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- PDB-6bzv: Structure of the Hepatitis C virus envelope glycoprotein E2 antig... -

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Basic information

Entry
Database: PDB / ID: 6bzv
TitleStructure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the GL precursor of the broadly neutralizing antibody 19B3
Components
  • 19B3 GL Heavy Chain
  • 19B3 GL Light Chain
  • E2 AS412 peptide
KeywordsIMMUNE SYSTEM / Hepatitis C virus / antibodies / broadly neutralizing antibodies / rational vaccine design / AS412 / E2 / VIRAL PROTEIN
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 / RNA-directed RNA polymerase / ribonucleoprotein complex / 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. / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.654 Å
AuthorsTzarum, N. / Aleman, F. / 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)AI106005 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI123365 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Immunogenetic and structural analysis of a class of HCV broadly neutralizing antibodies and their precursors.
Authors: Aleman, F. / Tzarum, N. / Kong, L. / Nagy, K. / Zhu, J. / Wilson, I.A. / Law, M.
History
DepositionDec 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 2, 2022Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: 19B3 GL Heavy Chain
F: 19B3 GL Light Chain
A: 19B3 GL Heavy Chain
B: 19B3 GL Light Chain
C: 19B3 GL Heavy Chain
D: 19B3 GL Light Chain
G: 19B3 GL Heavy Chain
H: 19B3 GL Light Chain
I: E2 AS412 peptide
J: E2 AS412 peptide
K: E2 AS412 peptide
L: E2 AS412 peptide


Theoretical massNumber of molelcules
Total (without water)197,71912
Polymers197,71912
Non-polymers00
Water2,792155
1
E: 19B3 GL Heavy Chain
F: 19B3 GL Light Chain
K: E2 AS412 peptide


Theoretical massNumber of molelcules
Total (without water)49,4303
Polymers49,4303
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 19B3 GL Heavy Chain
B: 19B3 GL Light Chain
J: E2 AS412 peptide


Theoretical massNumber of molelcules
Total (without water)49,4303
Polymers49,4303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 19B3 GL Heavy Chain
D: 19B3 GL Light Chain
I: E2 AS412 peptide


Theoretical massNumber of molelcules
Total (without water)49,4303
Polymers49,4303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 19B3 GL Heavy Chain
H: 19B3 GL Light Chain
L: E2 AS412 peptide


Theoretical massNumber of molelcules
Total (without water)49,4303
Polymers49,4303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.128, 124.767, 102.407
Angle α, β, γ (deg.)90.00, 91.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
19B3 GL Heavy Chain


Mass: 24029.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
19B3 GL Light Chain


Mass: 23845.271 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide
E2 AS412 peptide


Mass: 1554.710 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: P27958*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 40% 1,2 propanediol, 0.1 M acetate pH 4.5, final pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 49110 / % possible obs: 95.5 % / Redundancy: 2.8 % / Net I/σ(I): 9.6
Reflection shellResolution: 2.65→2.7 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Blu-Icedata collection
RefinementResolution: 2.654→47.357 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.54
RfactorNum. reflection% reflection
Rfree0.2405 2392 4.87 %
Rwork0.1992 --
obs0.2013 49071 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.654→47.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13528 0 0 155 13683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313867
X-RAY DIFFRACTIONf_angle_d0.80918915
X-RAY DIFFRACTIONf_dihedral_angle_d13.4768277
X-RAY DIFFRACTIONf_chiral_restr0.0482133
X-RAY DIFFRACTIONf_plane_restr0.0062408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6542-2.70840.35231060.29912416X-RAY DIFFRACTION84
2.7084-2.76730.3411320.28862683X-RAY DIFFRACTION93
2.7673-2.83160.30671440.28082737X-RAY DIFFRACTION95
2.8316-2.90240.35351800.26362666X-RAY DIFFRACTION95
2.9024-2.98090.32281470.25882772X-RAY DIFFRACTION96
2.9809-3.06860.35491380.26462760X-RAY DIFFRACTION95
3.0686-3.16760.35661430.26332744X-RAY DIFFRACTION96
3.1676-3.28080.311370.24452769X-RAY DIFFRACTION95
3.2808-3.41210.2741440.23192769X-RAY DIFFRACTION96
3.4121-3.56740.27311220.20442800X-RAY DIFFRACTION96
3.5674-3.75540.25421570.19692769X-RAY DIFFRACTION96
3.7554-3.99060.24621290.19522775X-RAY DIFFRACTION96
3.9906-4.29850.19821530.17162741X-RAY DIFFRACTION96
4.2985-4.73070.13841160.14622857X-RAY DIFFRACTION97
4.7307-5.41440.17941550.14932796X-RAY DIFFRACTION97
5.4144-6.81830.21161350.1782804X-RAY DIFFRACTION96
6.8183-47.36470.18981540.1692821X-RAY DIFFRACTION96

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