[English] 日本語
Yorodumi
- PDB-5dsd: The crystal structure of the C-terminal domain of Ebola (Bundibug... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dsd
TitleThe crystal structure of the C-terminal domain of Ebola (Bundibugyo) nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Filoviridae
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
P40 nucleoprotein, subdomain 2, Borna disease virus / Ebola nucleoprotein / Ebola nucleoprotein
Similarity search - Domain/homology
Biological speciesBundibugyo virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsBaker, L. / Handing, K.B. / Utepbergenov, D. / Derewenda, U. / Derewenda, Z.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)HDTRA1-14-C-0006 United States
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Molecular architecture of the nucleoprotein C-terminal domain from the Ebola and Marburg viruses.
Authors: Baker, L.E. / Ellena, J.F. / Handing, K.B. / Derewenda, U. / Utepbergenov, D. / Engel, D.A. / Derewenda, Z.S.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2014
Title: The structure of the C-terminal domain of the Zaire ebolavirus nucleoprotein.
Authors: Dziubanska, P.J. / Derewenda, U. / Ellena, J.F. / Engel, D.A. / Derewenda, Z.S.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionSep 30, 2015ID: 5CIJ
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4874
Polymers12,2681
Non-polymers2203
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleoprotein
hetero molecules

A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9758
Polymers24,5352
Non-polymers4396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+2/31
Buried area2910 Å2
ΔGint-35 kcal/mol
Surface area12490 Å2
MethodPISA
3
A: Nucleoprotein
hetero molecules

A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9758
Polymers24,5352
Non-polymers4396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area2050 Å2
ΔGint-32 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.957, 108.957, 82.736
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Nucleoprotein


Mass: 12267.726 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 641-739)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bundibugyo virus / Gene: NP, DH33_45404gpNP / Plasmid: Parallel1-MBPHis / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: B8XCM7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.94 Å3/Da / Density % sol: 79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystallization solution: 1.33 M LiSO4, 0.1 M Tris pH 8.5. 1:1 ratio (250 nL: 250 nL) of precipitant to protein (at a concentration of 13.9 mg/ml). 60 mcL reservoir. Protein purification ...Details: Crystallization solution: 1.33 M LiSO4, 0.1 M Tris pH 8.5. 1:1 ratio (250 nL: 250 nL) of precipitant to protein (at a concentration of 13.9 mg/ml). 60 mcL reservoir. Protein purification buffer 50mM Tris-HCl, 150 mM NaCl; pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.99 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 14, 2014
Diffraction measurementDetails: 0.50 degrees, -1.0 sec, detector distance 350.62 mm
Method: \w scans
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionAv R equivalents: 0.084 / Number: 184210
ReflectionResolution: 2.3→80 Å / Num. obs: 12398 / % possible obs: 94.3 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.084 / Net I/av σ(I): 31.34 / Net I/σ(I): 20.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.432 / % possible all: 64.7
Cell measurementReflection used: 184210

-
Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
REFMAC5.8.0103refinement
SBC-Collectdata collection
HKL-3000phasing
SCALEPACKdata scaling
PHENIXmodel building
HKL-3000data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QB0

4qb0


Resolution: 2.31→80 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.2071 / WRfactor Rwork: 0.1698 / FOM work R set: 0.8163 / SU B: 9.71 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1436 / SU Rfree: 0.1412 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 604 4.9 %RANDOM
Rwork0.1676 ---
obs0.1692 11792 94.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 243.89 Å2 / Biso mean: 81.78 Å2 / Biso min: 46.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å20 Å2
2--0.68 Å2-0 Å2
3----2.2 Å2
Refinement stepCycle: final / Resolution: 2.31→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 13 113 987
Biso mean--115.8 79.01 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019908
X-RAY DIFFRACTIONr_bond_other_d0.0010.02806
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9361225
X-RAY DIFFRACTIONr_angle_other_deg0.89931866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6785104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.10224.90251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3615153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.807153
X-RAY DIFFRACTIONr_chiral_restr0.0710.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02222
X-RAY DIFFRACTIONr_mcbond_it13.6963.935413
X-RAY DIFFRACTIONr_mcbond_other13.6293.925412
X-RAY DIFFRACTIONr_mcangle_it14.3635.917515
LS refinement shellResolution: 2.312→2.372 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 27 -
Rwork0.278 534 -
all-561 -
obs--59.49 %
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)
16.9694-4.8245-5.653410.90716.152922.4559-0.2281-0.0362-0.52990.8334-0.38090.72541.9299-1.40080.6090.8102-0.13670.04810.6334-0.0990.0736-8.65266.0327.423
25.22560.835-0.347513.26045.30526.0221-0.07260.2498-0.3232-0.0731-0.21510.65020.0341-0.60760.28770.40490.0005-0.00960.4396-0.06580.0621-4.86857.11713.558
33.43090.34352.03978.38680.2656.5105-0.1390.0581-0.50160.004-0.03940.147-0.20020.08320.17840.5052-0.0008-0.0070.4583-0.03440.12313.44555.95817.46
44.0368-2.6128-1.76629.64492.15894.7331-0.6915-0.2001-0.41830.6160.18320.31460.2982-0.19340.50830.41920.04250.13370.44130.01550.08455.88846.05724.51
512.2717-3.0546-6.43579.0614-0.443115.8036-0.7594-0.7271-1.32640.76810.30450.27321.02970.19330.45480.47570.0380.3090.28580.05110.376412.66231.19522.992
65.5817-5.3055-0.77656.68941.07375.6811-0.1280.6475-1.0672-0.2807-0.21640.93180.2186-0.4450.34450.5341-0.10770.20180.4981-0.14080.33398.45138.77814.976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A637 - 645
2X-RAY DIFFRACTION2A646 - 661
3X-RAY DIFFRACTION3A662 - 671
4X-RAY DIFFRACTION4A672 - 698
5X-RAY DIFFRACTION5A699 - 715
6X-RAY DIFFRACTION6A716 - 739

+
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