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- PDB-7byf: The crystal structure of mouse ORF10-Rae1-Nup98 complex -

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Basic information

Entry
Database: PDB / ID: 7byf
TitleThe crystal structure of mouse ORF10-Rae1-Nup98 complex
Components
  • 10 protein
  • Peptidase S59 domain-containing protein
  • mRNA export factor
KeywordsPROTEIN BINDING / complex
Function / homology
Function and homology information


Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Transcriptional regulation by small RNAs / : / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript ...Regulation of Glucokinase by Glucokinase Regulatory Protein / Nuclear Pore Complex (NPC) Disassembly / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Transcriptional regulation by small RNAs / : / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / RNA export from nucleus / nucleocytoplasmic transport / mitotic spindle pole / mRNA transport / nuclear pore / regulation of mitotic spindle organization / ubiquitin binding / fibrillar center / nuclear envelope / protein transport / cell division / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
Herpesvirus Orf11 / Herpesvirus dUTPase protein / Nup98, Gle2-binding sequence / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller ...Herpesvirus Orf11 / Herpesvirus dUTPase protein / Nup98, Gle2-binding sequence / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / 10 protein / Peptidase S59 domain-containing protein / mRNA export factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Murid herpesvirus 4 (Murine herpesvirus 68)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsGao, P. / Feng, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Molecular mechanism underlying selective inhibition of mRNA nuclear export by herpesvirus protein ORF10.
Authors: Feng, H. / Tian, H. / Wang, Y. / Zhang, Q. / Lin, N. / Liu, S. / Yu, Y. / Deng, H. / Gao, P.
History
DepositionApr 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA export factor
B: Peptidase S59 domain-containing protein
F: 10 protein
C: 10 protein
D: mRNA export factor
E: Peptidase S59 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,29334
Polymers183,3876
Non-polymers4,90628
Water7,584421
1
A: mRNA export factor
B: Peptidase S59 domain-containing protein
C: 10 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,12416
Polymers91,6943
Non-polymers2,43013
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-324 kcal/mol
Surface area33830 Å2
MethodPISA
2
F: 10 protein
D: mRNA export factor
E: Peptidase S59 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,17018
Polymers91,6943
Non-polymers2,47615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-339 kcal/mol
Surface area33790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.397, 150.630, 101.618
Angle α, β, γ (deg.)90.000, 111.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 6 molecules ADBEFC

#1: Protein mRNA export factor / Rae1 protein homolog / mRNA-associated protein mrnp 41


Mass: 39054.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rae1, Mrnp41
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q8C570
#2: Protein Peptidase S59 domain-containing protein


Mass: 6370.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nup98
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q3TPG3
#3: Protein 10 protein / Protein G10


Mass: 46268.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Gene: GAMMAHV.ORF10, 10, ORF10
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: O41931

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Non-polymers , 3 types, 449 molecules

#4: Chemical...
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Hg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M di-Sodium tartrate, 20% PEG 3350, pH 7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.903 Å / Num. obs: 63997 / % possible obs: 99.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 13
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.597 / Num. unique obs: 12416

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→48.903 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.03 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2331 1961 3.06 %
Rwork0.184 62035 -
obs0.1855 63996 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.16 Å2 / Biso mean: 41.4789 Å2 / Biso min: 16.94 Å2
Refinement stepCycle: final / Resolution: 2.5→48.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12389 0 28 421 12838
Biso mean--43.42 36.76 -
Num. residues----1577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912740
X-RAY DIFFRACTIONf_angle_d0.98117346
X-RAY DIFFRACTIONf_chiral_restr0.0571953
X-RAY DIFFRACTIONf_plane_restr0.0062217
X-RAY DIFFRACTIONf_dihedral_angle_d14.5387667
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.56220.40021310.2682402889
2.5622-2.63150.32861380.2538428895
2.6315-2.70890.31721360.2468437296
2.7089-2.79640.33171390.2321435296
2.7964-2.89630.30631350.2228444298
2.8963-3.01230.27721420.2261440998
3.0123-3.14930.29791400.2274443698
3.1493-3.31530.24611410.1985448799
3.3153-3.5230.25421420.1925452699
3.523-3.79490.22581430.17794531100
3.7949-4.17660.21430.1575450499
4.1766-4.78050.17231430.13164543100
4.7805-6.02120.1721440.1445455999
6.0212-48.9030.17021440.1559455899

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