- PDB-4ypi: Structure of Ebola virus nucleoprotein N-terminal fragment bound ... -
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Basic information
Entry
Database: PDB / ID: 4ypi
Title
Structure of Ebola virus nucleoprotein N-terminal fragment bound to a peptide derived from Ebola VP35
Components
Nucleoprotein
Polymerase cofactor VP35
Keywords
RNA BINDING PROTEIN / protein complex. / Ebola virus / nucleoprotein / VP35 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information
suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / molecular sequestering activity / viral RNA genome packaging ...suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / molecular sequestering activity / viral RNA genome packaging / positive regulation of protein sumoylation / : / helical viral capsid / viral transcription / viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / negative regulation of gene expression / RNA binding Similarity search - Function
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
R01AI081914
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
U19AI109945
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
U19AI109664
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
U19AI109664
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
HHSN272201200026C
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
P41GM103832
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
P50GM1003297
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
R01AI059536
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
R01AI077519
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
R01AI107056
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01GM053163
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
P41GM103399
United States
Department of Energy (DOE, United States)
DE-AC02-06CH11357
United States
Defense Threat Reduction Agency (DTRA)
DTRA 1_21_1_0002
United States
Defense Threat Reduction Agency (DTRA)
HDTRA1_12_1_0051
United States
Defense Threat Reduction Agency (DTRA)
HDTRA1_14_1_0013
United States
Citation
Journal: Cell Rep / Year: 2015 Title: An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions. Authors: Daisy W Leung / Dominika Borek / Priya Luthra / Jennifer M Binning / Manu Anantpadma / Gai Liu / Ian B Harvey / Zhaoming Su / Ariel Endlich-Frazier / Juanli Pan / Reed S Shabman / Wah Chiu / ...Authors: Daisy W Leung / Dominika Borek / Priya Luthra / Jennifer M Binning / Manu Anantpadma / Gai Liu / Ian B Harvey / Zhaoming Su / Ariel Endlich-Frazier / Juanli Pan / Reed S Shabman / Wah Chiu / Robert A Davey / Zbyszek Otwinowski / Christopher F Basler / Gaya K Amarasinghe / Abstract: During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In ...During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20-48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
ID
Density Matthews (Å3/Da)
Density % sol (%)
3
3.77
67.4
1
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop Details: streak seeding in well solution containing 100 mM Tris pH 7.2, 50 mM Hepes pH 7, and 23% PEG400 PH range: 7-7.4
Resolution: 3.7→3.72 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2 / % possible all: 10.2
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0049
refinement
HKL-2000
datacollection
HKL-2000
datascaling
PDB_EXTRACT
3.15
dataextraction
HKL-3000
datascaling
HKL-3000
phasing
SHELXDE
phasing
HKL-3000
datareduction
Refinement
Method to determine structure: SAD / Resolution: 3.71→25 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.868 / SU B: 113.728 / SU ML: 0.723 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.832 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.285
1163
5 %
RANDOM
Rwork
0.2529
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-
-
obs
0.2546
21925
84.75 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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