[English] 日本語
Yorodumi
- PDB-2i8b: Crystal structure of the C-terminal domain of Ebola virus VP30 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i8b
TitleCrystal structure of the C-terminal domain of Ebola virus VP30
ComponentsMinor nucleoprotein VP30
KeywordsVIRAL PROTEIN / VP30 Ebola virus protein / transcription / RNA binding
Function / homology
Function and homology information


symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / positive regulation of viral transcription / viral nucleocapsid / host cell cytoplasm / single-stranded RNA binding / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding / zinc ion binding / identical protein binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1160 / Transcriptional activator VP30, Filoviridae type / Ebola virus-specific transcription factor VP30 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional activator VP30 / Transcriptional activator VP30
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMuziol, T.M. / Hartlieb, B. / Becker, S. / Weissenhorn, W.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystal structure of the C-terminal domain of Ebola virus VP30 reveals a role in transcription and nucleocapsid association.
Authors: Hartlieb, B. / Muziol, T. / Weissenhorn, W. / Becker, S.
History
DepositionSep 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Minor nucleoprotein VP30
B: Minor nucleoprotein VP30


Theoretical massNumber of molelcules
Total (without water)35,0712
Polymers35,0712
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-32 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.370, 63.590, 80.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEGLNAA142 - 15722 - 37
21ILEGLNBB142 - 15722 - 37
32GLUPHEAA163 - 18143 - 61
42GLUPHEBB163 - 18143 - 61
53SERARGAA182 - 19562 - 75
63SERARGBB182 - 19562 - 75
74GLNSERAA203 - 21683 - 96
84GLNSERBB203 - 21683 - 96
95GLYGLNAA219 - 24899 - 128
105GLYGLNBB219 - 24899 - 128
116SERARGAA254 - 262134 - 142
126SERARGBB254 - 262134 - 142

-
Components

#1: Protein Minor nucleoprotein VP30 / Transcription activator VP30


Mass: 17535.570 Da / Num. of mol.: 2 / Fragment: C-terminal domain, residues 142-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Genus: Ebola-like viruses / Gene: VP30 / Plasmid: pProEx Htb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon + / References: UniProt: Q05323, UniProt: Q77DJ5*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M ammonium acetate, 15mM magnesium acetate tetrahydrate, 0.05M sodium cacodylate, 10%(v/v) isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97630, 0.97950
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: May 9, 2005 / Details: toroidal mirror
RadiationMonochromator: Si Channel cut crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
20.97951
ReflectionResolution: 2→25 Å / Num. all: 20848 / Num. obs: 20788 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 5.7 / Num. unique all: 2793 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
CCP4(SCALA)data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.898 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: hydrogens have been added in the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.24055 1101 5.3 %RANDOM
Rwork0.19504 ---
all0.19736 20788 --
obs0.19736 20788 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.549 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å20 Å2
2---3.03 Å20 Å2
3---5.01 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 0 174 2228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222121
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.9692880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2165269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93723.40791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30215396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4471518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021553
X-RAY DIFFRACTIONr_nbd_refined0.2060.2979
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2138
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.215
X-RAY DIFFRACTIONr_mcbond_it0.7351.51343
X-RAY DIFFRACTIONr_mcangle_it1.26322112
X-RAY DIFFRACTIONr_scbond_it1.9023877
X-RAY DIFFRACTIONr_scangle_it3.1134.5762
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 807 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.515
loose thermal2.7210
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 67 -
Rwork0.238 1451 -
obs--100 %
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)
12.0415-0.52610.64240.9835-0.12030.30990.0106-0.0750.06410.0017-0.03340.160.01370.00770.0228-0.0116-0.00590.0339-0.026-0.0036-0.04184.2732.734.676
20.9733-0.1571-0.24250.6695-0.14570.11350.0071-0.07850.16390.00430.0031-0.04880.05290.0513-0.01010.0153-0.0052-0.03480.0043-0.0181-0.062228.31929.7695.251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA140 - 26620 - 146
2X-RAY DIFFRACTION2BB135 - 26615 - 146

+
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