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- PDB-2bku: Kap95p:RanGTP complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2bku
TitleKap95p:RanGTP complex
Components
  • GTP-BINDING NUCLEAR PROTEIN RAN
  • IMPORTIN BETA-1 SUBUNIT
KeywordsNUCLEAR TRANSPORT / IMPORTIN-BETA / RANGTP / GTP BINDING / PROTEIN TRANSPORT
Function / homology
Function and homology information


Initiation of Nuclear Envelope (NE) Reformation / regulation of protein desumoylation / RISC complex binding / pre-miRNA binding / regulation of nucleocytoplasmic transport / nuclear pore complex assembly / phosphatidylcholine biosynthetic process / pre-miRNA export from nucleus / nuclear export signal receptor activity / import into nucleus ...Initiation of Nuclear Envelope (NE) Reformation / regulation of protein desumoylation / RISC complex binding / pre-miRNA binding / regulation of nucleocytoplasmic transport / nuclear pore complex assembly / phosphatidylcholine biosynthetic process / pre-miRNA export from nucleus / nuclear export signal receptor activity / import into nucleus / snRNA import into nucleus / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / GTP metabolic process / RISC complex / protein targeting to membrane / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / mitotic sister chromatid segregation / mRNA transport / ribosomal subunit export from nucleus / nuclear pore / Neutrophil degranulation / protein export from nucleus / guanyl-nucleotide exchange factor activity / positive regulation of protein export from nucleus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / small GTPase binding / protein import into nucleus / disordered domain specific binding / melanosome / nuclear envelope / cell division / GTPase activity / protein-containing complex binding / GTP binding / magnesium ion binding / protein-containing complex / nucleus / cytoplasm / cytosol
Similarity search - Function
Importin beta family / HEAT repeat / HEAT-like repeat / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. ...Importin beta family / HEAT repeat / HEAT-like repeat / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 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 / Alpha Horseshoe / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTP-binding nuclear protein Ran / Importin subunit beta-1
Similarity search - Component
Biological speciesCANIS FAMILIARIS (dog)
SACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLee, S.J. / Matsuura, Y. / Liu, S.M. / Stewart, M.
CitationJournal: Nature / Year: 2005
Title: Structural Basis for Nuclear Import Complex Dissociation by Rangtp
Authors: Lee, S.J. / Matsuura, Y. / Liu, S.M. / Stewart, M.
History
DepositionFeb 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.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_conn.ptnr2_label_seq_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: GTP-BINDING NUCLEAR PROTEIN RAN
B: IMPORTIN BETA-1 SUBUNIT
C: GTP-BINDING NUCLEAR PROTEIN RAN
D: IMPORTIN BETA-1 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,4858
Polymers230,3904
Non-polymers1,0954
Water1,11762
1
A: GTP-BINDING NUCLEAR PROTEIN RAN
B: IMPORTIN BETA-1 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7424
Polymers115,1952
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: GTP-BINDING NUCLEAR PROTEIN RAN
D: IMPORTIN BETA-1 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7424
Polymers115,1952
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)107.021, 127.879, 161.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13B
23D
14B
24D
15B
25D
16B
26D
17B
27D
18B
28D
19B
29D
110B
210D
111B
211D
112B
212D
113B
213D
114B
214D
115B
215D
116B
216D
117B
217D
118B
218D
119B
219D
120B
220D
121B
221D
122B
222D
123B
223D
124B
224D
125B
225D
126B
226D
127B
227D
128B
228D
129B
229D
130B
230D
131B
231D
132B
232D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A9 - 223
2111C9 - 223
1122B1 - 32
2122D1 - 32
1132B33 - 75
2132D33 - 75
1142B84 - 106
2142D84 - 106
1152B129 - 164
2152D129 - 164
1162B177 - 188
2162D177 - 188
1172B211 - 250
2172D211 - 250
1182B251 - 264
2182D251 - 264
1192B313 - 360
2192D313 - 360
11102B361 - 371
21102D361 - 371
11112B396 - 445
21112D396 - 445
11122B446 - 474
21122D446 - 474
11132B491 - 533
21132D491 - 533
11142B534 - 556
21142D534 - 556
11152B567 - 588
21152D567 - 588
11162B589 - 630
21162D589 - 630
11172B631 - 670
21172D631 - 670
11185B671 - 712
21185D671 - 712
11192B713 - 741
21192D713 - 741
11202B768 - 820
21202D768 - 820
11212B821 - 861
21212D821 - 861
11222B77 - 83
21222D77 - 83
11232B108 - 128
21232D108 - 128
11242B194 - 210
21242D194 - 210
11252B266 - 308
21252D266 - 308
11262B310 - 312
21262D310 - 312
11272B373 - 395
21272D373 - 395
11282B476 - 490
21282D476 - 490
11296B558 - 566
21296D558 - 566
11305B741 - 745
21305D741 - 745
11315B746 - 767
21315D746 - 767
11321B165 - 176
21321D165 - 176

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32

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Components

#1: Protein GTP-BINDING NUCLEAR PROTEIN RAN / GTPASE RAN / RAS-LIKE PROTEIN TC4


Mass: 20335.584 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANIS FAMILIARIS (dog) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P62825
#2: Protein IMPORTIN BETA-1 SUBUNIT / KARYOPHERIN BETA-1 SUBUNIT / IMPORTIN 95


Mass: 94859.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q06142
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGTP-BINDING PROTEIN INVOLVED IN NUCLEOCYTOPLASMIC TRANSPORT. REQUIRED FOR THE IMPORT OF PROTEIN AND ...GTP-BINDING PROTEIN INVOLVED IN NUCLEOCYTOPLASMIC TRANSPORT. REQUIRED FOR THE IMPORT OF PROTEIN AND EXPORT OF RNA FROM THE NUCLEUS

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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: 2.4 Å3/Da / Density % sol: 48.79 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 61240 / % possible obs: 99.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 62.13 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGK, 1WA5

1qgk

1wa5


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.876 / SU B: 15.54 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 3098 5.1 %RANDOM
Rwork0.223 ---
obs0.226 58092 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.14 Å20 Å20 Å2
2--3.61 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15976 0 66 62 16104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02216337
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214823
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.96422194
X-RAY DIFFRACTIONr_angle_other_deg0.773334560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05952043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8425.418742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.319152816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6591572
X-RAY DIFFRACTIONr_chiral_restr0.0580.22556
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218152
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023104
X-RAY DIFFRACTIONr_nbd_refined0.220.24315
X-RAY DIFFRACTIONr_nbd_other0.1660.215238
X-RAY DIFFRACTIONr_nbtor_refined0.1780.28227
X-RAY DIFFRACTIONr_nbtor_other0.0830.29249
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2355
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.281
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.2152
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.83613245
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.6461016510
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2667077
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.488105684
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2713tight positional0.050.1
2B190tight positional0.040.1
3B256tight positional0.050.1
4B137tight positional0.050.1
5B211tight positional0.060.1
6B71tight positional0.070.1
7B238tight positional0.060.1
8B83tight positional0.050.1
9B285tight positional0.060.1
10B64tight positional0.050.1
11B296tight positional0.050.1
12B169tight positional0.050.1
13B254tight positional0.050.1
14B137tight positional0.070.1
15B131tight positional0.060.1
16B249tight positional0.050.1
17B236tight positional0.060.1
19B170tight positional0.070.1
20B310tight positional0.060.1
21B244tight positional0.060.1
22B42tight positional0.050.1
23B124tight positional0.040.1
24B102tight positional0.070.1
25B256tight positional0.070.1
26B17tight positional0.040.1
27B137tight positional0.050.1
28B89tight positional0.050.1
32B97tight positional0.040.1
2B302medium positional0.120.3
3B382medium positional0.120.3
4B205medium positional0.130.3
5B322medium positional0.130.3
6B97medium positional0.130.3
7B356medium positional0.190.3
8B157medium positional0.150.3
9B417medium positional0.140.3
10B95medium positional0.10.3
11B453medium positional0.130.3
12B240medium positional0.10.3
13B372medium positional0.130.3
14B183medium positional0.150.3
15B207medium positional0.160.3
16B378medium positional0.120.3
17B362medium positional0.140.3
18B249medium positional0.180.3
19B244medium positional0.190.3
20B462medium positional0.120.3
21B427medium positional0.180.3
22B70medium positional0.110.3
23B181medium positional0.10.3
24B146medium positional0.160.3
25B391medium positional0.140.3
26B26medium positional0.080.3
27B206medium positional0.160.3
28B130medium positional0.110.3
30B30medium positional0.060.3
31B130medium positional0.10.3
18B389loose positional0.31
29B37loose positional0.321
30B45loose positional0.141
31B202loose positional0.161
1A2713tight thermal2.315
2B190tight thermal1.345
3B256tight thermal1.735
4B137tight thermal1.315
5B211tight thermal1.895
6B71tight thermal2.35
7B238tight thermal1.715
8B83tight thermal1.655
9B285tight thermal1.455
10B64tight thermal2.415
11B296tight thermal2.915
12B169tight thermal2.675
13B254tight thermal2.985
14B137tight thermal3.25
15B131tight thermal3.675
16B249tight thermal2.335
17B236tight thermal2.095
19B170tight thermal3.55
20B310tight thermal2.895
21B244tight thermal2.055
22B42tight thermal2.285
23B124tight thermal1.395
24B102tight thermal1.515
25B256tight thermal1.515
26B17tight thermal1.715
27B137tight thermal2.55
28B89tight thermal2.765
32B97tight thermal0.965
2B302medium thermal2.0610
3B382medium thermal1.8810
4B205medium thermal1.710
5B322medium thermal2.4410
6B97medium thermal2.0910
7B356medium thermal2.9410
8B157medium thermal2.0310
9B417medium thermal2.1310
10B95medium thermal2.6610
11B453medium thermal4.0210
12B240medium thermal3.0510
13B372medium thermal3.6210
14B183medium thermal3.3610
15B207medium thermal4.3310
16B378medium thermal2.7610
17B362medium thermal2.7910
18B249medium thermal5.610
19B244medium thermal4.410
20B462medium thermal3.9510
21B427medium thermal2.8910
22B70medium thermal4.1310
23B181medium thermal1.7810
24B146medium thermal2.3310
25B391medium thermal2.3710
26B26medium thermal1.0910
27B206medium thermal3.210
28B130medium thermal3.1410
30B30medium thermal1.1910
31B130medium thermal6.0710
18B389loose thermal5.9720
29B37loose thermal13.5720
30B45loose thermal1.2520
31B202loose thermal6.7720
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.356 223
Rwork0.314 4154

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