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- PDB-6uym: Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v6 red... -

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Basic information

Entry
Database: PDB / ID: 6uym
TitleStructure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v6 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 / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHepatitis C virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.848 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 2.2Oct 23, 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

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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)136,31713
Polymers134,3626
Non-polymers1,9557
Water00
1
E: Envelope glycoprotein E2
H: Fab AR3C heavy chain
L: Fab AR3C light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2697
Polymers67,1813
Non-polymers1,0884
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-16 kcal/mol
Surface area27530 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)68,0486
Polymers67,1813
Non-polymers8673
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-24 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.101, 90.840, 94.033
Angle α, β, γ (deg.)84.500, 78.110, 77.090
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Envelope glycoprotein E2


Mass: 19286.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus (isolate H) / Strain: isolate H / Production host: Homo sapiens (human)
#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)
#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.: 5
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
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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3500, 0.2M Na-thiocyanate, pH=6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.848→30 Å / Num. obs: 29145 / % possible obs: 88.5 % / Redundancy: 3.7 % / CC1/2: 0.96 / Net I/σ(I): 14.2
Reflection shellResolution: 2.85→2.9 Å / Num. unique obs: 836 / CC1/2: 0.88

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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: 2.848→29.474 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 33.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 1551 5.33 %
Rwork0.2145 27571 -
obs0.217 29122 87.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.05 Å2 / Biso mean: 66.289 Å2 / Biso min: 29.72 Å2
Refinement stepCycle: final / Resolution: 2.848→29.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8733 0 126 0 8859
Biso mean--103.89 --
Num. residues----1145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029124
X-RAY DIFFRACTIONf_angle_d0.65112447
X-RAY DIFFRACTIONf_chiral_restr0.051400
X-RAY DIFFRACTIONf_plane_restr0.0041577
X-RAY DIFFRACTIONf_dihedral_angle_d11.2185372
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8483-2.94020.3201740.2804137248
2.9402-3.04510.2966820.2873188465
3.0451-3.16690.32981400.2888222879
3.1669-3.31090.30861420.2837250888
3.3109-3.48520.33481110.2687275394
3.4852-3.70320.31571460.2449273596
3.7032-3.98840.29221390.2296282998
3.9884-4.38860.24991840.1874280899
4.3886-5.0210.20311820.1659283199
5.021-6.31570.20761510.1936283399
6.3157-29.4740.25752000.194279099

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