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- PDB-7rfb: Crystal structure of broadly neutralizing antibody mAb1198 in com... -

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Basic information

Entry
Database: PDB / ID: 7rfb
TitleCrystal structure of broadly neutralizing antibody mAb1198 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain
Components
  • envelope glycoprotein E2
  • mAb1198 Heavy Chain
  • mAb1198 Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HCV glycoprotein / broadly neutralizing antibodies / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell lipid droplet / host cell mitochondrion / viral nucleocapsid / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell ...host cell lipid droplet / host cell mitochondrion / viral nucleocapsid / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Hepacivirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFlyak, A.I. / Bjorkman, P.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI127469 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99 AI153465 United States
CitationJournal: Immunity / Year: 2022
Title: Analysis of antibodies from HCV elite neutralizers identifies genetic determinants of broad neutralization.
Authors: Weber, T. / Potthoff, J. / Bizu, S. / Labuhn, M. / Dold, L. / Schoofs, T. / Horning, M. / Ercanoglu, M.S. / Kreer, C. / Gieselmann, L. / Vanshylla, K. / Langhans, B. / Janicki, H. / Stroh, L. ...Authors: Weber, T. / Potthoff, J. / Bizu, S. / Labuhn, M. / Dold, L. / Schoofs, T. / Horning, M. / Ercanoglu, M.S. / Kreer, C. / Gieselmann, L. / Vanshylla, K. / Langhans, B. / Janicki, H. / Stroh, L.J. / Knops, E. / Nierhoff, D. / Spengler, U. / Kaiser, R. / Bjorkman, P.J. / Krey, T. / Bankwitz, D. / Pfeifer, N. / Pietschmann, T. / Flyak, A.I. / Klein, F.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: mAb1198 Heavy Chain
B: mAb1198 Light Chain
C: envelope glycoprotein E2
D: envelope glycoprotein E2
H: mAb1198 Heavy Chain
L: mAb1198 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,21018
Polymers155,9056
Non-polymers6,30612
Water00
1
A: mAb1198 Heavy Chain
B: mAb1198 Light Chain
C: envelope glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,24510
Polymers77,9523
Non-polymers3,2937
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint4 kcal/mol
Surface area32160 Å2
MethodPISA
2
D: envelope glycoprotein E2
H: mAb1198 Heavy Chain
L: mAb1198 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9658
Polymers77,9523
Non-polymers3,0135
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint1 kcal/mol
Surface area31890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.090, 102.431, 131.520
Angle α, β, γ (deg.)90.000, 92.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules CD

#3: Protein envelope glycoprotein E2


Mass: 28946.479 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 214-475)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Plasmid: pCMV / Cell line (production host): HEK293expi / Production host: Homo sapiens (human) / References: UniProt: A0A2P0NE26

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Antibody , 2 types, 4 molecules AHBL

#1: Antibody mAb1198 Heavy Chain


Mass: 25090.092 Da / Num. of mol.: 2
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)
#2: Antibody mAb1198 Light Chain


Mass: 23915.758 Da / Num. of mol.: 2
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 , 3 types, 12 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.: 3
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 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.: 3
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
#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.: 6 / Source method: obtained synthetically / 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
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: 2.94 Å3/Da / Density % sol: 58.14 % / Mosaicity: 0.43 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 17% PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→80.78 Å / Num. obs: 47758 / % possible obs: 96.3 % / Redundancy: 3.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.06 / Rrim(I) all: 0.111 / Net I/σ(I): 6.4 / Num. measured all: 148614 / Scaling rejects: 150
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.793.10.8881386944180.610.5861.0691.597.4
10.8-80.7830.08223947870.9890.0520.0971095.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 6MEH & 6MEI

6meh

6mei


Resolution: 2.7→46.16 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2617 2318 4.87 %
Rwork0.2148 45328 -
obs0.2171 47646 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.94 Å2 / Biso mean: 91.7578 Å2 / Biso min: 44.02 Å2
Refinement stepCycle: final / Resolution: 2.7→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10070 0 417 0 10487
Biso mean--119.03 --
Num. residues----1320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.760.39681360.32882662279897
2.76-2.820.36921470.30492669281697
2.82-2.880.31021260.2942670279696
2.88-2.950.34991390.2892668280796
2.95-3.030.34391390.28882604274394
3.03-3.120.30611410.26832580272194
3.12-3.220.29131510.26112714286598
3.22-3.340.27861460.25182670281697
3.34-3.470.31121290.23522686281597
3.47-3.630.30071250.22352696282195
3.63-3.820.28691210.22362545266692
3.82-4.060.26531290.20112735286498
4.06-4.370.22721250.18892708283397
4.37-4.810.22161590.16032667282696
4.81-5.510.20091210.17412676279795
5.51-6.930.25461390.20972740287997
6.94-46.160.24091450.21092638278393
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)
18.9145-1.39435.046.2198-3.59869.12270.46150.1303-0.3833-0.37960.28980.9870.8818-1.1512-0.72780.6125-0.103-0.03570.6759-0.03280.55611.2313.015-4.902
24.57890.44170.88034.3845-2.75344.38240.56350.669-0.3216-2.1498-0.65980.01030.8720.42050.11361.50.4677-0.15670.7723-0.13250.71390.20426.895-39.777
32.37671.54511.52945.4597-3.63417.9883-0.27970.4272-0.2782-1.5320.3462-0.47790.72070.2128-0.08730.53120.00650.04660.5417-0.14080.67321.311.5378.785
47.6622-0.62894.33963.47111.65083.8972-0.121.0522-0.2283-0.1143-0.07980.5350.39280.84560.18120.51080.0856-0.06010.6591-0.05841.099231.042-14.30395.689
56.30176.1603-3.99918.8613-4.80542.8634-0.6957-0.458-0.675-0.93790.037-1.43030.42290.21730.55780.5050.0391-0.02260.4846-0.07950.611129.2570.26287.62
63.0052-0.5639-0.33064.7955-0.72732.6458-0.2131-0.5084-0.07880.145-0.079-0.2688-0.2330.03960.26510.4590.01560.05290.5783-0.05740.498626.363-0.08592.323
77.30495.76085.88864.51844.63514.81970.497-1.45070.50041.1978-1.07080.21850.3907-0.74270.42880.7030.10150.13510.9862-0.00480.643912.5280.678100.058
83.2436-0.2715-0.14693.9073-3.57498.8469-0.04820.4750.05190.1012-0.1001-0.43860.0540.57790.110.3783-0.02540.02140.3975-0.10810.504918.63520.57159.666
94.5913-2.90171.50454.3275-1.53222.57740.00870.57180.1421-0.2726-0.0285-0.2465-0.22490.16560.05860.461-0.14540.05850.6921-0.09170.36662.73339.55833.701
109.5753-1.66014.72353.6607-3.88928.71490.22-0.1133-0.5792-0.25580.46570.58610.6134-0.866-0.63180.5398-0.09860.03390.4804-0.05180.6222-2.06513.13961.031
115.38311.0451-2.62743.9816-2.16188.50180.00070.8341-0.4958-0.7243-0.03310.10520.5824-0.10230.00780.5581-0.0372-0.04610.7423-0.24450.4978-4.54926.77826.163
125.6043-1.2806-0.42525.727-3.07088.84990.17030.68150.4728-0.0083-0.5567-0.80560.02960.62530.36850.39360.00060.0190.60790.10160.579222.01420.288-5.261
136.8486-2.81211.07346.896-2.01363.99610.20160.24480.4644-0.7319-1.0284-1.19350.00691.05420.66580.63140.11190.16470.85890.16040.56457.59239.342-31.417
147.3004-0.15360.5817.8394-3.88513.482-0.19020.6488-0.9531-1.28140.0442-0.43260.42880.63040.15690.8698-0.10960.09890.6161-0.04910.736823.9513.97511.257
151.53132.30630.40363.93331.63252.48310.3468-0.2383-1.25790.21590.64580.33531.74110.532-0.24721.39930.0962-0.53410.86380.38882.667827.499-17.15331.549
160.26870.1213-0.57450.90260.6131.9488-0.1068-0.2397-2.35610.6258-0.6194-1.49690.29920.97630.68080.7155-0.1188-0.22180.90010.35761.70631.8590.78523.584
172.53160.6181-1.96832.54361.40922.85120.238-0.8171-0.70630.7936-0.7665-1.4273-1.29991.25360.6110.9916-0.3432-0.3661.12770.2540.869634.0211.1928.388
181.0519-2.13771.11657.3942-0.52292.3366-0.2237-0.914-1.79071.1706-0.6357-1.343-0.0330.83430.75410.752-0.1152-0.13170.88930.5171.460327.197-8.74730.086
197.80691.5527-3.49214.8416-3.01968.3359-0.198-0.1491-1.0460.3161-0.131-0.21530.03530.49760.25940.6922-0.0212-0.07430.5290.08740.624516.1940.30127.668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN L AND RESID 2:113 )L2 - 113
2X-RAY DIFFRACTION2( CHAIN L AND RESID 114:213 )L114 - 213
3X-RAY DIFFRACTION3( CHAIN C AND RESID 420:464 )C420 - 464
4X-RAY DIFFRACTION4( CHAIN C AND RESID 465:484 )C465 - 484
5X-RAY DIFFRACTION5( CHAIN C AND RESID 485:509 )C485 - 509
6X-RAY DIFFRACTION6( CHAIN C AND RESID 510:624 )C510 - 624
7X-RAY DIFFRACTION7( CHAIN C AND RESID 625:645 )C625 - 645
8X-RAY DIFFRACTION8( CHAIN A AND RESID 1:125 )A1 - 125
9X-RAY DIFFRACTION9( CHAIN A AND RESID 126:214 )A126 - 214
10X-RAY DIFFRACTION10( CHAIN B AND RESID 2:113 )B2 - 113
11X-RAY DIFFRACTION11( CHAIN B AND RESID 114:213 )B114 - 213
12X-RAY DIFFRACTION12( CHAIN H AND RESID 1:125 )H1 - 125
13X-RAY DIFFRACTION13( CHAIN H AND RESID 126:213 )H126 - 213
14X-RAY DIFFRACTION14( CHAIN D AND RESID 421:458 )D421 - 458
15X-RAY DIFFRACTION15( CHAIN D AND RESID 459:485 )D459 - 485
16X-RAY DIFFRACTION16( CHAIN D AND RESID 486:509 )D486 - 509
17X-RAY DIFFRACTION17( CHAIN D AND RESID 510:550 )D510 - 550
18X-RAY DIFFRACTION18( CHAIN D AND RESID 551:607 )D551 - 607
19X-RAY DIFFRACTION19( CHAIN D AND RESID 608:645 )D608 - 645

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