[English] 日本語
Yorodumi
- PDB-5e05: Structure of Sin Nombre virus nucleoprotein in shot-axis crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 500000
TitleStructure of Sin Nombre virus nucleoprotein in shot-axis crystal form
ComponentsNucleocapsid protein
KeywordsNUCLEAR PROTEIN / hantavirus / Sin Nombre virus / nucleoprotein
Function / homology
Function and homology information


regulation of translation / viral nucleocapsid / endonuclease activity / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Hantavirus nucleocapsid protein / Hantavirus nucleocapsid protein
Similarity search - Domain/homology
PHOSPHATE ION / Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesSin Nombre virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGuo, Y. / Wang, W.M. / Lou, Z.Y.
CitationJournal: J.Virol. / Year: 2015
Title: Crystal Structure of the Core Region of Hantavirus Nucleocapsid Protein Reveals the Mechanism for Ribonucleoprotein Complex Formation
Authors: Guo, Y. / Wang, W. / Sun, Y. / Ma, C. / Wang, X. / Wang, X. / Liu, P. / Shen, S. / Li, B. / Lin, J. / Deng, F. / Wang, H. / Lou, Z.
History
DepositionSep 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2532
Polymers32,1581
Non-polymers951
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-8 kcal/mol
Surface area13640 Å2
Unit cell
Length a, b, c (Å)49.742, 74.908, 154.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Nucleocapsid protein


Mass: 32158.184 Da / Num. of mol.: 1 / Fragment: UNP residues 112-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sin Nombre virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q9E1J8, UniProt: Q89462*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 200 mM HEPES (pH 7.5), 200 mM lithium sulfate monohydrate, 23% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13234 / % possible obs: 100 % / Redundancy: 7.8 % / Net I/σ(I): 31

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5000000 / Resolution: 2.3→41.438 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 648 4.91 %
Rwork0.1826 --
obs0.1849 13200 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→41.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 5 45 2196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082200
X-RAY DIFFRACTIONf_angle_d1.0972977
X-RAY DIFFRACTIONf_dihedral_angle_d15.219815
X-RAY DIFFRACTIONf_chiral_restr0.042327
X-RAY DIFFRACTIONf_plane_restr0.005381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.298-2.47540.25741470.20412416X-RAY DIFFRACTION98
2.4754-2.72450.28251210.20622474X-RAY DIFFRACTION100
2.7245-3.11860.26711130.21652527X-RAY DIFFRACTION100
3.1186-3.92860.2261360.18112501X-RAY DIFFRACTION100
3.9286-41.44470.19331310.15872634X-RAY DIFFRACTION100
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)
10.4607-0.07-0.21520.41980.29271.3757-0.0045-0.10310.1169-0.03590.0051-0.0209-0.22820.03580.01870.17130.0067-0.01860.1723-0.00150.190834.636555.677757.2135
23.1207-0.5862.23312.88151.83173.42620.3026-0.9264-0.8308-0.8295-0.02312.31782.03721.0341-0.28720.98170.0175-0.11430.6733-0.00470.815635.461470.398657.1641
30.04360.023-0.0230.08250.03040.0370.1328-0.058-0.00260.11790.0726-0.08380.05720.03010.02390.2659-0.0266-0.00980.20320.08280.277932.819552.060452.635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1chain A and (residue 114 through 397)114 - 397
2X-RAY DIFFRACTION2chain A and (residue 401 through 401)401
3X-RAY DIFFRACTION3chain A and (residue 501 through 545)501 - 545

+
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