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- PDB-8w0v: Crystal structure of broadly neutralizing antibody hcab55 in comp... -

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Basic information

Entry
Database: PDB / ID: 8w0v
TitleCrystal structure of broadly neutralizing antibody hcab55 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain
Components
  • Envelope glycoprotein E2
  • hcab55 Fab Heavy Chain
  • hcab55 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: 2.59 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: hcab55 Fab Heavy Chain
L: hcab55 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4908
Polymers77,9223
Non-polymers2,5675
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint6 kcal/mol
Surface area31490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.019, 88.840, 175.400
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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Protein , 1 types, 1 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 / Strain: 1b09 / Plasmid: pCMV / Cell line (production host): HEK293expi / Production host: Homo sapiens (human) / References: UniProt: A0A2P0NE15

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Antibody , 2 types, 2 molecules HL

#2: Antibody hcab55 Fab Heavy Chain


Mass: 25447.586 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 hcab55 Fab Light Chain


Mass: 23528.180 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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Sugars , 4 types, 5 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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.: 2
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: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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.: 1
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: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 0.2 M lithium citrate tribasic tetrahydrate 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: Jun 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.59→88.84 Å / Num. obs: 32994 / % possible obs: 99 % / Redundancy: 5.6 % / CC1/2: 0.982 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.076 / Rrim(I) all: 0.183 / Χ2: 1 / Net I/σ(I): 6.8 / Num. measured all: 183914
Reflection shellResolution: 2.59→2.71 Å / % possible obs: 99.5 % / Redundancy: 5.6 % / Rmerge(I) obs: 1.21 / Num. measured all: 22282 / Num. unique obs: 3974 / CC1/2: 0.595 / Rpim(I) all: 0.554 / Rrim(I) all: 1.335 / Χ2: 1.04 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→45.67 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 1610 4.89 %
Rwork0.2023 --
obs0.2049 32909 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5033 0 170 0 5203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095341
X-RAY DIFFRACTIONf_angle_d1.1097281
X-RAY DIFFRACTIONf_dihedral_angle_d6.641824
X-RAY DIFFRACTIONf_chiral_restr0.058840
X-RAY DIFFRACTIONf_plane_restr0.009916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.670.36831360.31442813X-RAY DIFFRACTION99
2.67-2.770.41791450.30792806X-RAY DIFFRACTION99
2.77-2.880.30421460.28032750X-RAY DIFFRACTION97
2.88-3.010.32151310.2512855X-RAY DIFFRACTION99
3.01-3.170.26731310.24632858X-RAY DIFFRACTION99
3.17-3.370.29391410.23232839X-RAY DIFFRACTION99
3.37-3.630.27081610.21622785X-RAY DIFFRACTION98
3.63-3.990.22991640.18852846X-RAY DIFFRACTION99
3.99-4.570.21031330.15252856X-RAY DIFFRACTION98
4.57-5.760.21631610.15352917X-RAY DIFFRACTION100
5.76-45.670.24471610.19012974X-RAY DIFFRACTION97
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)
10.4769-0.003-0.4960.3721-0.26790.6806-0.00120.0554-0.14950.0632-0.04320.0917-0.3028-0.0569-00.42410.0664-0.07560.3896-0.1260.369616.563-15.988-28.663
20.59430.0664-0.26130.4287-0.00060.10710.20830.28770.0263-0.0971-0.07930.4894-0.08530.028-0.00040.44440.0369-0.03910.62330.0040.5349-3.507-14.421-11.111
31.0044-0.73140.08040.56870.07880.49180.11190.1576-0.1680.1197-0.1150.01110.2750.1504-0.00020.38330.0705-0.06890.4507-0.03230.41219.093-24.875-12.27
40.64680.01580.36790.4495-0.43430.610.0174-0.1476-0.06330.1738-0.02860.21370.21280.17-0.00010.44530.0011-0.03270.3793-0.02720.5441.764-17.552-8.533
50.90150.1114-0.09480.6145-0.07420.0130.17980.1055-0.1214-0.0404-0.19050.1023-0.1087-0.0368-00.40630.0238-0.00710.3368-0.01680.36428.675-10.031-12.209
60.3582-0.2669-0.19610.27680.20680.1686-0.0824-0.33050.30850.29360.0514-0.23180.0224-0.36370.00020.40980.00720.02150.3994-0.02380.399814.19-3.453-4.569
70.9445-0.48310.81160.8066-0.35321.3677-0.0339-0.13090.16070.01090.0542-0.0442-0.21270.2599-0.00030.44040.0048-0.05520.4313-0.06730.416814.383-8.636-51.671
80.53140.50380.61421.5321-0.05561.1748-0.1342-0.03480.03430.0220.01940.0857-0.0406-0.150500.380.06140.00360.29890.00510.3543-4.357-25.661-79.218
90.7531-0.6469-0.60091.3050.26820.84730.18850.0135-0.1211-0.2138-0.1315-0.05010.52520.47980.00160.53180.2709-0.08090.7013-0.04950.479821.894-28.856-53.191
100.5422-0.821-0.23421.86070.4352.0391-0.20180.1981-0.01560.04670.1983-0.0499-0.1050.1939-0.00060.3552-0.0341-0.01490.35020.00420.38899.087-30.227-87.101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 421:451 )C421 - 451
2X-RAY DIFFRACTION2( CHAIN C AND RESID 452:490 )C452 - 490
3X-RAY DIFFRACTION3( CHAIN C AND RESID 491:550 )C491 - 550
4X-RAY DIFFRACTION4( CHAIN C AND RESID 551:590 )C551 - 590
5X-RAY DIFFRACTION5( CHAIN C AND RESID 591:624 )C591 - 624
6X-RAY DIFFRACTION6( CHAIN C AND RESID 625:645 )C625 - 645
7X-RAY DIFFRACTION7( CHAIN H AND RESID 1:113 )H1 - 113
8X-RAY DIFFRACTION8( CHAIN H AND RESID 114:215 )H114 - 215
9X-RAY DIFFRACTION9( CHAIN L AND RESID 2:107 )L2 - 107
10X-RAY DIFFRACTION10( CHAIN L AND RESID 108:213 )L108 - 213

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