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- PDB-6uyd: Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 red... -

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Basic information

Entry
Database: PDB / ID: 6uyd
TitleStructure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 redesigned core from genotype 1a bound to broadly neutralizing antibody AR3C
Components
  • Envelope glycoprotein E2
  • Fab AR3C heavy chain
  • Fab AR3C light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HCV / E2 core / Vaccine design / self-assembly nanoparticle / broadly neutralizing antibodies / bNAbs / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of hexokinase activity / symbiont-mediated perturbation of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / hepacivirin / TBC/RABGAPs / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / symbiont-mediated perturbation of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / hepacivirin / TBC/RABGAPs / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / SH3 domain binding / kinase binding / nucleoside-triphosphate phosphatase / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase 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 / ribonucleoprotein complex / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : ...Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHepatitis C virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å
AuthorsTzarum, N. / Wilson, I.A. / Zhu, J.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI124337 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI129698 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI123861 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI079031 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI123365 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI106005 United States
CitationJournal: Sci Adv / Year: 2020
Title: Proof of concept for rational design of hepatitis C virus E2 core nanoparticle vaccines.
Authors: He, L. / Tzarum, N. / Lin, X. / Shapero, B. / Sou, C. / Mann, C.J. / Stano, A. / Zhang, L. / Nagy, K. / Giang, E. / Law, M. / Wilson, I.A. / Zhu, J.
History
DepositionNov 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Envelope glycoprotein E2
H: Fab AR3C heavy chain
L: Fab AR3C light chain
A: Fab AR3C heavy chain
B: Fab AR3C light chain
F: Envelope glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,52412
Polymers134,7906
Non-polymers1,7346
Water9,368520
1
E: Envelope glycoprotein E2
H: Fab AR3C heavy chain
L: Fab AR3C light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4837
Polymers67,3953
Non-polymers1,0884
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-20 kcal/mol
Surface area27280 Å2
MethodPISA
2
A: Fab AR3C heavy chain
B: Fab AR3C light chain
F: Envelope glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0415
Polymers67,3953
Non-polymers6462
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-30 kcal/mol
Surface area27840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.492, 93.655, 96.799
Angle α, β, γ (deg.)90.000, 100.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HALB

#2: Antibody Fab AR3C heavy chain


Mass: 24627.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Fab AR3C light chain


Mass: 23266.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 522 molecules EF

#1: Protein Envelope glycoprotein E2


Mass: 19500.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus (isolate H) / Production host: Homo sapiens (human) / References: UniProt: P27958*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 6 molecules

#4: 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 genetically manipulated 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
#5: 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


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

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3500, 0.2M di-ammonium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.897→30 Å / Num. obs: 121242 / % possible obs: 99 % / Redundancy: 4.5 % / CC1/2: 0.89 / Net I/σ(I): 25.8
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 5954 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
PDB_EXTRACT3.25data extraction
SCALEPACKdata scaling
PHASERphasing
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MWF

4mwf


Resolution: 1.897→29.914 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 6108 5.04 %
Rwork0.2078 115081 -
obs0.2096 121189 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.01 Å2 / Biso mean: 47.5896 Å2 / Biso min: 21.57 Å2
Refinement stepCycle: final / Resolution: 1.897→29.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8893 0 112 520 9525
Biso mean--80.9 47.51 -
Num. residues----1168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089261
X-RAY DIFFRACTIONf_angle_d0.99312636
X-RAY DIFFRACTIONf_chiral_restr0.0591411
X-RAY DIFFRACTIONf_plane_restr0.0071610
X-RAY DIFFRACTIONf_dihedral_angle_d13.1535456
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8973-1.91880.39671850.3831349191
1.9188-1.94140.37272030.3577377798
1.9414-1.96510.37662010.3382379898
1.9651-1.98990.31522050.3182379698
1.9899-2.01610.33092110.3048385298
2.0161-2.04370.30751880.2989382899
2.0437-2.07290.34331990.2907379199
2.0729-2.10390.29511740.271388099
2.1039-2.13670.31452200.2748375499
2.1367-2.17180.31512100.2631380899
2.1718-2.20920.26722200.2464380099
2.2092-2.24930.30512070.2403383599
2.2493-2.29260.26032250.2325381199
2.2926-2.33940.2751830.2376387299
2.3394-2.39020.2821950.234385199
2.3902-2.44580.30412270.2358379499
2.4458-2.50690.27622250.2339382599
2.5069-2.57470.29291710.2366387699
2.5747-2.65040.30521990.2325386299
2.6504-2.73590.28751950.2384388099
2.7359-2.83360.24231890.2311386299
2.8336-2.9470.28742370.22353863100
2.947-3.0810.24751860.2265385099
3.081-3.24320.26342050.2273389299
3.2432-3.44610.27482070.22043870100
3.4461-3.71180.2342050.1934391199
3.7118-4.08440.18442170.17243875100
4.0844-4.67350.18082170.1393876100
4.6735-5.88080.17581890.15133957100
5.8808-29.9140.20892130.1831394499

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