[English] 日本語
Yorodumi
- PDB-5w2b: Crystal structure of C-terminal domain of Ebola (Reston) nucleopr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w2b
TitleCrystal structure of C-terminal domain of Ebola (Reston) nucleoprotein in complex with Fab fragment
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • Nucleoprotein
Keywordsviral protein/immune system / Ebola virus / nucleoprotein / Fab / antibody-antigen interaction / VIRAL PROTEIN / viral protein-immune system complex
Function / homology
Function and homology information


viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Ebola nucleoprotein / Ebola nucleoprotein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Reston ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRadwanska, M.J. / Derewenda, U. / Kossiakoff, A.A. / Derewenda, Z.S.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: The structure of the C-terminal domain of the nucleoprotein from the Bundibugyo strain of the Ebola virus in complex with a pan-specific synthetic Fab.
Authors: Radwanska, M.J. / Jaskolowski, M. / Davydova, E. / Derewenda, U. / Miyake, T. / Engel, D.A. / Kossiakoff, A.A. / Derewenda, Z.S.
History
DepositionJun 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Fab Heavy Chain
L: Fab Light Chain
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)60,9383
Polymers60,9383
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-34 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.508, 88.516, 137.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Fab Heavy Chain


Mass: 25216.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab Light Chain


Mass: 23258.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 12462.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reston ebolavirus / Strain: Reston-89 / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: Q8JPY1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mM xylitol, 20 mM myo-Inositol, 20 mM D-Fructose, 20 mM L-Rhamnose monohydrate, 20 mM D-Sorbitol, 0.1 M BES pH 7.5, 0.1 M triethanolamine (TEA) pH 7.5, 10% w/v PEG 8000, 20% w/v 1,5-Pentanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 14, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 28393 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 50.8 Å2 / Rpim(I) all: 0.034 / Χ2: 1.173 / Net I/σ(I): 3.21
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 5 % / Num. unique obs: 1835 / CC1/2: 0.836 / Rpim(I) all: 0.249

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data collection
HKL-3000data processing
HKL-3000data scaling
PHENIX1.9_1692phasing
PHENIX1.9_1692model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VKD

5vkd


Resolution: 2.25→40.623 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.45
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 1417 5 %Random selection
Rwork0.1979 ---
obs0.2007 28332 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→40.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4131 0 0 111 4242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074242
X-RAY DIFFRACTIONf_angle_d1.0145762
X-RAY DIFFRACTIONf_dihedral_angle_d14.7581516
X-RAY DIFFRACTIONf_chiral_restr0.04633
X-RAY DIFFRACTIONf_plane_restr0.005732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.246-2.32630.36521370.26462600X-RAY DIFFRACTION98
2.3263-2.41940.34261390.25492636X-RAY DIFFRACTION100
2.4194-2.52950.29541400.23672667X-RAY DIFFRACTION100
2.5295-2.66290.3031410.23612664X-RAY DIFFRACTION100
2.6629-2.82970.31391400.23612666X-RAY DIFFRACTION100
2.8297-3.04810.31711400.22862675X-RAY DIFFRACTION100
3.0481-3.35470.28261420.2252690X-RAY DIFFRACTION100
3.3547-3.83980.2431420.20022702X-RAY DIFFRACTION100
3.8398-4.83650.21751450.16922746X-RAY DIFFRACTION100
4.8365-40.62930.21781510.17122869X-RAY DIFFRACTION100

+
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