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- PDB-3vyc: Crystal structure of unliganded Saccharomyces cerevisiae CRM1 (Xpo1p) -

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Basic information

Entry
Database: PDB / ID: 3vyc
TitleCrystal structure of unliganded Saccharomyces cerevisiae CRM1 (Xpo1p)
ComponentsExportin-1
KeywordsPROTEIN TRANSPORT / HEAT repeat / nuclear export
Function / homology
Function and homology information


nuclear export signal receptor activity / spindle pole body / protein localization to kinetochore / U4 snRNA binding / nuclear export / nuclear import signal receptor activity / MAPK6/MAPK4 signaling / ribosomal large subunit export from nucleus / U5 snRNA binding / ribosomal small subunit export from nucleus ...nuclear export signal receptor activity / spindle pole body / protein localization to kinetochore / U4 snRNA binding / nuclear export / nuclear import signal receptor activity / MAPK6/MAPK4 signaling / 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 / protein export from nucleus / kinetochore / small GTPase binding / perinuclear region of cytoplasm / 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsSaito, N. / Matsuura, Y.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: A 2.1- angstrom -resolution crystal structure of unliganded CRM1 reveals the mechanism of autoinhibition
Authors: Saito, N. / Matsuura, Y.
History
DepositionSep 22, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exportin-1


Theoretical massNumber of molelcules
Total (without water)118,7581
Polymers118,7581
Non-polymers00
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.782, 116.782, 118.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 118758.406 Da / Num. of mol.: 1
Mutation: a deletion mutant in which residues 377-413 and 971-984 are deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: CRM1 / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P30822
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.4263.99
2
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.2M KF, 16% PEG3350, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL41XU20.97896, 0.97927, 0.96405
Detector
TypeIDDetectorDate
RAYONIX MX225HE1CCDJul 14, 2010
RAYONIX MX225HE2CCDJul 14, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SIGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.978961
30.979271
40.964051
ReflectionResolution: 2.1→48.34 Å / Num. all: 93284 / Num. obs: 93097 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.21 Å / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
BSSdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→41.67 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.53 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 4716 5.1 %RANDOM
Rwork0.1867 ---
obs0.1882 93065 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 175.29 Å2 / Biso mean: 62.498 Å2 / Biso min: 24.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--0.68 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7802 0 0 378 8180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197943
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.96310758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6015969
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49625.112358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.528151468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9581534
X-RAY DIFFRACTIONr_chiral_restr0.1130.21266
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215817
LS refinement shellResolution: 2.096→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 326 -
Rwork0.277 6280 -
all-6606 -
obs--96.69 %
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)
10.13090.0631-0.14440.0308-0.06880.16340.0825-0.134-0.01510.0427-0.0589-0.013-0.08490.1734-0.02350.2744-0.0634-0.23380.4018-0.15750.424211.3225-1.85051.4027
24.1736-3.2531-2.03755.48290.31531.7970.21970.44-0.8336-1.1833-0.40311.04470.5354-0.12610.18350.59240.1885-0.34880.1788-0.25420.405814.86375.85344.3253
30.30160.8931-0.00415.29840.85030.2860.0327-0.0391-0.0777-0.6643-0.19380.338-0.22080.00880.16110.50430.3557-0.29130.4155-0.19260.286718.149715.85466.2454
40.4245-1.42061.316423.4662-0.59725.18550.0154-0.1114-0.34990.19981.3555-1.6714-0.5908-0.6318-1.37090.22050.3774-0.0340.7213-0.28920.815335.255521.532914.382
53.13050.9769-0.09394.44781.50640.5796-0.0650.2316-0.307-1.0567-0.01280.3822-0.38290.04040.07780.60680.3471-0.14070.5339-0.13080.140120.459333.09229.4689
60.829-0.24690.61610.42890.36171.3080.15370.1878-0.0518-0.1943-0.14320.0526-0.12550.0663-0.01050.36910.1140.05850.3313-0.00670.201420.79742.970426.5347
70.6313-0.15760.53650.0801-0.30531.7410.10760.0653-0.0733-0.08250.0034-0.01730.0409-0.0036-0.11090.29490.05450.06540.2642-0.01040.301226.942740.847746.1871
80.4591-0.49880.28560.5761-0.29210.4352-0.0803-0.1107-0.04560.08360.1676-0.0372-0.1657-0.1487-0.08740.28520.06820.03840.2920.02220.31125.669141.461465.7124
90.2857-0.3353-0.06631.1773-0.07360.2663-0.0971-0.13660.02820.13230.13930.0469-0.027-0.0487-0.04220.27610.0280.03210.31650.00310.279137.39920.203580.4018
100.23350.3009-0.20230.960.22820.8159-0.075-0.0147-0.00280.0622-0.03430.01730.1064-0.1960.10940.2988-0.03540.03830.33690.01780.277134.78660.64270.998
110.98550.1030.05770.14050.3861.1711-0.01740.0707-0.05390.0486-0.0319-0.00330.1121-0.00430.04940.3179-0.00950.00530.2718-0.00440.264647.54980.078161.5177
121.1934-0.0451-1.98450.00220.07513.3056-0.1162-0.102-0.06230.00930.00260.0110.15010.18190.11360.3289-0.00970.00190.3313-0.06080.237854.829-2.355446.0121
130.1428-0.0552-0.51320.25110.1611.86650.04790.01290.00910.0493-0.0168-0.0032-0.1153-0.0246-0.03110.341-0.01780.01620.2882-0.04250.237854.94971.681128.9824
140.0646-0.0809-0.32382.22521.67142.4750.0138-0.01770.06230.02130.115-0.03460.13640.1543-0.12880.22550.18220.02930.3501-0.12170.360143.096224.949439.2292
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 56
2X-RAY DIFFRACTION2A64 - 110
3X-RAY DIFFRACTION3A111 - 166
4X-RAY DIFFRACTION4A167 - 187
5X-RAY DIFFRACTION5A188 - 249
6X-RAY DIFFRACTION6A250 - 356
7X-RAY DIFFRACTION7A357 - 485
8X-RAY DIFFRACTION8A486 - 607
9X-RAY DIFFRACTION9A608 - 727
10X-RAY DIFFRACTION10A728 - 777
11X-RAY DIFFRACTION11A778 - 874
12X-RAY DIFFRACTION12A875 - 930
13X-RAY DIFFRACTION13A931 - 1037
14X-RAY DIFFRACTION14A1038 - 1084

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