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- PDB-5xoj: Crystal structure of Xpo1p-PKI-Nup42p-Gsp1p-GTP complex -

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Basic information

Entry
Database: PDB / ID: 5xoj
TitleCrystal structure of Xpo1p-PKI-Nup42p-Gsp1p-GTP complex
Components
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein
  • Nup42p
  • cAMP-dependent protein kinase inhibitor alphaCAMP-dependent pathway
KeywordsGTP BINDING PROTEIN / exportin / nucleoporin
Function / homology
Function and homology information


MAPK6/MAPK4 signaling / nuclear export signal receptor activity / negative regulation of cAMP-dependent protein kinase activity / spindle pole body / protein localization to kinetochore / U4 snRNA binding / nuclear export / cAMP-dependent protein kinase inhibitor activity / nuclear import signal receptor activity / negative regulation of protein import into nucleus ...MAPK6/MAPK4 signaling / nuclear export signal receptor activity / negative regulation of cAMP-dependent protein kinase activity / spindle pole body / protein localization to kinetochore / U4 snRNA binding / nuclear export / cAMP-dependent protein kinase inhibitor activity / nuclear import signal receptor activity / negative regulation of protein import into nucleus / protein kinase A catalytic subunit binding / ribosomal large subunit export from nucleus / U5 snRNA binding / ribosomal small subunit export from nucleus / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / U1 snRNA binding / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / kinetochore / small GTPase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1/5 ...Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / : / Exportin-1 / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKoyama, M. / Shirai, N. / Matsuura, Y.
CitationJournal: Genes Cells / Year: 2017
Title: Crystal structure of the Xpo1p nuclear export complex bound to the SxFG/PxFG repeats of the nucleoporin Nup42p
Authors: Koyama, M. / Hirano, H. / Shirai, N. / Matsuura, Y.
History
DepositionMay 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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
C: Exportin-1
D: cAMP-dependent protein kinase inhibitor alpha
E: Nup42p
F: Nup42p
G: Nup42p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,4938
Polymers158,9456
Non-polymers5472
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-63 kcal/mol
Surface area48970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.640, 107.560, 149.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ACD

#1: Protein GTP-binding nuclear protein / Gsp1p


Mass: 20672.861 Da / Num. of mol.: 1 / Fragment: UNP residues 1-182 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain AWRI796) (yeast)
Strain: AWRI796 / Gene: AWRI796_3356 / Production host: Escherichia coli (E. coli) / References: UniProt: E7KFU1
#2: Protein Exportin-1 / Karyopherin / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 120270.070 Da / Num. of mol.: 1 / Mutation: residues 377-413 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Production host: Escherichia coli (E. coli) / References: UniProt: P30822
#3: Protein cAMP-dependent protein kinase inhibitor alpha / CAMP-dependent pathway / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 8022.581 Da / Num. of mol.: 1 / Mutation: S35L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKIA, PRKACN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61925

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Protein/peptide , 1 types, 3 molecules EFG

#4: Protein/peptide Nup42p


Mass: 3326.603 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain FostersB) (yeast)
References: UniProt: E7Q297

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Non-polymers , 3 types, 496 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: PEG20000, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→31.582 Å / Num. obs: 81567 / % possible obs: 97.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 30.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.057 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.7 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) all% possible all
2.2-2.240.79820.560.40396.4
11.43-31.580.03225.40.9980.01693.7

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WYG

3wyg


Resolution: 2.2→31.582 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9
RfactorNum. reflection% reflection
Rfree0.2195 4145 5.09 %
Rwork0.1909 --
obs0.1924 81506 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.09 Å2 / Biso mean: 40.6537 Å2 / Biso min: 11.04 Å2
Refinement stepCycle: final / Resolution: 2.2→31.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9723 0 33 494 10250
Biso mean--26.49 44.34 -
Num. residues----1212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029949
X-RAY DIFFRACTIONf_angle_d0.65613486
X-RAY DIFFRACTIONf_chiral_restr0.0251561
X-RAY DIFFRACTIONf_plane_restr0.0031699
X-RAY DIFFRACTIONf_dihedral_angle_d15.4723656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2250.33061390.30172511265097
2.225-2.25120.30071260.28532519264596
2.2512-2.27860.27911440.26972490263496
2.2786-2.30740.27021400.25422521266197
2.3074-2.33780.27371440.25242519266396
2.3378-2.36980.27531190.24122538265797
2.3698-2.40360.26781480.23512534268297
2.4036-2.43950.25531390.2282534267397
2.4395-2.47760.27551270.21572568269597
2.4776-2.51820.30291370.22652523266097
2.5182-2.56160.26571400.21812570271097
2.5616-2.60820.25051330.21532542267598
2.6082-2.65830.2621290.2152553268297
2.6583-2.71260.26521140.20932580269498
2.7126-2.77150.23151310.2022567269898
2.7715-2.83590.20561430.19992582272597
2.8359-2.90680.22191460.19812561270798
2.9068-2.98530.24621430.19662563270698
2.9853-3.07310.23611290.19532584271398
3.0731-3.17220.23841550.18652570272598
3.1722-3.28550.19851160.19232625274198
3.2855-3.41690.19681500.18162565271598
3.4169-3.57220.2241390.1692575271498
3.5722-3.76020.19751600.17032627278798
3.7602-3.99540.21221510.16332595274698
3.9954-4.30320.181430.15662616275998
4.3032-4.73490.17711160.1532671278799
4.7349-5.41710.19941440.16632656280099
5.4171-6.81370.22631410.20472715285699
6.8137-31.58490.16041590.1642787294698
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)
11.6025-0.6523-0.58610.9796-0.93471.9349-0.0972-0.31460.40520.0662-0.02760.1051-0.20180.13420.09270.21150.0552-0.06010.1928-0.02820.2581-4.527126.3381-32.7518
22.68231.07860.71734.93310.50085.2822-0.2007-0.56980.01740.8695-0.12270.3844-0.288-0.21050.36260.41140.1267-0.03530.284-0.06970.3272-5.056725.4987-20.5642
30.5601-0.53540.10820.4871-0.29060.7354-0.461-0.4670.25490.66530.3212-0.2367-0.7407-0.45620.09750.48540.0644-0.14680.1566-0.10750.4127-5.357428.4188-25.0615
45.7581.4271-0.18171.6053-0.81361.9242-0.2905-0.06980.1630.08990.2385-0.1647-0.5222-0.16730.09220.35090.0707-0.05020.2047-0.02150.2451-8.681127.1202-33.2185
51.6104-0.7933-0.07440.4631-0.40081.92320.00680.2829-0.03810.0351-0.06870.1703-0.3247-0.07980.11830.28550.0567-0.05770.1486-0.0040.2366-9.141327.0744-40.1253
61.9851-0.30490.22161.47-1.37744.5872-0.025-0.0386-0.1004-0.17790.00590.16270.2444-0.28370.01960.13520.0137-0.02930.1345-0.02730.195-5.090811.8108-36.8742
74.7781.22964.65851.14162.01635.2420.00450.4026-0.1101-0.4931-0.1341-0.1932-0.52040.3590.22250.29240.0666-0.04930.2324-0.04880.2352-1.013724.5871-45.5133
82.0515-0.3409-0.45841.3776-0.12392.4363-0.1469-0.1435-0.09950.18990.0633-0.0254-0.07710.05970.11420.20470.0184-0.02490.15920.00570.20893.047912.9674-30.1017
93.50191.2315-0.3062.87530.20792.5842-0.25220.04460.22350.0215-0.1274-0.5191-0.8770.54960.34510.283-0.0495-0.0910.21540.04270.33519.027827.9987-32.2347
100.6258-0.22-1.64162.4871.87498.1334-0.1245-0.3020.13590.1332-0.0242-0.5650.2180.71450.11680.4314-0.0106-0.12240.44890.05180.528313.682330.9984-26.1367
111.1553-1.0601-0.19342.28030.49991.55670.16510.2052-0.1088-0.1232-0.11190.11080.0176-0.258-0.04360.29360.0478-0.0590.2774-0.01690.2837-20.129435.3898-46.111
121.9489-0.1307-0.13881.3301-0.11321.64840.01330.20480.1059-0.3082-0.00540.198-0.1419-0.0961-0.0060.38390.0789-0.09220.213-0.01640.2185-8.932119.8983-62.5583
133.0132-0.38130.61071.89890.53743.04480.07380.2619-0.1466-0.2155-0.1879-0.1956-0.01690.07270.10030.2020.04350.060.22550.02710.18610.296411.8749-60.325
141.6227-0.32230.37751.5934-0.70832.73040.02280.15710.1059-0.2063-0.0689-0.18770.02870.23240.06810.1579-0.04160.05090.22050.04850.17923.38467.0317-46.8185
151.7179-0.9862-2.04760.72661.42282.3818-0.105-0.11250.08020.37350.18440.18520.0675-0.0963-0.050.39970.03780.02370.42390.07560.26358.72219.3488-18.0734
160.89230.358-0.16550.6096-0.19622.1570.1334-0.1937-0.01450.2023-0.1061-0.1429-0.10940.2307-0.01080.2247-0.0665-0.08190.28370.03210.209524.86312.027-10.028
172.2091-0.10460.32291.08350.07771.41130.1761-0.39390.00130.3437-0.09120.181-0.1406-0.0931-0.08640.3514-0.06730.08220.35240.03290.2863-7.60150.63163.7072
181.4216-0.22070.53811.695-0.60241.63440.04270.03390.04950.01770.10440.1085-0.0435-0.2645-0.12950.1827-0.01010.03260.35330.05540.33-20.6687-1.0597-13.0494
191.1176-0.2607-0.08970.96740.2931.62550.1024-0.3474-0.1220.0805-0.06980.29610.0346-0.1707-0.01760.287-0.0773-0.04540.43120.09160.5097-26.7181-3.7871-27.8788
201.11450.4804-0.20841.5983-0.28961.3706-0.04650.0426-0.1754-0.58880.16420.47020.3945-0.4039-0.09520.4297-0.1068-0.1670.3815-0.00010.5237-28.8298-4.5373-46.1391
213.3601-4.54642.84636.9114-2.24375.7436-0.0314-0.2486-1.08010.04660.1124-0.55380.74520.6065-0.09260.4413-0.0356-0.09070.72560.1920.561137.9691-4.5046-5.3469
222.7746-0.25750.6667.87660.18843.78440.0945-0.14040.39480.2022-0.2033-0.4414-0.04980.50490.16540.3397-0.2272-0.16430.70140.0580.237934.42813.6684-2.4584
230.38411.1271-0.49223.7299-0.40423.2004-0.0458-0.2295-0.08410.2118-0.1955-0.9471-0.37620.88240.24360.9427-0.285-0.02920.5665-0.02710.502633.735916.6614-0.6477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 10:26)A10 - 26
2X-RAY DIFFRACTION2(chain A and resid 27:36)A27 - 36
3X-RAY DIFFRACTION3(chain A and resid 37:60)A37 - 60
4X-RAY DIFFRACTION4(chain A and resid 61:73)A61 - 73
5X-RAY DIFFRACTION5(chain A and resid 74:89)A74 - 89
6X-RAY DIFFRACTION6(chain A and resid 90:108)A90 - 108
7X-RAY DIFFRACTION7(chain A and resid 109:119)A109 - 119
8X-RAY DIFFRACTION8(chain A and resid 120:160)A120 - 160
9X-RAY DIFFRACTION9(chain A and resid 161:173)A161 - 173
10X-RAY DIFFRACTION10(chain A and resid 174:179)A174 - 179
11X-RAY DIFFRACTION11(chain C and resid 10:71)C10 - 71
12X-RAY DIFFRACTION12(chain C and resid 72:213)C72 - 213
13X-RAY DIFFRACTION13(chain C and resid 214:262)C214 - 262
14X-RAY DIFFRACTION14(chain C and resid 266:433)C266 - 433
15X-RAY DIFFRACTION15(chain C and resid 434:468)C434 - 468
16X-RAY DIFFRACTION16(chain C and resid 469:652)C469 - 652
17X-RAY DIFFRACTION17(chain C and resid 653:807)C653 - 807
18X-RAY DIFFRACTION18(chain C and resid 808:873)C808 - 873
19X-RAY DIFFRACTION19(chain C and resid 874:958)C874 - 958
20X-RAY DIFFRACTION20(chain C and resid 959:1054)C959 - 1054
21X-RAY DIFFRACTION21(chain D and resid 34:38)D34 - 38
22X-RAY DIFFRACTION22(chain D and resid 39:45)D39 - 45
23X-RAY DIFFRACTION23(chain D and resid 46:52)D46 - 52

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