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- PDB-9lt9: Crystal structure of Gle1 from Debaryomyces hansenii -

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Basic information

Entry
Database: PDB / ID: 9lt9
TitleCrystal structure of Gle1 from Debaryomyces hansenii
ComponentsmRNA export factor GLE1
KeywordsRNA BINDING PROTEIN / Nuclear Pore Complex
Function / homology
Function and homology information


nuclear pore cytoplasmic filaments / inositol hexakisphosphate binding / poly(A)+ mRNA export from nucleus / translation initiation factor binding / phospholipid binding / protein transport / nuclear membrane / cytoplasm
Similarity search - Function
mRNA export factor GLE1-like / GLE1-like superfamily / GLE1-like protein
Similarity search - Domain/homology
mRNA export factor GLE1
Similarity search - Component
Biological speciesDebaryomyces hansenii (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsJang, M.J. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Molecular Structure of the mRNA Export Factor Gle1 from Debaryomyces hansenii
Authors: Jang, M.J. / Lee, S.J. / Chang, J.H.
History
DepositionFeb 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA export factor GLE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9003
Polymers33,7161
Non-polymers1842
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.222, 70.697, 87.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein mRNA export factor GLE1 / Nucleoporin GLE1


Mass: 33715.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Debaryomyces hansenii (yeast) / Gene: DEHA2F19668g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6BKR9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / Details: Tris (pH 8.5) and 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 47692 / % possible obs: 99.3 % / Redundancy: 10.4 % / Biso Wilson estimate: 17.75 Å2 / CC1/2: 0.993 / Net I/σ(I): 49.5
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 4729 / CC1/2: 0.927

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→35.85 Å / SU ML: 0.1545 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7142
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1934 1998 4.2 %
Rwork0.1716 45610 -
obs0.1725 47608 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.19 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 12 480 2864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682461
X-RAY DIFFRACTIONf_angle_d0.97623339
X-RAY DIFFRACTIONf_chiral_restr0.0838369
X-RAY DIFFRACTIONf_plane_restr0.0158421
X-RAY DIFFRACTIONf_dihedral_angle_d6.0674330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.28051300.22962982X-RAY DIFFRACTION91.61
1.53-1.580.2491440.21773274X-RAY DIFFRACTION100
1.58-1.620.2261410.19273216X-RAY DIFFRACTION99.97
1.62-1.670.23071430.1873255X-RAY DIFFRACTION99.79
1.67-1.730.21631420.1893258X-RAY DIFFRACTION99.79
1.73-1.80.23281440.18593255X-RAY DIFFRACTION99.68
1.8-1.890.22691430.19083268X-RAY DIFFRACTION99.59
1.89-1.980.21461410.19193223X-RAY DIFFRACTION98.56
1.99-2.110.20491420.17263266X-RAY DIFFRACTION99.36
2.11-2.270.19311430.16973255X-RAY DIFFRACTION98.52
2.27-2.50.20341420.17433266X-RAY DIFFRACTION98.67
2.5-2.860.19331450.16763281X-RAY DIFFRACTION99.07
2.86-3.610.17921460.15793348X-RAY DIFFRACTION99.01
3.61-35.850.15851520.15843463X-RAY DIFFRACTION98.56
Refinement TLS params.Method: refined / Origin x: 33.8352779543 Å / Origin y: 42.5181010523 Å / Origin z: 33.2027657599 Å
111213212223313233
T0.128854587088 Å20.0052158603977 Å2-0.000747084802247 Å2-0.124994328936 Å2-0.00921581945979 Å2--0.12605734291 Å2
L0.364462319586 °20.102588519671 °2-0.124379655948 °2-0.359708439831 °2-0.13336068236 °2--0.339861312176 °2
S-0.00047100280493 Å °0.00140954906834 Å °-0.0349550561128 Å °-0.0283288154033 Å °-0.00719352980461 Å °-0.0280559302542 Å °0.0246534684599 Å °0.00808293074937 Å °-0.000414770999591 Å °
Refinement TLS groupSelection details: all

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