[English] 日本語
Yorodumi
- PDB-3v7o: Crystal structure of the C-terminal domain of Ebola virus VP30 (s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v7o
TitleCrystal structure of the C-terminal domain of Ebola virus VP30 (strain Reston-89)
ComponentsMinor nucleoprotein VP30
KeywordsTRANSCRIPTION / Ebola / VP30 / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Smt / nucleoprotein
Function / homology
Function and homology information


viral nucleocapsid / host cell cytoplasm / RNA binding / metal ion binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1160 / Transcriptional activator VP30, Filoviridae type / Ebola virus-specific transcription factor VP30 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ubiquitin-like (UB roll) / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Minor nucleoprotein VP30
Similarity search - Component
Biological speciesReston ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structure of the Reston ebolavirus VP30 C-terminal domain.
Authors: Clifton, M.C. / Kirchdoerfer, R.N. / Atkins, K. / Abendroth, J. / Raymond, A. / Grice, R. / Barnes, S. / Moen, S. / Lorimer, D. / Edwards, T.E. / Myler, P.J. / Saphire, E.O.
History
DepositionDec 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Sep 13, 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 / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,6954
Polymers51,5712
Non-polymers1242
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-27 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.310, 93.740, 111.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Minor nucleoprotein VP30 / Transcription activator VP30


Mass: 25785.299 Da / Num. of mol.: 2 / Fragment: UNP residues 142 - 272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reston ebolavirus / Strain: Reston-89 / Gene: VP30 / Plasmid: pEMB001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8JPX6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: EbreA.17250.a at 18.3 mg/ml. 10% PEG6000, 0.1M HEPES pH 7.0, Cryoprotectant 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionHighest resolution: 2.25 Å / Num. obs: 25173 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.18
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.25-2.310.5063.151100
2.31-2.370.4423.58199.9
2.37-2.440.3914.11199.9
2.44-2.520.3314.781100
2.52-2.60.2655.83199.9
2.6-2.690.2266.71199.9
2.69-2.790.1938.09199.9
2.79-2.90.1699.011100
2.9-3.030.13211.241100
3.03-3.180.10913.47199.9
3.18-3.350.07418.231100
3.35-3.560.05723.161100
3.56-3.80.04627.67199.9
3.8-4.110.0432.56199.9
4.11-4.50.03634.24199.8
4.5-5.030.03536.3199.8
5.03-5.810.03732.61199.8
5.81-7.120.03930.561100
7.12-10.060.02343.041100
10.060.01947.81183.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å19.63 Å
Translation2.8 Å19.63 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I8B

2i8b


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.341 / SU ML: 0.118 / SU R Cruickshank DPI: 0.2023 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1280 5.1 %RANDOM
Rwork0.19307 ---
obs0.19478 23841 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.562 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20 Å2
2--1.35 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 8 150 2712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192605
X-RAY DIFFRACTIONr_bond_other_d0.0010.021750
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9623522
X-RAY DIFFRACTIONr_angle_other_deg0.89934269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2665329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75524.052116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21415461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8441519
X-RAY DIFFRACTIONr_chiral_restr0.0730.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022889
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02526
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 95 -
Rwork0.241 1577 -
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)
11.386-0.2087-0.64580.3438-0.17411.1353-0.01480.0738-0.1212-0.0695-0.04170.00120.1378-0.06410.05650.0774-0.014-0.00820.0407-0.01650.09235.695-28.5671-8.0233
21.8774-0.16130.52471.0601-0.45012.7089-0.0222-0.06180.07040.0237-0.04810.0778-0.1361-0.18040.07030.03950.0093-0.00160.0466-0.01620.10567.1834-20.8681-6.7162
32.7038-6.18593.730330.49664.415515.41540.0152-0.2024-0.1386-1.2422-0.36310.9149-1.003-0.99240.34790.22290.08260.03020.3303-0.10350.40796.0289-29.7744-33.6077
43.19310.32-0.11872.77040.11712.99720.09020.36830.0706-0.1444-0.0042-0.064-0.0243-0.0158-0.0860.0429-0.0099-0.00930.07760.04270.0404-15.6696-10.8708-22.4483
54.2934-3.3478-4.61796.14225.52286.34310.02320.235-0.2458-0.1065-0.2980.1915-0.0416-0.36670.27480.09270.0088-0.0220.0854-0.07570.089110.8947-39.5771-30.3106
62.60990.95460.98261.93040.73964.5829-0.0630.2950.0062-0.26660.1069-0.0833-0.03590.425-0.04390.08510.01270.01630.0772-0.02120.036921.7902-30.2631-31.6893
70.07840.081-0.58170.2601-0.33155.2236-0.03720.0027-0.0181-0.00280.1130.01870.39860.2674-0.07580.10480.0406-0.01280.1127-0.03550.160619.4342-36.1416-14.8845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 60
2X-RAY DIFFRACTION2A61 - 112
3X-RAY DIFFRACTION3A113 - 124
4X-RAY DIFFRACTION4B-77 - -2
5X-RAY DIFFRACTION5B-1 - 20
6X-RAY DIFFRACTION6B21 - 97
7X-RAY DIFFRACTION7B98 - 125

+
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