[English] 日本語
Yorodumi
- PDB-5yow: The post-fusion structure of the Heartland virus Gc glycoprotein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yow
TitleThe post-fusion structure of the Heartland virus Gc glycoprotein
ComponentsGlycoprotein polyprotein
KeywordsVIRAL PROTEIN / Bunyavirus / Heartland virus / Glycoprotein / Gc
Function / homologyPhlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain / virion component => GO:0044423 / membrane => GO:0016020 / Glycoprotein polyprotein
Function and homology information
Biological speciesHeartland virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWu, Y. / Gao, F. / Qi, J.X. / Chai, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81330082 China
National Natural Science Foundation of China81301465 China
CitationJournal: J. Virol. / Year: 2018
Title: The Postfusion Structure of the Heartland Virus Gc Glycoprotein Supports Taxonomic Separation of the Bunyaviral Families Phenuiviridae and Hantaviridae.
Authors: Zhu, Y. / Wu, Y. / Chai, Y. / Qi, J. / Peng, R. / Feng, W.H. / Gao, G.F.
History
DepositionOct 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoprotein polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2612
Polymers46,5441
Non-polymers7171
Water3,657203
1
A: Glycoprotein polyprotein
hetero molecules

A: Glycoprotein polyprotein
hetero molecules

A: Glycoprotein polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,7836
Polymers139,6323
Non-polymers2,1503
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area18610 Å2
ΔGint19 kcal/mol
Surface area48490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.875, 117.875, 117.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

21A-652-

HOH

31A-674-

HOH

41A-713-

HOH

51A-763-

HOH

-
Components

#1: Protein Glycoprotein polyprotein


Mass: 46544.152 Da / Num. of mol.: 1 / Fragment: G2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heartland virus / Production host: Trichoplusia (butterflies/moths) / References: UniProt: J3SPZ8
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 6% (v/v) 2-propanol, 0.1M sodium acetate trihydrate, pH 4.5, 26%(v/v) polyethylene glycol monomethyl ether 550

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 32160 / % possible obs: 100 % / Redundancy: 12.8 % / Rpim(I) all: 0.032 / Net I/σ(I): 23.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.65 / Num. unique obs: 3200 / CC1/2: 0.538 / Rpim(I) all: 0.495 / Χ2: 0.982 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data processing
ADSCdata collection
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G47

5g47


Resolution: 2.1→39.292 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 2003 6.23 %
Rwork0.1821 --
obs0.1853 32128 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 48 203 3421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113292
X-RAY DIFFRACTIONf_angle_d1.2464456
X-RAY DIFFRACTIONf_dihedral_angle_d7.1081982
X-RAY DIFFRACTIONf_chiral_restr0.065510
X-RAY DIFFRACTIONf_plane_restr0.007560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.15270.31861420.26862149X-RAY DIFFRACTION100
2.1527-2.21090.26681420.24192125X-RAY DIFFRACTION100
2.2109-2.2760.271380.23482122X-RAY DIFFRACTION100
2.276-2.34950.32381460.22782141X-RAY DIFFRACTION100
2.3495-2.43340.30331460.2122108X-RAY DIFFRACTION100
2.4334-2.53080.24951410.21532136X-RAY DIFFRACTION100
2.5308-2.6460.26041440.20152167X-RAY DIFFRACTION100
2.646-2.78550.26281410.19962104X-RAY DIFFRACTION100
2.7855-2.95990.25481440.21182171X-RAY DIFFRACTION100
2.9599-3.18840.23051430.19792130X-RAY DIFFRACTION100
3.1884-3.5090.23831450.18422154X-RAY DIFFRACTION100
3.509-4.01640.21821410.16922159X-RAY DIFFRACTION100
4.0164-5.05850.19291430.13132197X-RAY DIFFRACTION100
5.0585-39.29850.21281470.17092262X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 118.9233 Å / Origin y: 101.5321 Å / Origin z: 105.925 Å
111213212223313233
T0.2991 Å20.013 Å20.0272 Å2-0.3267 Å2-0.0005 Å2--0.2866 Å2
L1.2596 °20.8967 °20.8384 °2-0.8873 °20.6742 °2--0.7057 °2
S-0.0537 Å °0.2052 Å °-0.1327 Å °-0.0679 Å °0.1406 Å °-0.1738 Å °0.015 Å °0.1352 Å °-0.0995 Å °
Refinement TLS groupSelection details: all

+
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