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- PDB-6b4h: Crystal structure of Chaetomium thermophilum Gle1 CTD-Nup42 GBM-I... -

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Basic information

Entry
Database: PDB / ID: 6b4h
TitleCrystal structure of Chaetomium thermophilum Gle1 CTD-Nup42 GBM-IP6 complex
Components
  • Nucleoporin AMO1
  • Nucleoporin GLE1
KeywordsTRANSPORT PROTEIN / Complex / Nuclear Pore Complex / mRNA export / DEAD-box helicase
Function / homology
Function and homology information


poly(A)+ mRNA export from nucleus / mRNA transport / nuclear pore / protein transport / nuclear membrane / metal ion binding
Similarity search - Function
mRNA export factor GLE1-like / GLE1-like superfamily / GLE1-like protein / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Nucleoporin AMO1 / mRNA export factor GLE1
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å
AuthorsLin, D.H. / Correia, A.R. / Cai, S.W. / Huber, F.M. / Jette, C.A. / Hoelz, A.
CitationJournal: Nat Commun / Year: 2018
Title: Structural and functional analysis of mRNA export regulation by the nuclear pore complex.
Authors: Lin, D.H. / Correia, A.R. / Cai, S.W. / Huber, F.M. / Jette, C.A. / Hoelz, A.
History
DepositionSep 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 26, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Oct 14, 2020Group: Derived calculations / Structure summary / Category: chem_comp / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_label_atom_id ..._chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Nucleoporin AMO1
A: Nucleoporin GLE1
B: Nucleoporin AMO1
C: Nucleoporin GLE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,42916
Polymers87,8174
Non-polymers4,61212
Water6,341352
1
D: Nucleoporin AMO1
C: Nucleoporin GLE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2158
Polymers43,9092
Non-polymers2,3066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-118 kcal/mol
Surface area18960 Å2
MethodPISA
2
A: Nucleoporin GLE1
B: Nucleoporin AMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2158
Polymers43,9092
Non-polymers2,3066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-121 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.160, 73.276, 117.665
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules DBAC

#1: Protein Nucleoporin AMO1 / Nuclear pore protein AMO1


Mass: 8425.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: AMO1, CTHT_0020020 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S381
#2: Protein Nucleoporin GLE1 / Nuclear pore protein GLE1 / RNA export factor GLE1


Mass: 35483.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: GLE1, CTHT_0027940 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S7F3

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Non-polymers , 4 types, 364 molecules

#3: Chemical
ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H18O24P6
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 10 mM zinc sulfate heptahydrate, 0.1 M MES pH 6.3, 18 % (w/v) PEG MME 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.17→35 Å / Num. obs: 52814 / % possible obs: 98.4 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.043 / Rsym value: 0.111 / Net I/σ(I): 11.1
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5249 / CC1/2: 0.87 / Rpim(I) all: 0.498 / Rsym value: 1.316 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.17→34.847 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.78
RfactorNum. reflection% reflection
Rfree0.2302 2594 4.93 %
Rwork0.1925 --
obs0.1944 52582 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.17→34.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6029 0 244 352 6625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036441
X-RAY DIFFRACTIONf_angle_d0.5338780
X-RAY DIFFRACTIONf_dihedral_angle_d14.973906
X-RAY DIFFRACTIONf_chiral_restr0.038895
X-RAY DIFFRACTIONf_plane_restr0.0041095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.20940.38111560.37132579X-RAY DIFFRACTION98
2.2094-2.25190.33411390.31822633X-RAY DIFFRACTION99
2.2519-2.29790.38481350.31282618X-RAY DIFFRACTION98
2.2979-2.34780.32021400.29012636X-RAY DIFFRACTION99
2.3478-2.40240.30321280.2812615X-RAY DIFFRACTION98
2.4024-2.46250.33921290.27532642X-RAY DIFFRACTION98
2.4625-2.5290.25291380.2452570X-RAY DIFFRACTION97
2.529-2.60340.29261380.23452634X-RAY DIFFRACTION97
2.6034-2.68740.2561290.21392580X-RAY DIFFRACTION97
2.6874-2.78350.23871330.21152640X-RAY DIFFRACTION99
2.7835-2.89490.26851510.20712649X-RAY DIFFRACTION99
2.8949-3.02650.24151390.1972645X-RAY DIFFRACTION99
3.0265-3.1860.23311410.19242661X-RAY DIFFRACTION98
3.186-3.38550.26031270.18742571X-RAY DIFFRACTION97
3.3855-3.64660.2551200.17942661X-RAY DIFFRACTION98
3.6466-4.01310.19561110.15972705X-RAY DIFFRACTION99
4.0131-4.59270.19741520.14042682X-RAY DIFFRACTION99
4.5927-5.7820.18441250.15612643X-RAY DIFFRACTION97
5.782-34.85150.17521630.17432624X-RAY DIFFRACTION95

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