[English] 日本語
Yorodumi
- PDB-6wzq: Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P21 form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wzq
TitleStructure of SARS-CoV-2 Nucleocapsid dimerization domain, P21 form
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / COVID-19 / nucleocapsid / RNA binding
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 ...: / 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 / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / 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 / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsYe, Q. / Corbett, K.D.
Citation
Journal: Protein Sci. / Year: 2020
Title: Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein.
Authors: Ye, Q. / West, A.M.V. / Silletti, S. / Corbett, K.D.
#1: Journal: Biorxiv / Year: 2020
Title: Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein.
Authors: Ye, Q. / West, A.M.V. / Silletti, S. / Corbett, K.D.
#2: Journal: Protein Sci. / Year: 2020
Title: Architecture and self-assembly of the SARS-CoV-2 ucleocapsid protein
Authors: Ye, Q. / West, A.M.V. / Silletti, S. / Corbett, K.D.
History
DepositionMay 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Sep 9, 2020Group: Database references / Category: citation / citation_author
Revision 1.4Apr 7, 2021Group: Database references / Category: citation / citation_author
Revision 1.5Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,93810
Polymers62,3624
Non-polymers5766
Water8,881493
1
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4695
Polymers31,1812
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-61 kcal/mol
Surface area12070 Å2
MethodPISA
2
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4695
Polymers31,1812
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-51 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.146, 43.546, 74.233
Angle α, β, γ (deg.)90.000, 94.870, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 15590.458 Da / Num. of mol.: 4
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5, 50 mM Ammonium Sulfate, and 38% polyethylene glycol (PEG) 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→74 Å / Num. obs: 80163 / % possible obs: 98.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Net I/σ(I): 16
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2 / Num. unique obs: 3906 / CC1/2: 0.796 / Rrim(I) all: 0.877

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WXO

6wxo


Resolution: 1.45→73.97 Å / SU ML: 0.144 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 20.7015
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1802 3919 4.89 %
Rwork0.1673 76201 -
obs0.168 80120 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.5 Å2
Refinement stepCycle: LAST / Resolution: 1.45→73.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3637 0 30 493 4160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093785
X-RAY DIFFRACTIONf_angle_d0.9225127
X-RAY DIFFRACTIONf_chiral_restr0.0804527
X-RAY DIFFRACTIONf_plane_restr0.0081675
X-RAY DIFFRACTIONf_dihedral_angle_d21.70181401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.460.30961170.28882404X-RAY DIFFRACTION88.89
1.46-1.480.29921370.26322689X-RAY DIFFRACTION97.55
1.48-1.50.26641250.25022698X-RAY DIFFRACTION97.08
1.5-1.520.26931370.2362577X-RAY DIFFRACTION96.34
1.52-1.550.28171550.22362764X-RAY DIFFRACTION99.56
1.55-1.570.22491150.21812710X-RAY DIFFRACTION99.65
1.57-1.590.24551230.20572751X-RAY DIFFRACTION99.76
1.59-1.620.20631320.19212768X-RAY DIFFRACTION99.62
1.62-1.650.2321410.19012707X-RAY DIFFRACTION99.41
1.65-1.680.21431450.18932757X-RAY DIFFRACTION99.83
1.68-1.710.221240.18592736X-RAY DIFFRACTION99.51
1.71-1.740.26231470.19272722X-RAY DIFFRACTION99.38
1.74-1.780.21051180.18992722X-RAY DIFFRACTION99.51
1.78-1.820.19691410.1862768X-RAY DIFFRACTION99.22
1.82-1.870.23381510.17452681X-RAY DIFFRACTION99.02
1.87-1.920.19561300.17182733X-RAY DIFFRACTION99.1
1.92-1.980.18921490.16642715X-RAY DIFFRACTION98.59
1.98-2.040.19891500.1672722X-RAY DIFFRACTION98.93
2.04-2.110.18961480.16292673X-RAY DIFFRACTION98.46
2.11-2.20.17681220.16452803X-RAY DIFFRACTION99.83
2.2-2.30.16991360.15712771X-RAY DIFFRACTION99.9
2.3-2.420.17841550.1592726X-RAY DIFFRACTION99.83
2.42-2.570.19411480.16822769X-RAY DIFFRACTION99.93
2.57-2.770.19531560.17092754X-RAY DIFFRACTION99.79
2.77-3.050.18841240.16512756X-RAY DIFFRACTION99.55
3.05-3.490.16961360.16472773X-RAY DIFFRACTION98.78
3.49-4.390.13451550.13842726X-RAY DIFFRACTION97.07
4.39-73.970.15762020.1622826X-RAY DIFFRACTION99.61
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)
11.01576948675-0.0941243664726-0.2949170118163.998942038440.3629217316171.390133265830.0642687264618-0.130679751902-0.05158593450920.604098270551-0.090859416885-0.3384830079130.1470468583580.07661234200970.009571119727910.206504227629-0.0274869832256-0.0792741180310.1927289401230.01741459671590.1662721300237.221511991014.1320229875424.3224027882
20.6546413687440.2912192802980.2394699920762.906811476330.1023638642371.693246921870.02220829154730.02804411861020.0413881381806-0.218335696102-0.0841535767024-0.0798322691966-0.1275944087140.06067097794770.06219146935630.1464795777780.00721182967641-0.01080382363050.1706747305820.007318717792710.1459175766365.5639046316314.814556066511.0529991376
30.4543765885770.0922926193934-0.3500138700363.399135552130.08093636156750.8950344130080.01201247867070.0752505484510.0171716598769-0.350341410811-0.0369446395428-0.0848344433507-0.073814156328-0.0717942624280.02991736023290.1544885364310.004674343376260.01463665286290.1964885917290.0005246038114290.176592807651-34.415070225920.282053843425.2684199618
41.30473023224-0.2479339865220.1439691099292.69605643183-0.03339147988211.45704923325-0.02082733561270.192374807353-0.0800662312043-0.9704506421950.0130373896529-0.659273595031-0.02956821069030.2058709079580.02558803572650.381662224673-0.003253139153390.2256499513410.233953740601-0.02439911585810.293965686468-25.26413823379.7284673714815.1021751224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

+
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