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- PDB-1z3h: The exportin Cse1 in its cargo-free, cytoplasmic state -

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Basic information

Entry
Database: PDB / ID: 1z3h
TitleThe exportin Cse1 in its cargo-free, cytoplasmic state
ComponentsImportin alpha re-exporter
KeywordsPROTEIN TRANSPORT / Cse1 / Exportin / Nuclear transport / HEAT repeat
Function / homology
Function and homology information


nuclear export signal receptor activity / snRNA import into nucleus / protein export from nucleus / positive regulation of protein export from nucleus / small GTPase binding / protein import into nucleus / nuclear envelope / cell cycle / cell division / protein-containing complex / cytosol
Similarity search - Function
Exportin-2, C-terminal / CAS/CSE protein, C-terminus / Exportin-2, central domain / Cse1 / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin alpha re-exporter
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsCook, A. / Fernandez, E. / Lindner, D. / Ebert, J. / Schlenstedt, G. / Conti, E.
CitationJournal: Mol.Cell / Year: 2005
Title: The structure of the nuclear export receptor cse1 in its cytosolic state reveals a closed conformation incompatible with cargo binding
Authors: Cook, A. / Fernandez, E. / Lindner, D. / Ebert, J. / Schlenstedt, G. / Conti, E.
History
DepositionMar 12, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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_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 alpha re-exporter
B: Importin alpha re-exporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,0783
Polymers221,0532
Non-polymers241
Water0
1
A: Importin alpha re-exporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5512
Polymers110,5271
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Importin alpha re-exporter


Theoretical massNumber of molelcules
Total (without water)110,5271
Polymers110,5271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.520, 113.040, 122.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Importin alpha re-exporter / Chromosome segregation protein CSE1


Mass: 110526.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Cse1 / Plasmid: PQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): DL-41 / References: UniProt: P33307
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, MgCl2, glycerol, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.93
SYNCHROTRONSLS X06SA21.02
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMar 5, 2004
MARRESEARCH2CCDJun 13, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1SAGITALLY FOCUSED Si(111)
Radiation wavelength
IDWavelength (Å)Relative weight
10.931
21.021
ReflectionRedundancy: 13.2 % / Av σ(I) over netI: 3.7 / Number: 33873 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / D res high: 3.3 Å / D res low: 122.06 Å / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
10.4449.4996.910.0780.07810.8
7.3810.4498.710.0750.07512.4
6.027.3898.710.0840.08413
5.226.0298.810.0910.09113.1
4.675.2298.910.0880.08813.3
4.264.6798.610.0950.09513.3
3.944.2698.710.1230.12313.4
3.693.9498.510.170.1713.5
3.483.6998.510.2510.25113.5
3.33.4898.510.3910.39113.6
ReflectionResolution: 3.3→50 Å / Num. all: 44757 / Num. obs: 41661 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.2 % / Biso Wilson estimate: 96.017 Å2 / Rsym value: 0.102
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.391 / % possible all: 98.5

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
19.016.41972.673SE134.442.69
237.747-27.55784.104SE601.5
314.7852.02159.577SE123.382.43
431.862-31.25104.424SE601.25
531.4768.705107.899SE122.152.05
633.2121.147109.723SE01.38
752.516-34.29687.75SE601.36
852.672-31.85481.356SE601.28
922.07542.63599.39SE150.142.34
1025.47645.515103.488SE130.12.25
1132.016-33.40897.368SE91.81.48
1247.282-28.512102.069SE601.14
134.18439.09979.905SE601.05
1411.5464.9654.791SE600.86
1529.669-6.33183.453SE600.87
168.68763.746132.795SE179.782.31
173.18147.57995.944SE600.88
1850.41514.99872.31SE02.07
1925.788-16.23145.779SE600.79
2015.7052.14373.261SE600.88
2122.581-18.27641.234SE600.83
2214.76759.16119.886SE172.52.39
2311.8962.832115.168SE600.64
2453.9463.07875.584SE600.91
2555.071-10.353101.189SE600.87
264.616-10.5736.355SE600.73
276.879-16.36519.51SE600.77
2814.82958.19133.185SE600.76
2927.107-27.57478.775SE600.71
3042.269-28.34592.997SE600.57
31134.2034.245113.772SE600.59
3223.69826.10214.558SE600.53
33103.6899.25970.808SE600.4
3464.24725.24159.929SE600.42

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Processing

Software
NameVersionClassificationNB
SHARPphasing
SOLOMONphasing
CNSrefinement
PDB_EXTRACT1.6data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.1→122 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residue side chains that were not visible in the final 2Fo-Fc map have been placed in the model but the B factors for these atoms have been set above 200. The protein was treated with ...Details: Residue side chains that were not visible in the final 2Fo-Fc map have been placed in the model but the B factors for these atoms have been set above 200. The protein was treated with subtilisin during purification. This resulted in two fragments of 100 kDa and 10 kDa respectively that co-purify and are both present in the crystal
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2096 5 %RANDOM
Rwork0.241 ---
all0.287 33873 --
obs0.287 33834 99.6 %-
Solvent computationBsol: 30.849 Å2
Displacement parametersBiso mean: 77.326 Å2
Baniso -1Baniso -2Baniso -3
1-16.882 Å20 Å20 Å2
2---22.698 Å20 Å2
3---5.816 Å2
Refinement stepCycle: LAST / Resolution: 3.1→122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14786 0 1 0 14787
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5430
LS refinement shellResolution: 3.1→3.2 Å
RfactorNum. reflection% reflection
Rfree0.406 186 -
Rwork0.377 --
obs-3737 100 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param

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