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- PDB-8w0w: Crystal structure of broadly neutralizing antibody hcab64 in comp... -

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Basic information

Entry
Database: PDB / ID: 8w0w
TitleCrystal structure of broadly neutralizing antibody hcab64 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain
Components
  • Envelope glycoprotein E2
  • hcab64 Fab Heavy Chain
  • hcab64 Fab Light Chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HCV glycoprotein / broadly neutralizing antibodies / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


host cell lipid droplet / host cell mitochondrion / lipid droplet / viral nucleocapsid / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / viral envelope / structural molecule activity / virion membrane / membrane / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesHepacivirus hominis
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsFlyak, A.I. / Wilcox, X.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI159822 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R00 AI153465 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99 AI153465 United States
CitationJournal: Immunity / Year: 2024
Title: Convergent evolution and targeting of diverse E2 epitopes by human broadly neutralizing antibodies are associated with HCV clearance.
Authors: Ogega, C.O. / Skinner, N.E. / Schoenle, M.V. / Wilcox, X.E. / Frumento, N. / Wright, D.A. / Paul, H.T. / Sinnis-Bourozikas, A. / Clark, K.E. / Figueroa, A. / Bjorkman, P.J. / Ray, S.C. / ...Authors: Ogega, C.O. / Skinner, N.E. / Schoenle, M.V. / Wilcox, X.E. / Frumento, N. / Wright, D.A. / Paul, H.T. / Sinnis-Bourozikas, A. / Clark, K.E. / Figueroa, A. / Bjorkman, P.J. / Ray, S.C. / Flyak, A.I. / Bailey, J.R.
History
DepositionFeb 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Envelope glycoprotein E2
H: hcab64 Fab Heavy Chain
L: hcab64 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7669
Polymers78,1393
Non-polymers2,6266
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint14 kcal/mol
Surface area31460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.680, 88.231, 174.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody hcab64 Fab Heavy Chain


Mass: 25655.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293expi / Production host: Homo sapiens (human)
#3: Antibody hcab64 Fab Light Chain


Mass: 23537.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293expi / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 269 molecules C

#1: Protein Envelope glycoprotein E2


Mass: 28946.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus hominis / Plasmid: pCMV / Cell line (production host): HEK293expi / Production host: Homo sapiens (human) / References: UniProt: A0A2P0NE15
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 6 molecules

#4: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: 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.: 2
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

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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: 3.39 Å3/Da / Density % sol: 63.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 8% Tacsimate and 20% PEG 3,350

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.13→87.35 Å / Num. obs: 59648 / % possible obs: 99.1 % / Redundancy: 6.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.071 / Rrim(I) all: 0.179 / Χ2: 0.93 / Net I/σ(I): 7.2 / Num. measured all: 365813
Reflection shellResolution: 2.13→2.19 Å / % possible obs: 99.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 3.063 / Num. measured all: 28522 / Num. unique obs: 4582 / CC1/2: 0.366 / Rpim(I) all: 1.32 / Rrim(I) all: 3.342 / Χ2: 0.93 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→53.99 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 2967 4.99 %
Rwork0.1948 --
obs0.1963 59489 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→53.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5067 0 173 268 5508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015380
X-RAY DIFFRACTIONf_angle_d1.0827334
X-RAY DIFFRACTIONf_dihedral_angle_d19.3731945
X-RAY DIFFRACTIONf_chiral_restr0.062842
X-RAY DIFFRACTIONf_plane_restr0.009923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.160.30551410.30452634X-RAY DIFFRACTION98
2.16-2.20.36011680.30842668X-RAY DIFFRACTION99
2.2-2.240.32581330.2952634X-RAY DIFFRACTION99
2.24-2.290.3211540.28622607X-RAY DIFFRACTION98
2.29-2.330.29361360.27472659X-RAY DIFFRACTION98
2.33-2.380.3191330.26552710X-RAY DIFFRACTION99
2.38-2.440.28461250.24832683X-RAY DIFFRACTION99
2.44-2.50.27771270.24142661X-RAY DIFFRACTION99
2.5-2.570.28281310.23532667X-RAY DIFFRACTION99
2.57-2.640.26571410.22872702X-RAY DIFFRACTION99
2.64-2.730.26081510.2252674X-RAY DIFFRACTION99
2.73-2.830.24891180.21922639X-RAY DIFFRACTION98
2.83-2.940.27761300.20592717X-RAY DIFFRACTION99
2.94-3.070.23891640.1982675X-RAY DIFFRACTION99
3.07-3.230.18161140.18692729X-RAY DIFFRACTION99
3.23-3.440.20431550.18162697X-RAY DIFFRACTION99
3.44-3.70.20331400.17382698X-RAY DIFFRACTION98
3.7-4.070.20571710.16482720X-RAY DIFFRACTION100
4.07-4.660.18781500.14412742X-RAY DIFFRACTION99
4.66-5.870.16731330.15712734X-RAY DIFFRACTION97
5.87-53.990.21151520.19952872X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5647-1.9003-0.27653.9907-0.77624.3356-0.02220.23970.4782-0.368-0.1647-0.6032-0.43550.3460.16930.3830.0503-0.030.4567-0.05080.37618.545-15.402-28.21
21.9946-0.0651-0.50932.7228-1.47922.08430.11530.50640.1557-0.5841-0.16280.27720.3734-0.20270.10460.52690.0375-0.06770.5855-0.040.5411-3.008-14.365-11.363
33.7103-1.4615-0.05552.7087-0.82342.50680.04840.1972-0.4521-0.0314-0.07950.17970.51120.21240.00650.30710.0485-0.05790.2978-0.01790.318119.687-24.31-12.233
42.0236-0.0944-0.4632.55150.56472.23450.14180.03780.06540.1751-0.14940.1953-0.0923-0.19310.00560.2850.0314-0.01860.2618-0.00990.32397.633-11.242-8.935
52.6797-0.88271.09812.5738-0.75366.137-0.1473-0.230.3417-0.02880.0477-0.2322-0.77980.64110.08380.4018-0.078-0.05730.3552-0.0760.337514.898-8.008-51.669
62.29550.9290.4394.88570.37643.5013-0.12030.05780.0925-0.1183-0.06290.1915-0.1855-0.19270.14450.19980.0546-0.01260.2231-0.00120.2722-4.417-25.161-79.191
71.9766-0.67990.01165.3260.49724.53330.0642-0.0996-0.17470.3490.2287-0.410.7651.092-0.2190.41450.2524-0.08920.6417-0.0530.302222.036-28.289-52.85
82.4629-0.6310.37913.1260.07965.1992-0.09390.1984-0.0699-0.11750.1053-0.11670.01080.2712-0.02360.1721-0.03080.01280.2219-0.02960.27049.313-30.061-86.521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 420:451 )C420 - 451
2X-RAY DIFFRACTION2( CHAIN C AND RESID 452:489 )C452 - 489
3X-RAY DIFFRACTION3( CHAIN C AND RESID 490:550 )C490 - 550
4X-RAY DIFFRACTION4( CHAIN C AND RESID 551:645 )C551 - 645
5X-RAY DIFFRACTION5( CHAIN H AND RESID 1:113 )H1 - 113
6X-RAY DIFFRACTION6( CHAIN H AND RESID 114:215 )H114 - 215
7X-RAY DIFFRACTION7( CHAIN L AND RESID 2:107 )L2 - 107
8X-RAY DIFFRACTION8( CHAIN L AND RESID 108:213 )L108 - 213

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