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

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Basic information

Entry
Database: PDB / ID: 6bzw
TitleStructure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the GL precursor of the broadly neutralizing antibody AP33
Components
  • AP33 GL Heavy Chain
  • AP33 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


Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / oxylipin biosynthetic process / lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily ...Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
Revision 1.6Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: AP33 GL Heavy Chain
D: AP33 GL Light Chain
A: AP33 GL Heavy Chain
B: AP33 GL Light Chain
E: AP33 GL Heavy Chain
F: AP33 GL Light Chain
G: AP33 GL Heavy Chain
H: AP33 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)197,57512
Polymers197,57512
Non-polymers00
Water11,908661
1
C: AP33 GL Heavy Chain
D: AP33 GL Light Chain
I: E2 AS412 peptide


Theoretical massNumber of molelcules
Total (without water)49,3943
Polymers49,3943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-32 kcal/mol
Surface area18920 Å2
MethodPISA
2
A: AP33 GL Heavy Chain
B: AP33 GL Light Chain
J: E2 AS412 peptide


Theoretical massNumber of molelcules
Total (without water)49,3943
Polymers49,3943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-34 kcal/mol
Surface area19080 Å2
MethodPISA
3
E: AP33 GL Heavy Chain
F: AP33 GL Light Chain
K: E2 AS412 peptide


Theoretical massNumber of molelcules
Total (without water)49,3943
Polymers49,3943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-32 kcal/mol
Surface area18990 Å2
MethodPISA
4
G: AP33 GL Heavy Chain
H: AP33 GL Light Chain
L: E2 AS412 peptide


Theoretical massNumber of molelcules
Total (without water)49,3943
Polymers49,3943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-31 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.356, 84.709, 192.919
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
AP33 GL Heavy Chain


Mass: 23993.758 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
AP33 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


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 4000, 20% (w/v) glycerol, 0.16 M ammonium-sulfate, 0.08 M acetate pH 4.6

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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: 2.2→50 Å / Num. obs: 93841 / % possible obs: 95.4 % / Redundancy: 2.4 % / Rpim(I) all: 0.089 / Net I/σ(I): 11.85
Reflection shellResolution: 2.2→2.24 Å / Rpim(I) all: 0.417

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6A

4g6a


Resolution: 2.2→49.155 Å / Cross valid method: FREE R-VALUE / σ(F): 53.61 / Phase error: 28.73
RfactorNum. reflection% reflection
Rfree0.2306 4749 5.06 %
Rwork0.1922 --
obs0.2127 93827 94.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→49.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13579 0 0 661 14240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213913
X-RAY DIFFRACTIONf_angle_d0.62918977
X-RAY DIFFRACTIONf_dihedral_angle_d13.6558321
X-RAY DIFFRACTIONf_chiral_restr0.0442157
X-RAY DIFFRACTIONf_plane_restr0.0052409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.202-2.240.31552120.27844140X-RAY DIFFRACTION83
2.24-2.28070.30742180.28994291X-RAY DIFFRACTION89
2.2807-2.32460.34272360.25854433X-RAY DIFFRACTION89
2.3246-2.3720.32872550.26284374X-RAY DIFFRACTION90
2.372-2.42360.31932080.25244510X-RAY DIFFRACTION91
2.4236-2.480.34422440.24884392X-RAY DIFFRACTION91
2.48-2.5420.32132030.24784451X-RAY DIFFRACTION90
2.542-2.61070.28111890.24614451X-RAY DIFFRACTION90
2.6107-2.68750.30812190.23454465X-RAY DIFFRACTION92
2.6875-2.77430.27972310.2384547X-RAY DIFFRACTION92
2.7743-2.87340.27122180.22594574X-RAY DIFFRACTION93
2.8734-2.98840.30392260.21564556X-RAY DIFFRACTION93
2.9884-3.12440.2432010.19794600X-RAY DIFFRACTION93
3.1244-3.28910.22342770.19294416X-RAY DIFFRACTION90
3.2891-3.49510.19992400.18484526X-RAY DIFFRACTION91
3.4951-3.76490.21212350.17744579X-RAY DIFFRACTION92
3.7649-4.14360.18522170.17264536X-RAY DIFFRACTION92
4.1436-4.74270.17062070.16064497X-RAY DIFFRACTION90
4.7427-5.97350.23012690.18914443X-RAY DIFFRACTION89
5.9735-47.65030.25332520.23064460X-RAY DIFFRACTION88

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