[English] 日本語
Yorodumi
- PDB-6h3s: Schmallenberg Virus Glycoprotein Gc Head/Stalk Domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h3s
TitleSchmallenberg Virus Glycoprotein Gc Head/Stalk Domains
ComponentsEnvelopment polyprotein
KeywordsVIRAL PROTEIN / Envelope Glycoprotein
Function / homology
Function and homology information


modulation by virus of host process / host cell Golgi membrane / 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
Bunyavirus glycoprotein G2 / Bunyavirus nonstructural protein NSm / Bunyavirus glycoprotein G2 / Bunyavirus glycoprotein G1 / Bunyavirus glycoprotein G1
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesBovine Schmallenberg virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.023 Å
AuthorsHellert, J. / Aebischer, A. / Wernike, K. / Haouz, A. / Brocchi, E. / Reiche, S. / Guardado-Calvo, P. / Beer, M. / Rey, F.A.
Funding support1items
OrganizationGrant numberCountry
Innovative Medicines Initiative115760
CitationJournal: Nat Commun / Year: 2019
Title: Orthobunyavirus spike architecture and recognition by neutralizing antibodies.
Authors: Hellert, J. / Aebischer, A. / Wernike, K. / Haouz, A. / Brocchi, E. / Reiche, S. / Guardado-Calvo, P. / Beer, M. / Rey, F.A.
History
DepositionJul 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Envelopment polyprotein
A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,85822
Polymers95,7392
Non-polymers2,11920
Water5,513306
1
B: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,93412
Polymers47,8701
Non-polymers1,06511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,92410
Polymers47,8701
Non-polymers1,0549
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.226, 95.226, 204.739
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 47869.551 Da / Num. of mol.: 2 / Fragment: Glycoprotein Gc Head/Stalk Domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine Schmallenberg virus / Gene: GP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: H2AM12
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.5 uL of 12.3 mg/mL EndoH/EndoD-deglycosylated SBV Gc(465-874) in 17.6 mM Tris-Cl pH 8.0, 132 mM NaCl, 0.5 M ammonium sulfate were added to 0.75 uL of reservoir solution containing 0.1 M ...Details: 0.5 uL of 12.3 mg/mL EndoH/EndoD-deglycosylated SBV Gc(465-874) in 17.6 mM Tris-Cl pH 8.0, 132 mM NaCl, 0.5 M ammonium sulfate were added to 0.75 uL of reservoir solution containing 0.1 M MES pH6.5, 5%w/v PEG 400, 2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91908 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91908 Å / Relative weight: 1
ReflectionResolution: 2.01→47.93 Å / Num. obs: 38793 / % possible obs: 60.9 % / Observed criterion σ(I): 1.2 / Redundancy: 17.6 % / Biso Wilson estimate: 45.58 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.02 / Rrim(I) all: 0.1 / Net I/σ(I): 20.6
Reflection shellResolution: 2.01→2.28 Å / Redundancy: 15.6 % / Rmerge(I) obs: 1.91 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1940 / CC1/2: 0.66 / Rpim(I) all: 0.49 / Rrim(I) all: 1.97 / % possible all: 9.8

-
Processing

Software
NameVersionClassification
STARANISOdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.023→47.613 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.3
RfactorNum. reflection% reflection
Rfree0.2404 2283 5.89 %
Rwork0.2095 --
obs0.2113 38789 62.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.93 Å2 / Biso mean: 64.8412 Å2 / Biso min: 26.62 Å2
Refinement stepCycle: final / Resolution: 2.023→47.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6474 0 116 306 6896
Biso mean--79.88 55.93 -
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036734
X-RAY DIFFRACTIONf_angle_d0.5619144
X-RAY DIFFRACTIONf_chiral_restr0.0421032
X-RAY DIFFRACTIONf_plane_restr0.0031148
X-RAY DIFFRACTIONf_dihedral_angle_d15.9154124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0225-2.06650.88320.750456582
2.0665-2.11460.6054110.49961801915
2.1146-2.16750.5617230.437236238510
2.1675-2.22610.4826380.386259763517
2.2261-2.29160.3736500.332280385322
2.2916-2.36550.3478660.3271046111229
2.3655-2.45010.3321910.31831460155140
2.4501-2.54820.35151540.31842432258668
2.5482-2.66410.34612130.30683463367694
2.6641-2.80460.3232290.29736493878100
2.8046-2.98030.27732280.288836503878100
2.9803-3.21030.27442300.247736613891100
3.2103-3.53330.2582310.21137043935100
3.5333-4.04440.23932320.175537103942100
4.0444-5.09450.16272360.149337613997100
5.0945-47.62620.20862490.178139724221100
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)
11.0760.42190.24971.2409-0.15672.75340.0586-0.12460.03350.1577-0.12310.2466-0.1788-1.0319-0.0090.17240.00180.05280.6585-0.12080.2649-7.498831.191617.6869
29.42580.7737-1.58673.1336-1.78595.0754-0.4299-1.8601-0.80021.2552-0.16110.63160.967-0.47320.34311.1788-0.23780.21671.11190.05050.4905-6.869622.266545.6109
30.94960.1801-0.98950.6867-0.54851.43990.1661-0.1171-0.6714-0.079-0.11240.64940.7053-0.0265-0.09490.8123-0.40740.09561.2234-0.04080.7774-18.29719.361226.6717
44.50030.6364-0.22532.7763-0.40890.2013-0.2701-0.4572-0.98690.1640.5264-0.02281.4583-0.91640.17460.839-0.48710.19351.04190.15940.7003-2.09375.276634.6743
55.4139-1.0356-1.11592.34530.50182.0253-0.1752-0.2630.41730.58560.01220.2210.5592-0.28310.16380.5205-0.12510.13350.3506-0.14410.82920.603110.810819.0514
61.8899-0.11611.39181.72010.81273.8433-0.2540.28280.3746-0.18530.0999-0.0723-0.58790.81330.11010.2992-0.09890.02660.29760.0330.380445.890518.581613.2302
74.67052.64322.13974.76433.56657.3421-0.0742-1.0628-0.47992.22010.5405-1.15750.53210.4797-0.40851.14830.159-0.17840.5105-0.00680.528144.97179.551341.3863
81.2721-0.5023-0.12651.5722-1.1051.4197-0.32450.06220.78220.38640.5712-0.5713-1.04240.4315-0.27330.8411-0.2771-0.19190.9038-0.11521.02856.75430.682233.5951
95.3008-0.6506-0.02742.1587-0.00991.7555-0.609-0.23650.51081.15070.5029-0.4260.36970.5570.12330.66680.1686-0.2290.4125-0.13310.416940.420629.066143.1733
102.5077-0.38090.78251.95060.26813.6260.03690.2224-0.28390.1945-0.1662-0.28550.18550.38860.12020.3088-0.0018-0.05230.3011-0.05620.337617.643333.576427.5028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 467:498) or (resseq 522:687))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 499:521))A499 - 521
3X-RAY DIFFRACTION3chain 'A' and ((resseq 688:712))A688 - 712
4X-RAY DIFFRACTION4chain 'A' and ((resseq 713:799))A713 - 799
5X-RAY DIFFRACTION5chain 'A' and ((resseq 800:874))A800 - 874
6X-RAY DIFFRACTION6chain 'B' and ((resseq 467:498) or (resseq 522:687))B0
7X-RAY DIFFRACTION7chain 'B' and ((resseq 499:521))B499 - 521
8X-RAY DIFFRACTION8chain 'B' and ((resseq 688:712))B688 - 712
9X-RAY DIFFRACTION9chain 'B' and ((resseq 713:799))B713 - 799
10X-RAY DIFFRACTION10chain 'B' and ((resseq 800:874))B800 - 874

+
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://pdbjlvh1.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