[English] 日本語
Yorodumi
- PDB-9foj: LGTV TP21. Langat virus, strain TP21 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9foj
TitleLGTV TP21. Langat virus, strain TP21
Components
  • Envelope protein E
  • Small envelope protein M
KeywordsVIRUS / Flavivirus / Langat virus / recombinant virus
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated activation of host apoptosis / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated activation of host apoptosis / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. ...Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-CPL / Genome polyprotein
Similarity search - Component
Biological speciesLangat virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsBisikalo, K. / Rosendal, E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-05851 Sweden
Citation
Journal: J Virol / Year: 2025
Title: Influence of the pre-membrane and envelope proteins on structure, pathogenicity, and tropism of tick-borne encephalitis virus.
Authors: Ebba Rosendal / Kyrylo Bisikalo / Stefanie M A Willekens / Marie Lindgren / Jiří Holoubek / Pavel Svoboda / Amanda Lappalainen / Ebba Könighofer / Ekaterina Mirgorodskaya / Rickard ...Authors: Ebba Rosendal / Kyrylo Bisikalo / Stefanie M A Willekens / Marie Lindgren / Jiří Holoubek / Pavel Svoboda / Amanda Lappalainen / Ebba Könighofer / Ekaterina Mirgorodskaya / Rickard Nordén / Federico Morini / William Rosenbaum / Daniel Růžek / Ulf Ahlgren / Maria Anastasina / Andres Merits / Sarah J Butcher / Emma Nilsson / Anna K Överby /
Abstract: Tick-borne encephalitis virus (TBEV) is a neurotropic flavivirus that causes thousands of human infections annually. Viral tropism in the brain is determined by the presence of necessary receptors, ...Tick-borne encephalitis virus (TBEV) is a neurotropic flavivirus that causes thousands of human infections annually. Viral tropism in the brain is determined by the presence of necessary receptors, entry factors, and the ability of the virus to overcome host defenses. The viral structural proteins, pre-membrane (prM), and envelope (E) play an important role in receptor binding, membrane fusion, particle maturation, and antibody neutralization. To understand how these proteins influence virus distribution and tropism in the brain, we generated a chimeric virus harboring the prM and ectodomain of E from TBEV in the background of the low-pathogenic Langat virus (LGTV). We solved the atomic structures of both the chimeric virus and LGTV to compare them to the known TBEV structure. We show that this chimeric virus remains low-pathogenic, while being structurally and antigenically similar to TBEV. Using 3D optical whole brain imaging combined with immunohistochemistry, we found that both LGTV and the chimeric virus primarily infect the cerebral cortex, with no significant differences in their localization or tropism. In contrast, TBEV shows high infection of the cerebellum and a strong preference toward Purkinje cells, indicating that factors other than the prM and E proteins are important for determining TBEV tropism in the brain. Together, this provides new insights into the roles of the structural and non-structural proteins of tick-borne flaviviruses.
IMPORTANCE: Although an effective vaccine exists, there is no treatment for those infected by the tick-borne encephalitis virus (TBEV). This study aimed to better understand how the virus's surface ...IMPORTANCE: Although an effective vaccine exists, there is no treatment for those infected by the tick-borne encephalitis virus (TBEV). This study aimed to better understand how the virus's surface proteins influence viral tropism and pathogenicity. We created a chimeric virus with prM and E proteins of TBEV in the genetic background of the low-pathogenic Langat virus (LGTV). The chimeric virus remained low pathogenic, similar to LGTV. Both viruses infected similar brain regions, while TBEV showed a strong preference for the cerebellum and Purkinje cells. This means that other parts of the virus, such as non-structural proteins or NCR, likely decide how the virus behaves in the brain. This study also presents the first cryogenic electron microscopy structure of LGTV, the first whole-brain imaging of TBEV infection in mouse brain, and a new model system to study surface proteins in tick-borne flaviviruses-laying groundwork for future studies on viral tropism, antibody cross-reactivity, and virus-receptor interaction.
#1: Journal: Biorxiv / Year: 2024
Title: The influence of the pre-membrane and envelope proteins on structure, pathogenicity and tropism of tick-borne encephalitis virus
Authors: Rosendal, E. / Bisikalo, K. / Willekens, S.M. / Lindgren, M. / Holoubek, J. / Svoboda, P. / Lappalainen, A. / Konighofer, E. / Mirgorodskaya, E. / Norden, R. / Morini, F. / Rosenbaum, W. / ...Authors: Rosendal, E. / Bisikalo, K. / Willekens, S.M. / Lindgren, M. / Holoubek, J. / Svoboda, P. / Lappalainen, A. / Konighofer, E. / Mirgorodskaya, E. / Norden, R. / Morini, F. / Rosenbaum, W. / Ruzek, D. / Ahlgren, U. / Anastasina, M. / Merits, A. / Butcher, S.J. / Nilsson, E. / Overby, A.K.
History
DepositionJun 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 2.0Nov 27, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / pdbx_modification_feature / pdbx_struct_sheet_hbond / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
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 / _em_admin.last_update / _pdbx_modification_feature.modified_residue_auth_asym_id / _pdbx_modification_feature.modified_residue_label_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Revision 2.1Sep 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 2.2Oct 1, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,29415
Polymers185,4726
Non-polymers5,8229
Water00
1
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,477,637900
Polymers11,128,343360
Non-polymers349,294540
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

-
Components

#1: Protein Envelope protein E


Mass: 53574.301 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Langat virus (strain TP21) / Cell line (production host): A549 MAVS -/- / Production host: Homo sapiens (human) / References: UniProt: P29837
#2: Protein Small envelope protein M / Matrix protein


Mass: 8249.828 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Langat virus (strain TP21) / Cell line (production host): A549 MAVS -/- / Production host: Homo sapiens (human) / References: UniProt: P29837
#3: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CPL / 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE


Mass: 758.060 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H80NO8P / Comment: phospholipid*YM
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Langat virus (strain TP21) / Type: VIRUS / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Langat virus (strain TP21)
Source (recombinant)Organism: Homo sapiens (human) / Cell: A549 MAVS -/-
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Virus shellDiameter: 500 nm / Triangulation number (T number): 3
Buffer solutionpH: 8
Details: VP-SFM growth medium, supplemented with rapamycin and glutamate.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Alignment procedure: BASIC
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1430

-
Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
14ISOLDEmodel refinement
15Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 15306
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12857 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

+
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