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- PDB-7f60: Crystal structure of auxiliary protein in complex with human nucl... -

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Basic information

Entry
Database: PDB / ID: 7f60
TitleCrystal structure of auxiliary protein in complex with human nuclear protein
Components
  • Nuclear pore complex protein Nup98-Nup96
  • ORF6 protein
  • mRNA export factor
KeywordsVIRAL PROTEIN / immune system / auxiliary protein
Function / homology
Function and homology information


Translation of Accessory Proteins / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body ...Translation of Accessory Proteins / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / Transport of Ribonucleoproteins into the Host Nucleus / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / nuclear localization sequence binding / positive regulation of mRNA splicing, via spliceosome / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / : / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / mitotic spindle pole / Vpr-mediated nuclear import of PICs / : / host cell Golgi membrane / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / serine-type peptidase activity / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / nuclear periphery / protein sequestering activity / SUMOylation of chromatin organization proteins / HCMV Late Events / ubiquitin binding / Transcriptional regulation by small RNAs / promoter-specific chromatin binding / RHO GTPases Activate Formins / molecular condensate scaffold activity / ISG15 antiviral mechanism / fibrillar center / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / microtubule binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / nuclear membrane / transcription coactivator activity / host cell endoplasmic reticulum membrane / nuclear body / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / cell division / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Non-structural protein NS6, betacoronavirus / Betacoronavirus NS6 protein / Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / 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. ...Non-structural protein NS6, betacoronavirus / Betacoronavirus NS6 protein / Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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
ORF6 protein / Nuclear pore complex protein Nup98-Nup96 / mRNA export factor RAE1
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGao, X. / Cui, S.
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport
Authors: Gao, X. / Tian, H. / Zhu, K. / Li, Q. / Hao, W. / Wang, L. / Qin, B. / Deng, H. / Cui, S.
History
DepositionJun 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA export factor
B: mRNA export factor
C: Nuclear pore complex protein Nup98-Nup96
D: Nuclear pore complex protein Nup98-Nup96
E: ORF6 protein
F: ORF6 protein


Theoretical massNumber of molelcules
Total (without water)492,1526
Polymers492,1526
Non-polymers00
Water00
1
A: mRNA export factor
D: Nuclear pore complex protein Nup98-Nup96
E: ORF6 protein


Theoretical massNumber of molelcules
Total (without water)246,0763
Polymers246,0763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-14 kcal/mol
Surface area17180 Å2
MethodPISA
2
B: mRNA export factor
C: Nuclear pore complex protein Nup98-Nup96
F: ORF6 protein


Theoretical massNumber of molelcules
Total (without water)246,0763
Polymers246,0763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-17 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.345, 87.531, 48.230
Angle α, β, γ (deg.)90.000, 93.680, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 41017.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAE1, MRNP41
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P78406
#2: Protein Nuclear pore complex protein Nup98-Nup96


Mass: 197780.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP98, ADAR2
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P52948, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Protein ORF6 protein / ORF6 / Accessory protein 6 / Non-structural protein 6 / ns6 / Protein X3


Mass: 7278.505 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P0DTC6

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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: 0.41 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1m Bis-tris ph5.5,45%PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.85→48.27 Å / Num. obs: 36291 / % possible obs: 99 % / Redundancy: 3.52 % / Rmerge(I) obs: 0.37 / Net I/σ(I): 3.47
Reflection shellResolution: 2.85→3.02 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5780 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OWR

4owr


Resolution: 2.85→48.24 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2756 904 4.83 %
Rwork0.2357 17797 -
obs0.2377 18701 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.92 Å2 / Biso mean: 40.8356 Å2 / Biso min: 22.32 Å2
Refinement stepCycle: final / Resolution: 2.85→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6153 0 0 0 6153
Num. residues----777
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-3.020.38611420.34252850299295
3.02-3.260.32451520.297229463098100
3.26-3.590.31071380.273629893127100
3.59-4.10.28351640.22229833147100
4.11-5.170.22141670.18162971313899
5.17-48.240.24311410.21153058319999
Refinement TLS params.Method: refined / Origin x: -24.3858 Å / Origin y: -2.8648 Å / Origin z: 10.1328 Å
111213212223313233
T0.2835 Å20.0193 Å20.0047 Å2-0.3095 Å2-0.0603 Å2--0.26 Å2
L0.0621 °20.0377 °2-0.0421 °2-1.0346 °2-0.0403 °2--0.1379 °2
S0.0477 Å °-0.0182 Å °0.0033 Å °0.0235 Å °-0.0676 Å °0.1647 Å °0.001 Å °0.0114 Å °0.0144 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA31 - 365
2X-RAY DIFFRACTION1allB31 - 365
3X-RAY DIFFRACTION1allC158 - 213
4X-RAY DIFFRACTION1allD158 - 213
5X-RAY DIFFRACTION1allE53 - 61
6X-RAY DIFFRACTION1allF55 - 61

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