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- PDB-7rfc: Crystal structure of broadly neutralizing antibody mAb1382 in com... -

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Basic information

Entry
Database: PDB / ID: 7rfc
TitleCrystal structure of broadly neutralizing antibody mAb1382 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain
Components
  • envelope glycoprotein E2
  • mAb1382 Heavy Chain
  • mAb1382 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 / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / ribonucleoprotein complex / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...host cell lipid droplet / host cell mitochondrion / viral nucleocapsid / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / ribonucleoprotein complex / fusion of virus membrane with host endosome membrane / viral envelope / 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: 3.24 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 9, 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: mAb1382 Heavy Chain
B: mAb1382 Light Chain
C: envelope glycoprotein E2
D: envelope glycoprotein E2
H: mAb1382 Heavy Chain
L: mAb1382 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,87519
Polymers155,5226
Non-polymers5,35313
Water00
1
A: mAb1382 Heavy Chain
B: mAb1382 Light Chain
C: envelope glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0639
Polymers77,7613
Non-polymers2,3026
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-14 kcal/mol
Surface area31130 Å2
MethodPISA
2
D: envelope glycoprotein E2
H: mAb1382 Heavy Chain
L: mAb1382 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,81210
Polymers77,7613
Non-polymers3,0517
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-3 kcal/mol
Surface area31430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.291, 140.184, 142.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 225)
21(chain H and (resid 2 through 144 or resid 146 through 225))
12(chain B and resid 1 through 214)
22chain L
13(chain C and (resid 421 through 475 or resid 484...
23(chain D and (resid 421 through 448 or resid 452...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 2 through 225)A2 - 225
211(chain H and (resid 2 through 144 or resid 146 through 225))H2 - 144
221(chain H and (resid 2 through 144 or resid 146 through 225))H146 - 225
112(chain B and resid 1 through 214)B1 - 214
212chain LL1 - 212
113(chain C and (resid 421 through 475 or resid 484...C421 - 475
123(chain C and (resid 421 through 475 or resid 484...C484 - 645
133(chain C and (resid 421 through 475 or resid 484...C4231 - 5562
143(chain C and (resid 421 through 475 or resid 484...C6231
213(chain D and (resid 421 through 448 or resid 452...D421 - 448
223(chain D and (resid 421 through 448 or resid 452...D452 - 475
233(chain D and (resid 421 through 448 or resid 452...D484 - 571
243(chain D and (resid 421 through 448 or resid 452...D576 - 645
253(chain D and (resid 421 through 448 or resid 452...D4231 - 5401
263(chain D and (resid 421 through 448 or resid 452...D5562

NCS ensembles :
ID
1
2
3

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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 mAb1382 Heavy Chain


Mass: 24965.896 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 mAb1382 Light Chain


Mass: 23848.504 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 , 4 types, 13 molecules

#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.: 7
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
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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
#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.: 4 / 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: 3.36 Å3/Da / Density % sol: 63.35 % / Mosaicity: 1.07 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.03 M citric acid, 0.07 M Bis-Tris propane, pH 7.6, 20% PEG3350

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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 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.24→83.67 Å / Num. obs: 33598 / % possible obs: 99.1 % / Redundancy: 5.2 % / CC1/2: 0.911 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.136 / Rrim(I) all: 0.312 / Net I/σ(I): 4 / Num. measured all: 174067 / Scaling rejects: 1430
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
3.24-3.45.11.1912269044150.4580.5721.3261.599.2
10.75-83.675.20.069526710190.9950.0320.0766.798.1

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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: 3.24→52.15 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2842 1813 5.44 %
Rwork0.2329 31520 -
obs0.2358 33333 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.85 Å2 / Biso mean: 72.5916 Å2 / Biso min: 35.32 Å2
Refinement stepCycle: final / Resolution: 3.24→52.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10010 0 352 0 10362
Biso mean--104.49 --
Num. residues----1304
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1300X-RAY DIFFRACTION10.036TORSIONAL
12H1300X-RAY DIFFRACTION10.036TORSIONAL
21B1298X-RAY DIFFRACTION10.036TORSIONAL
22L1298X-RAY DIFFRACTION10.036TORSIONAL
31C1398X-RAY DIFFRACTION10.036TORSIONAL
32D1398X-RAY DIFFRACTION10.036TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.24-3.330.321330.3012388252198
3.33-3.430.39521230.322420254399
3.43-3.540.43781140.35782360247496
3.54-3.660.40051520.32572404255699
3.66-3.810.3731590.33612349250897
3.81-3.980.43031300.35662361249196
3.98-4.190.27341340.217424572591100
4.19-4.450.22451600.18112406256699
4.45-4.80.22171150.16522429254498
4.8-5.280.20321310.16372465259699
5.28-6.040.24391680.18082435260399
6.04-7.610.23771360.21232493262999
7.61-52.150.24051580.18642553271197
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)
13.1390.8155-0.88813.7947-2.69084.113-0.0829-0.54760.32470.38910.26710.7226-0.2411-0.1918-0.18840.42740.10530.05490.49660.01650.624-4.613-7.33455.103
23.7288-1.38181.06911.62030.09654.6353-0.24630.091-0.35090.42960.36310.6710.1427-0.3265-0.09740.5776-0.04540.08430.33390.11280.7411-3.877-15.45557.572
31.58921.5575-1.32844.7776-2.93534.19310.18790.00470.26750.4071-0.1967-0.0524-0.4158-0.29150.03360.41390.08560.02150.3205-0.0190.50037.912.72528.027
45.04440.2836-2.36471.7444-0.61871.7979-0.33940.545-0.10960.03360.19710.2528-0.142-0.10030.14230.38710.0311-0.0720.29330.02970.567927.51927.768-0.328
54.36821.5442-1.54182.7128-1.01134.9166-0.07690.1248-0.51170.038-0.421-0.38040.42580.72150.53880.44490.08550.03130.41450.1680.669327.0042.25227.856
65.1469-1.27261.45457.1087-1.08114.6017-0.3834-0.48040.17980.23040.2264-0.0877-0.78670.23860.17130.3843-0.009-0.02960.46360.00470.519437.5831.54211.971
73.4063-0.6031.55865.12233.58934.93750.55141.55211.0080.330.0816-0.5234-0.64370.6371-0.34150.6810.0870.17440.8525-0.0161.07081.898-5.652-8.096
83.1775-0.8433-0.9950.22140.26340.3340.0123-0.39411.4958-0.80540.43870.133-0.84050.0592-0.23611.090.0182-0.14550.6169-0.05920.5229-7.265-3.758-16.985
94.52010.6506-1.15313.71171.41086.60360.0231.11170.5635-1.18040.8431-0.48920.24581.1985-0.99640.972-0.14620.1591.1405-0.22240.6667.503-17.56-30.295
104.20270.5613-0.93262.02251.54561.89-0.07410.1733-0.0617-0.28460.2787-0.36760.29550.5648-0.19740.82240.14510.01330.7426-0.06460.45562.576-21.013-19.813
113.26150.0961-0.18042.70790.89973.4160.0253-0.1707-0.49030.1176-0.32360.56530.3029-0.35030.31540.48060.0082-0.04440.4288-0.04740.6804-26.3170.0828.197
125.64711.5532-0.92695.1599-1.25443.07340.0952-0.05850.44120.36620.13840.3152-0.2541-0.3649-0.20110.37430.03270.10340.3933-0.02420.4215-33.62931.38321.574
132.0154-1.1083-0.33925.42695.18475.3873-0.00730.1078-0.024-0.74480.08720.0243-0.4057-0.0172-0.11060.5376-0.04650.01970.46710.12580.414-6.2078.1547.135
146.84271.1443-4.79423.2970.7965.9833-0.1193-1.05490.01340.7699-0.0388-0.3079-0.20030.350.20910.61310.0514-0.07390.51820.07680.4139-23.95928.35734.356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND RESID 421:526 )D421 - 526
2X-RAY DIFFRACTION2( CHAIN D AND RESID 527:645 )D527 - 645
3X-RAY DIFFRACTION3( CHAIN H AND RESID 2:124 )H2 - 124
4X-RAY DIFFRACTION4( CHAIN H AND RESID 125:214 )H125 - 214
5X-RAY DIFFRACTION5( CHAIN L AND RESID 1:109 )L1 - 109
6X-RAY DIFFRACTION6( CHAIN L AND RESID 110:212 )L110 - 212
7X-RAY DIFFRACTION7( CHAIN C AND RESID 421:436 )C421 - 436
8X-RAY DIFFRACTION8( CHAIN C AND RESID 437:455 )C437 - 455
9X-RAY DIFFRACTION9( CHAIN C AND RESID 456:501 )C456 - 501
10X-RAY DIFFRACTION10( CHAIN C AND RESID 502:645 )C502 - 645
11X-RAY DIFFRACTION11( CHAIN B AND RESID 1:109 )B1 - 109
12X-RAY DIFFRACTION12( CHAIN B AND RESID 110:213 )B110 - 213
13X-RAY DIFFRACTION13( CHAIN A AND RESID 1:124 )A1 - 124
14X-RAY DIFFRACTION14( CHAIN A AND RESID 125:215 )A125 - 215

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