99.94 %
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)
10.81360.53460.14711.27190.31080.9603-0.0343-0.15580.1175-0.3527-0.19120.00940.17920.65250.22550.1960.25480.07030.6776-0.02220.4687-10.805416.1747-23.6552
21.62340.9292-1.29960.9922-1.95934.31570.4273-0.4538-0.20910.2882-0.5601-0.0344-0.49081.12260.13280.1093-0.1245-0.07090.8399-0.05970.5807-6.7225.82252.3733
30.68260.3370.03180.1959-0.22794.05080.5539-0.0988-0.14370.3247-0.15620.0319-1.19111.546-0.39770.8034-0.4791-0.04040.8336-0.24820.5093-17.703424.889214.4681
47.64521.18122.11862.3552-1.01941.46330.3936-0.39940.11861.4002-0.21820.4895-0.77710.1764-0.17540.8885-0.18110.22880.6574-0.28610.3519-28.807420.410320.6143
52.7974-1.2430.31630.5871-0.38295.37720.39680.1824-0.4475-0.0754-0.170.225-0.96940.8889-0.22680.368-0.1909-0.0320.6056-0.09440.4535-23.62715.094921.0761
61.97122.05840.16033.3349-0.45440.37160.6903-0.281-0.14460.9072-0.47670.3257-0.1920.1828-0.21360.6548-0.17940.14630.6476-0.16120.2287-32.192612.697532.2984
70.97331.3940.17782.11140.41870.48830.1546-0.1619-0.03360.153-0.09730.0751-0.18950.0053-0.05730.17150.12340.09750.55060.06640.5296-48.9043-10.915424.9993
80.1801-0.0109-0.31830.317-0.80952.74390.15260.0239-0.0421-0.1314-0.03260.10450.09130.1154-0.120.17230.104-0.01920.3528-0.02650.6299-26.9115-39.549611.694
90.1651-0.16860.51230.273-0.8843.58090.01880.0059-0.09530.0212-0.1905-0.01910.0620.55980.17170.12450.0462-0.0480.6350.13820.5343-15.964-51.591743.7652
102.87840.1341-1.87034.0501-6.714512.7233-0.6102-0.3315-0.68770.1156-0.0484-0.199-0.3932-0.510.65870.5450.250.02120.84980.03820.3615-35.9036-50.992454.4116
1113.035118.007310.97429.825317.62510.69210.3813-0.6351-0.00421.8979-0.14030.18950.7313-0.2573-0.2410.71720.26040.42540.63460.16350.4133-37.6892-49.419269.9032
127.1195-9.145-5.546713.24148.63865.85560.2058-0.9485-0.8866-1.05220.2873-0.0225-0.9567-0.208-0.49320.450.57470.51581.29410.58121.1148-37.057-38.518559.3037
132.0786-1.7577-0.61153.09750.74480.21810.17150.03860.0769-0.1404-0.18590.1211-0.0120.00830.01440.27410.2771-0.11970.3204-0.05680.6052-32.70696.8502-11.2219
145.64373.47025.79727.09671.99576.05370.04790.17340.24530.1799-0.2780.63880.01670.20150.23010.33250.0576-0.06090.3506-0.03750.4082-39.8743-1.7751-9.4845
157.0629.33024.949412.4176.808413.46820.4213-0.0968-1.04310.7159-0.432-1.17630.7824-0.64220.01070.42480.18470.01330.3097-0.26190.7076-33.0087-10.7093-9.1591
1614.922-7.5752-0.22989.7075-1.36890.38040.00360.409-0.5526-0.49560.03080.42260.1252-0.0564-0.03440.37070.1096-0.00790.3977-0.08910.409-28.82320.2092-17.8596
170.3451-0.7749-0.3991.94570.55951.030.0505-0.0446-0.0425-0.1406-0.05050.1287-0.02050.263200.23380.2285-0.07250.3212-0.0460.5793-30.18677.4016-11.6997
181.06780.1582-0.06163.1898-3.2273.3798-0.1182-0.1427-0.1574-0.1222-0.0734-0.23720.12820.3190.19160.34590.216-0.03530.5134-0.08980.4891-21.58726.3116-2.5588
1921.31517.271810.441913.1512-9.393520.890.4530.6683-1.59681.624-0.0843-1.1165-1.17970.3277-0.36870.9443-0.0722-0.25810.65080.03070.3454-25.1898-6.23649.4581
200.0108-0.3002-0.115817.80167.42013.10970.33020.04860.05771.7386-0.5307-0.57940.7291-0.31830.20050.37130.1884-0.14050.76490.11220.6203-21.55067.70869.0902
210.47730.9378-0.18053.1093-0.21680.7535-0.1565-0.2421-0.042-0.15380.0930.17230.03410.36470.06350.23610.2218-0.04960.4658-0.00530.5829-34.16187.65330.8236
2213.75543.9203-0.96746.75-0.08132.1510.0986-0.06330.09550.2413-0.02240.0285-0.175-0.0623-0.07620.20440.1593-0.04430.3039-0.07220.5099-40.409718.9305-2.8311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 167
2X-RAY DIFFRACTION2A168 - 259
3X-RAY DIFFRACTION3A260 - 298
4X-RAY DIFFRACTION4A299 - 337
5X-RAY DIFFRACTION5A338 - 370
6X-RAY DIFFRACTION6A371 - 450
7X-RAY DIFFRACTION7A451 - 623
8X-RAY DIFFRACTION8A624 - 865
9X-RAY DIFFRACTION9A866 - 1044
10X-RAY DIFFRACTION10A1045 - 1062
11X-RAY DIFFRACTION11A1063 - 1071
12X-RAY DIFFRACTION12A1072 - 1088
13X-RAY DIFFRACTION13B6 - 27
14X-RAY DIFFRACTION14B28 - 33
15X-RAY DIFFRACTION15B34 - 41
16X-RAY DIFFRACTION16B42 - 48
17X-RAY DIFFRACTION17B49 - 92
18X-RAY DIFFRACTION18B93 - 126
19X-RAY DIFFRACTION19B127 - 131
20X-RAY DIFFRACTION20B132 - 141
21X-RAY DIFFRACTION21B142 - 166
22X-RAY DIFFRACTION22B167 - 176

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