[English] 日本語
Yorodumi
- PDB-6ya2: Crystal structure of TSWV glycoprotein N ectodomain (Trypsin treated) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ya2
TitleCrystal structure of TSWV glycoprotein N ectodomain (Trypsin treated)
ComponentsGlycoprotein
KeywordsVIRAL PROTEIN / Envelope protein / attachment / viral entry / receptor binding / viral assembly
Function / homology
Function and homology information


modulation by virus of host process / host cell Golgi membrane / host cell Golgi apparatus / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Envelope glycoprotein precursor/M polyprotein precursor, Tospovirus type / Bunyavirus glycoprotein G1 / Bunyavirus glycoprotein G1
Similarity search - Domain/homology
Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesTomato spotted wilt virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDessau, M. / Bahat, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Crystal structure of tomato spotted wilt virus G N reveals a dimer complex formation and evolutionary link to animal-infecting viruses
Authors: Bahat, Y. / Alter, J. / Dessau, M.
History
DepositionMar 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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: Glycoprotein
B: Glycoprotein
C: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5539
Polymers65,8203
Non-polymers1,7346
Water1,42379
1
A: Glycoprotein
B: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1716
Polymers43,8802
Non-polymers1,2914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-4 kcal/mol
Surface area21030 Å2
MethodPISA
2
C: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3823
Polymers21,9401
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint5 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.660, 76.010, 71.180
Angle α, β, γ (deg.)90.000, 106.560, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glycoprotein /


Mass: 21939.869 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: This construct is a S214C mutant construct based on 6YA0 entry.
Source: (gene. exp.) Tomato spotted wilt virus / Gene: Gn, Gc / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A3G1GK10, UniProt: O55647*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19% PEG 8,000 (w/v) 0.1 M tris pH 7.5 0.2 M magnesium chloride hexahydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→18.85 Å / Num. obs: 24477 / % possible obs: 98.5 % / Redundancy: 6.976 % / Biso Wilson estimate: 67.877 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.108 / Χ2: 1.026 / Net I/σ(I): 13.14 / Num. measured all: 170741 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.67.121.833119225275027000.561.97798.2
2.6-2.77.1551.3271.4416800235923480.7031.43199.5
2.7-2.87.0780.9372.1114290202320190.8221.01199.8
2.8-2.97.1250.7192.7212455175417480.870.77599.7
2.9-36.8570.5313.6210389152615150.9140.57599.3
3-3.56.6490.1978.5734434529851790.990.21497.8
3.5-47.2850.09318.1921717299629810.9970.199.5
4-57.0550.0530.1820877297129590.9990.05499.6
5-76.5220.04931.9612561200819260.9980.05395.9
7-107.4710.03245.7556037527500.9990.03499.7
10-137.2570.03151.316112212220.9990.033100
13-156.750.03249.6345969680.9990.03598.6
15-18.855.1610.0440.11320128620.9990.04448.4

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YA0

6ya0


Resolution: 2.5→18.85 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 1026 5.03 %
Rwork0.2129 19391 -
obs0.2145 20417 82.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.65 Å2 / Biso mean: 75.2674 Å2 / Biso min: 16.24 Å2
Refinement stepCycle: final / Resolution: 2.5→18.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 112 79 4438
Biso mean--143.49 57.06 -
Num. residues----551
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.630.3138590.2948109032
2.63-2.80.26171170.2975211564
2.8-3.010.37931520.2997294489
3.01-3.320.2991700.2515323897
3.32-3.790.24491760.21263334100
3.79-4.760.21991760.18223343100
Refinement TLS params.Method: refined / Origin x: -13.7352 Å / Origin y: -8.7137 Å / Origin z: 4.6998 Å
111213212223313233
T0.1986 Å20.022 Å2-0.0601 Å2-0.1594 Å2-0.0227 Å2--0.2165 Å2
L1.89 °20.2947 °20.0571 °2-1.076 °2-0.0304 °2--0.9243 °2
S0.0484 Å °-0.2075 Å °-0.1774 Å °0.0766 Å °-0.0214 Å °-0.0601 Å °-0.0012 Å °-0.0402 Å °-0.012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA109 - 296
2X-RAY DIFFRACTION1allA297 - 301
3X-RAY DIFFRACTION1allB107 - 296
4X-RAY DIFFRACTION1allB301 - 303
5X-RAY DIFFRACTION1allC110 - 295
6X-RAY DIFFRACTION1allC296 - 301
7X-RAY DIFFRACTION1allZ1 - 122

+
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