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- PDB-6wo5: Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from... -

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Basic information

Entry
Database: PDB / ID: 6wo5
TitleStructure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 1a bound to neutralizing antibody 212.1.1 and non neutralizing antibody E1
Components
  • Envelope glycoprotein E2
  • Fab 212.1.1 heavy chain
  • Fab 212.1.1 light chain
  • Fab E1 heavy chain
  • Fab E1 light chain
KeywordsIMMUNE SYSTEM/Viral Protein / HCV / broadly neutralizing antibodies / bNAbs / E2 core / IGHV1-69 / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral Protein complex
Function / homology
Function and homology information


positive regulation of hexokinase activity / modulation by virus 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 / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus 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 / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endoplasmic reticulum-Golgi intermediate compartment membrane / SH3 domain binding / kinase binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / entry receptor-mediated virion attachment to host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
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 non-structural protein NS4b ...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 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 / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
beta-D-mannopyranose / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.619 Å
AuthorsTzarum, N. / Wilson, I.A. / Law, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al123365 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al106005 United States
CitationJournal: Sci Adv / Year: 2020
Title: An alternate conformation of HCV E2 neutralizing face as an additional vaccine target.
Authors: Tzarum, N. / Giang, E. / Kadam, R.U. / Chen, F. / Nagy, K. / Augestad, E.H. / Velazquez-Moctezuma, R. / Keck, Z.Y. / Hua, Y. / Stanfield, R.L. / Dreux, M. / Prentoe, J. / Foung, S.K.H. / ...Authors: Tzarum, N. / Giang, E. / Kadam, R.U. / Chen, F. / Nagy, K. / Augestad, E.H. / Velazquez-Moctezuma, R. / Keck, Z.Y. / Hua, Y. / Stanfield, R.L. / Dreux, M. / Prentoe, J. / Foung, S.K.H. / Bukh, J. / Wilson, I.A. / Law, M.
History
DepositionApr 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab E1 heavy chain
B: Fab E1 light chain
C: Fab E1 heavy chain
D: Fab E1 light chain
H: Fab 212.1.1 heavy chain
L: Fab 212.1.1 light chain
G: Fab 212.1.1 heavy chain
I: Fab 212.1.1 light chain
E: Envelope glycoprotein E2
F: Envelope glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,71121
Polymers232,49310
Non-polymers4,21911
Water3,675204
1
A: Fab E1 heavy chain
B: Fab E1 light chain
H: Fab 212.1.1 heavy chain
L: Fab 212.1.1 light chain
E: Envelope glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,30411
Polymers116,2465
Non-polymers2,0586
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12190 Å2
ΔGint-37 kcal/mol
Surface area45800 Å2
MethodPISA
2
C: Fab E1 heavy chain
D: Fab E1 light chain
G: Fab 212.1.1 heavy chain
I: Fab 212.1.1 light chain
F: Envelope glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,40710
Polymers116,2465
Non-polymers2,1615
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-35 kcal/mol
Surface area45220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.793, 242.204, 100.729
Angle α, β, γ (deg.)90.000, 98.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 4 types, 8 molecules ACBDHGLI

#1: Antibody Fab E1 heavy chain


Mass: 23937.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab E1 light chain


Mass: 24304.039 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 212.1.1 heavy chain


Mass: 23838.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Fab 212.1.1 light chain


Mass: 23308.926 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, 206 molecules EF

#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
#5: Protein Envelope glycoprotein E2


Mass: 20856.525 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

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Sugars , 5 types, 11 molecules

#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 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.: 5 / 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
#10: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN

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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: 3.07 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: from 20% (w/v) PEG 3000, 0.2M NaCl, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.619→50 Å / Num. obs: 76536 / % possible obs: 96.2 % / Redundancy: 4.8 % / CC1/2: 0.96 / Net I/σ(I): 16.3
Reflection shellResolution: 2.619→2.67 Å / Num. unique obs: 2986 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-20003.25data reduction
Blu-Icedata collection
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MWF

4mwf


Resolution: 2.619→47.435 Å / SU ML: 0.37 / σ(F): 1.38 / Phase error: 28.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 3791 4.96 %
Rwork0.2028 --
obs0.2051 76477 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 2.619→47.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15246 0 276 204 15726
Biso mean--76.72 47.38 -
Num. residues----2016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415934
X-RAY DIFFRACTIONf_angle_d0.79921740
X-RAY DIFFRACTIONf_dihedral_angle_d14.3359495
X-RAY DIFFRACTIONf_chiral_restr0.0522508
X-RAY DIFFRACTIONf_plane_restr0.0052737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6194-2.65250.3361140.2972261X-RAY DIFFRACTION79
2.6525-2.68740.36061450.27972489X-RAY DIFFRACTION92
2.6874-2.72420.35591560.27692650X-RAY DIFFRACTION95
2.7242-2.76310.3421240.27012694X-RAY DIFFRACTION96
2.7631-2.80440.33821420.26482708X-RAY DIFFRACTION97
2.8044-2.84820.31121260.25662703X-RAY DIFFRACTION98
2.8482-2.89490.34391290.26432746X-RAY DIFFRACTION98
2.8949-2.94480.34461610.26892749X-RAY DIFFRACTION98
2.9448-2.99830.33671490.26342662X-RAY DIFFRACTION97
2.9983-3.0560.35411220.26882686X-RAY DIFFRACTION96
3.056-3.11840.2831460.25492633X-RAY DIFFRACTION95
3.1184-3.18620.35851530.24542718X-RAY DIFFRACTION99
3.1862-3.26030.29961550.24872784X-RAY DIFFRACTION99
3.2603-3.34180.29541350.23492730X-RAY DIFFRACTION99
3.3418-3.43210.26441500.24262731X-RAY DIFFRACTION99
3.4321-3.53310.29911560.23032728X-RAY DIFFRACTION98
3.5331-3.64710.27651450.2292712X-RAY DIFFRACTION98
3.6471-3.77730.25871260.21572665X-RAY DIFFRACTION95
3.7773-3.92850.2241410.19532734X-RAY DIFFRACTION97
3.9285-4.10720.24451230.18052735X-RAY DIFFRACTION99
4.1072-4.32360.18421400.16242787X-RAY DIFFRACTION99
4.3236-4.59430.18261370.14342753X-RAY DIFFRACTION99
4.5943-4.94870.18611570.1442653X-RAY DIFFRACTION97
4.9487-5.4460.18751370.14452726X-RAY DIFFRACTION98
5.446-6.23260.21641550.16512780X-RAY DIFFRACTION99
6.2326-7.84670.19711420.18652691X-RAY DIFFRACTION96
7.8467-47.44310.20081250.18022778X-RAY DIFFRACTION98

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