[English] 日本語
Yorodumi
- PDB-8tfd: Crystal structure of a stem-loop DNA aptamer complexed with SARS-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tfd
TitleCrystal structure of a stem-loop DNA aptamer complexed with SARS-CoV-2 nucleocapsid protein RNA-binding domain
Components
  • DNA aptamer
  • Nucleoprotein
KeywordsVIRAL PROTEIN / DNA binding protein / endonuclease / replication
Function / homology
Function and homology information


response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways ...response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / VEGFR2 mediated vascular permeability / molecular condensate scaffold activity / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / DDX58/IFIH1-mediated induction of interferon-alpha/beta / MHC class I protein complex / RNA stem-loop binding / Interleukin-1 signaling / Interferon alpha/beta signaling / viral capsid / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / Induction of Cell-Cell Fusion / Attachment and Entry / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / RNA binding / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsEsler, M. / Belica, C. / Shi, K. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA234228 United States
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain.
Authors: Esler, M.A. / Belica, C.A. / Rollie, J.A. / Brown, W.L. / Moghadasi, S.A. / Shi, K. / Harki, D.A. / Harris, R.S. / Aihara, H.
History
DepositionJul 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein
B: DNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7928
Polymers20,4202
Non-polymers3726
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint3 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.795, 54.133, 98.813
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

-
Components

#1: Protein Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 14254.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC9
#2: DNA chain DNA aptamer


Mass: 6164.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium formate,10% w/v Polyvinylpyrrolidone, 20% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→54.13 Å / Num. obs: 27808 / % possible obs: 92.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 21.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.025 / Rrim(I) all: 0.066 / Net I/σ(I): 16.6 / Num. measured all: 171070
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 43.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.416 / Num. measured all: 1371 / Num. unique obs: 636 / CC1/2: 0.758 / Rpim(I) all: 0.304 / Rrim(I) all: 0.519 / Net I/σ(I) obs: 1.3

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→47.48 Å / SU ML: 0.1703 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.2038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1887 1438 5.18 %
Rwork0.1591 26311 -
obs0.1606 27749 91.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.75 Å2
Refinement stepCycle: LAST / Resolution: 1.55→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 409 24 249 1670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01471492
X-RAY DIFFRACTIONf_angle_d1.41262100
X-RAY DIFFRACTIONf_chiral_restr0.085220
X-RAY DIFFRACTIONf_plane_restr0.0157204
X-RAY DIFFRACTIONf_dihedral_angle_d21.2361574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.610.3434900.34661563X-RAY DIFFRACTION55.38
1.61-1.670.28321250.23752090X-RAY DIFFRACTION75.31
1.67-1.750.26041090.19252562X-RAY DIFFRACTION89.3
1.75-1.840.20441520.16832781X-RAY DIFFRACTION98.99
1.84-1.950.17911580.17712823X-RAY DIFFRACTION99.87
1.95-2.10.22561550.18572852X-RAY DIFFRACTION99.87
2.1-2.320.21411600.16272838X-RAY DIFFRACTION99.87
2.32-2.650.1731690.16462861X-RAY DIFFRACTION99.7
2.65-3.340.18161540.15212901X-RAY DIFFRACTION99.58
3.34-47.480.16411660.13493040X-RAY DIFFRACTION99.66
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.98659017224-1.16639128916-0.03762279993394.087512688171.442797943026.351145725260.0396173119201-0.4236574627610.5657816524040.5422697792560.003894749721670.376765362252-0.331211040302-0.4551467361010.05034500297870.2095166726040.007053677166570.05413883920430.181388375075-0.02927925337650.173649924588-6.16260623909-3.4706201747933.3426555526
27.238214514382.287762029221.211922793455.504321532191.161277497282.64612018822-0.2761322824140.6182422146970.137556372352-0.5286495572190.165257274633-0.449308004994-0.0792900911790.4322046644520.02594154343180.194691379665-0.03705980298040.04217710963830.2101770787360.01926577917330.2133107618395.33689805471-0.49520629193718.6575197338
34.22820081991.2320487960.9479535386124.004460326060.520297562182.748674189770.00158315463996-0.0133873169105-0.1061174501950.00333575467383-0.04003489054330.2800826637040.156257846357-0.2082061488330.05770014670670.08890223230410.008327539232490.009539250383780.1273895523370.007014566714510.0983640113574-9.58009805015-6.8574526147321.4043374872
42.61440682948-0.5283793084862.27558971394.05892991479-0.9193848197575.88090270686-0.11189807946-0.196291692601-0.06426450319330.304358008028-0.0408479064387-0.583209401394-0.2088294256560.6422665841310.03330680533480.179803681297-0.0114999373376-0.03423851390350.2684901932660.03697852160980.27514966536112.65188377258.4125736894336.3755435882
58.844976704556.949883039282.995875696116.446690318332.537953847241.58574095651-0.04542486773220.00069889864562-0.1043298269550.006645019712160.0329661052047-0.276439448636-0.03206060237020.0308646597813-0.005233504929350.1492542313370.01905122190840.002618593780610.1381030165190.01890083996530.1325072425691.916174039351.6602263775128.4069741616
64.26312368658-0.6050792014581.051991353150.184182182561-0.03609718444551.0156609238-0.255468189250.06739184828430.32507773815-0.06351100414510.0476721745622-0.0747651825865-0.181570349464-0.1128742938910.1803063623980.1916448347060.02159090191-0.03057550483830.130565011173-0.0167851347850.232820734254-11.44694554055.5274409208721.636507256
74.471812465725.565985691133.051301199477.436055597032.904254644683.70179513867-0.1620045545270.1082060031240.100271123197-0.2274418112240.1032202507750.163309019231-0.0863370288919-0.1869532789680.01107599775690.1020401739590.00576042095384-0.006031764118690.152184242105-0.009869636162450.13236905929-11.7776269946-3.6017510134416.4387365539
81.59515827303-0.254151206082.157664936110.64497260377-0.5849058977835.30681087519-0.0800516148273-0.483688298126-0.04863183605350.1637768019360.0175977965130.2714695759070.00851786972248-0.8681956305050.003939368747090.169443086561-0.03410897914910.04790179362710.235991503326-0.007870600109080.178801477644-12.4033958676-5.9067233605132.2299721385
93.243006452382.05620050932-0.8331653264382.39098314350.1819692589830.6798224793820.0355434658090.0711429855764-0.0844095733959-0.04733393875910.160142143754-0.7208148115360.001733016561060.379010609493-0.1221349763160.144833149013-0.009614147243280.03009445531590.161728400334-0.03725384808930.2618657778713.25736801554-10.241334148418.5129157275
105.05904680946-1.02902480991-3.709375443133.46089658129-3.08322216687.252500666110.8853308388120.8933703490150.757366884934-0.801658790571-0.1380949858220.6205049603960.187938619403-0.989161672574-0.5847933687810.5389425827330.01452568161770.06130583509520.627481312448-0.003173011808580.394621336829-3.373324343720.43396269926353.3608509972
112.46742339464-0.004579783447142.354819144312.12039284015-0.6249539413132.953120889720.0486698023163-0.104972317558-0.1506824568320.214310962688-0.00620137879612-0.09728968835250.177938894720.114432065902-0.01672358419150.229983721410.0205033582875-0.003452302934010.2205989762890.005300253990850.1529035396766.65344869507-1.8882958173440.0817341446
125.09865573806-4.717802832-5.515087491464.631416356025.134749202076.22542695993-0.141574541356-0.3000163200410.1275051607640.2011559146190.111698473747-0.3748794345351.282572226950.6143923772560.05257102726320.4653224917780.08245840767430.05604592375060.3525176485510.05999314636430.2341825070492.76663404509-3.5951244650955.8826213642
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 47 through 56 )AA47 - 561 - 10
22chain 'A' and (resid 57 through 66 )AA57 - 6611 - 20
33chain 'A' and (resid 67 through 90 )AA67 - 9021 - 44
44chain 'A' and (resid 91 through 100 )AA91 - 10045 - 54
55chain 'A' and (resid 101 through 112 )AA101 - 11255 - 66
66chain 'A' and (resid 113 through 129 )AA113 - 12967 - 83
77chain 'A' and (resid 130 through 139 )AA130 - 13984 - 93
88chain 'A' and (resid 140 through 159 )AA140 - 15994 - 113
99chain 'A' and (resid 160 through 173 )AA160 - 173114 - 127
1010chain 'B' and (resid 1 through 5 )BG1 - 5
1111chain 'B' and (resid 6 through 15 )BG6 - 15
1212chain 'B' and (resid 16 through 20 )BG16 - 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more