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- PDB-8eqa: Crystal structure of human anti-N1 neuraminidase 2H08 Fab -

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Basic information

Entry
Database: PDB / ID: 8eqa
TitleCrystal structure of human anti-N1 neuraminidase 2H08 Fab
Components
  • 2H08 Fab heavy chain
  • 2H08 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / neuraminidase / H1N1 / broad protection / pandemic
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Immunity / Year: 2023
Title: Human anti-N1 monoclonal antibodies elicited by pandemic H1N1 virus infection broadly inhibit HxN1 viruses in vitro and in vivo.
Authors: Lena Hansen / Meagan McMahon / Hannah L Turner / Xueyong Zhu / Jackson S Turner / Gabriel Ozorowski / Daniel Stadlbauer / Juha Vahokoski / Aaron J Schmitz / Amena A Rizk / Wafaa B Alsoussi / ...Authors: Lena Hansen / Meagan McMahon / Hannah L Turner / Xueyong Zhu / Jackson S Turner / Gabriel Ozorowski / Daniel Stadlbauer / Juha Vahokoski / Aaron J Schmitz / Amena A Rizk / Wafaa B Alsoussi / Shirin Strohmeier / Wenli Yu / José Alberto Choreño-Parra / Luis Jiménez-Alvarez / Alfredo Cruz-Lagunas / Joaquín Zúñiga / Philip A Mudd / Rebecca J Cox / Ian A Wilson / Andrew B Ward / Ali H Ellebedy / Florian Krammer /
Abstract: Neuraminidase (NA) is one of the two influenza virus surface glycoproteins, and antibodies that target it are an independent correlate of protection. However, our current understanding of NA ...Neuraminidase (NA) is one of the two influenza virus surface glycoproteins, and antibodies that target it are an independent correlate of protection. However, our current understanding of NA antigenicity is incomplete. Here, we describe human monoclonal antibodies (mAbs) from a patient with a pandemic H1N1 virus infection in 2009. Two mAbs exhibited broad reactivity and inhibited NA enzyme activity of seasonal H1N1 viruses circulating before and after 2009, as well as viruses with avian or swine N1s. The mAbs provided robust protection from lethal challenge with human H1N1 and avian H5N1 viruses in mice, and both target an epitope on the lateral face of NA. In summary, we identified two broadly protective NA antibodies that share a novel epitope, inhibited NA activity, and provide protection against virus challenge in mice. Our work reaffirms that NA should be included as a target in future broadly protective or universal influenza virus vaccines.
History
DepositionOct 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 2H08 Fab light chain
H: 2H08 Fab heavy chain
A: 2H08 Fab light chain
B: 2H08 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1439
Polymers94,8164
Non-polymers3275
Water2,630146
1
L: 2H08 Fab light chain
H: 2H08 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5394
Polymers47,4082
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-94 kcal/mol
Surface area19160 Å2
MethodPISA
2
A: 2H08 Fab light chain
B: 2H08 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6045
Polymers47,4082
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-130 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.558, 110.568, 130.679
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-441-

HOH

21B-457-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain L
12chain B
22chain H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPCYSCYSchain AAC1 - 2141 - 215
21ASPASPCYSCYSchain LLA1 - 2141 - 215
12GLNGLNLYSLYSchain BBD1 - 2281 - 223
22GLNGLNLYSLYSchain HHB1 - 2281 - 223

NCS ensembles :
ID
1
2

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Components

#1: Antibody 2H08 Fab light chain


Mass: 23543.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 2H08 Fab heavy chain


Mass: 23864.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Zn acetate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 3, 2021
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.55→45.6 Å / Num. obs: 30277 / % possible obs: 98.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 40 Å2 / CC1/2: 0.983 / Rpim(I) all: 0.08 / Rsym value: 0.18 / Net I/σ(I): 8.6
Reflection shellResolution: 2.55→2.6 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1431 / CC1/2: 0.631 / Rpim(I) all: 0.39 / Rsym value: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PZF, 5UBY

6pzf

5uby


Resolution: 2.55→45.56 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 1431 4.74 %
Rwork0.2151 28789 -
obs0.2181 30220 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.61 Å2 / Biso mean: 45.6158 Å2 / Biso min: 16.96 Å2
Refinement stepCycle: final / Resolution: 2.55→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6564 0 5 146 6715
Biso mean--70.75 38.96 -
Num. residues----864
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1298X-RAY DIFFRACTION8.2TORSIONAL
12L1298X-RAY DIFFRACTION8.2TORSIONAL
21B1294X-RAY DIFFRACTION8.2TORSIONAL
22H1294X-RAY DIFFRACTION8.2TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.55-2.630.39961320.3246227179
2.63-2.740.34361270.2963279296
2.74-2.860.32431430.2798290199
2.86-3.010.33341580.26832899100
3.02-3.20.29181390.252931100
3.2-3.450.26821460.22672935100
3.45-3.80.28121450.20972938100
3.8-4.350.23481260.18352996100
4.35-5.480.18941520.15782986100
5.48-45.560.24391630.20213140100
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)
12.74040.1957-0.83162.6042-0.72582.68310.2152-0.59980.22190.5007-0.2202-0.04150.0698-0.1546-0.06730.4009-0.03540.01650.3891-0.06310.3019-23.53099.341742.4004
21.32620.47510.63052.64260.78921.17810.1166-0.0469-0.22880.13890.0222-0.25810.21390.1327-0.07380.237-0.03880.03420.29080.03330.3231-22.5499-8.70423.65
33.5145-0.0562-0.56782.20070.69232.88710.1904-0.0975-0.5734-0.0466-0.1634-0.40050.23140.15230.11560.2956-0.0094-0.01430.25970.09980.4107-25.0948-20.636417.1845
41.5878-0.55370.82222.0839-0.68321.1553-0.4535-0.1641-0.46420.17370.00470.62510.0225-0.23640.38090.28350.0063-0.02810.2982-0.01490.3934-25.041921.290317.8567
51.76690.9510.13112.8439-0.1172.7315-0.1187-0.06710.1096-0.05120.063-0.57490.05250.2866-0.00420.23780.0079-0.01870.3033-0.06050.342-17.472923.571925.1238
62.70730.38230.65362.2732-0.1451.7106-0.1733-0.1485-0.0187-0.18080.05320.237-0.2743-0.23220.06950.31380.0464-0.02980.2279-0.03760.2629-22.758920.570923.9915
71.94830.5146-0.19821.0438-0.61541.41290.01560.0419-0.0323-0.04760.02260.02080.0493-0.0986-0.02820.19220.0011-0.00790.2036-0.00720.2372-30.7991-4.6911.615
83.5305-1.7768-0.29594.03380.76923.20660.10290.1760.4214-0.50870.1568-0.46250.18880.1893-0.41640.3728-0.094-0.02510.3466-0.01470.3615-64.3507-9.554-42.6485
92.7759-0.07420.1612.78191.38272.2761-0.16050.58760.4269-0.79650.1639-0.5661-0.23390.23110.00830.5938-0.10490.08220.48540.01360.3206-56.2208-0.9952-43.5558
101.1104-0.10850.58221.5664-0.98691.7451-0.0320.4227-0.1859-0.54810.19720.16080.12330.0647-0.18670.4828-0.0765-0.01960.5016-0.05250.2886-59.8997-3.0581-40.7827
110.3548-0.51020.84783.1109-2.64072.78830.1645-0.0281-0.3371-0.74190.35870.14590.6809-0.0497-0.43620.37910.0072-0.11940.4763-0.10110.6899-55.7581-22.2336-32.0276
122.619-0.6494-2.62882.81441.92117.63980.639-0.3776-0.240.12260.1365-0.4466-0.9315-0.4274-0.83890.48860.1356-0.00430.35970.08920.5402-52.2615-20.8351-1.822
132.66760.4247-0.89151.61650.19545.735-0.28360.2812-1.2681-0.2896-0.45070.38250.05-0.0820.40420.33470.02560.00440.3671-0.1080.4638-57.9398-26.019-14.9028
140.4567-0.74740.55262.45940.04662.1650.00950.0095-0.68320.4911-0.58810.22190.0961-0.4430.52120.5297-0.07360.10430.45530.04020.6769-64.4825-26.6369-8.2488
150.16870.1644-1.0152.757-0.62946.230.2017-0.09180.51530.0614-0.3478-0.5632-0.5682-0.2793-0.07750.383-0.01380.03510.3342-0.12830.5672-51.9964-18.4461-26.9734
162.0006-0.3227-1.25952.47771.05643.0239-0.2977-0.215-0.32020.654-0.04660.12960.79250.04340.44830.50350.02550.1170.41380.17080.6286-57.0176-29.7728-5.5501
171.94480.0633-0.1932.078-0.83170.6652-0.23550.005-0.20820.0226-0.0146-0.37890.17710.15850.30490.2357-0.0312-0.01450.2966-0.03270.3463-56.637412.9433-22.7843
182.858-0.33830.06571.37781.32812.4578-0.0199-0.14040.7165-0.25280.11040.8819-0.1707-0.36490.01440.3127-0.0142-0.0560.30930.04960.586-64.293812.9266-30.287
190.77520.3022-0.51540.73080.05351.4459-0.03960.15550.54910.11940.03690.0913-0.028-0.21780.0090.26120.0076-0.040.25130.0890.3473-61.572811.529-24.0458
202.3474-0.41380.75993.9879-2.50912.56990.2610.66010.4307-0.64560.43180.62580.38350.0185-0.47740.3908-0.1534-0.04130.5882-0.04230.4578-54.5518.4487-36.9228
211.754-0.1623-0.45440.78330.260.99710.0471-0.0758-0.15260.03810.0238-0.1631-0.0860.042-0.07460.2593-0.0162-0.00180.29670.00240.3595-50.7018-10.1844-9.3698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 83 )L1 - 83
2X-RAY DIFFRACTION2chain 'L' and (resid 84 through 163 )L84 - 163
3X-RAY DIFFRACTION3chain 'L' and (resid 164 through 214 )L164 - 214
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 33 )H1 - 33
5X-RAY DIFFRACTION5chain 'H' and (resid 34 through 72 )H34 - 72
6X-RAY DIFFRACTION6chain 'H' and (resid 73 through 106 )H73 - 106
7X-RAY DIFFRACTION7chain 'H' and (resid 107 through 228 )H107 - 228
8X-RAY DIFFRACTION8chain 'A' and (resid 1 through 25 )A1 - 25
9X-RAY DIFFRACTION9chain 'A' and (resid 26 through 69 )A26 - 69
10X-RAY DIFFRACTION10chain 'A' and (resid 70 through 101 )A70 - 101
11X-RAY DIFFRACTION11chain 'A' and (resid 102 through 113 )A102 - 113
12X-RAY DIFFRACTION12chain 'A' and (resid 114 through 128 )A114 - 128
13X-RAY DIFFRACTION13chain 'A' and (resid 129 through 150 )A129 - 150
14X-RAY DIFFRACTION14chain 'A' and (resid 151 through 163 )A151 - 163
15X-RAY DIFFRACTION15chain 'A' and (resid 164 through 174 )A164 - 174
16X-RAY DIFFRACTION16chain 'A' and (resid 175 through 214 )A175 - 214
17X-RAY DIFFRACTION17chain 'B' and (resid 1 through 33 )B1 - 33
18X-RAY DIFFRACTION18chain 'B' and (resid 34 through 72 )B34 - 72
19X-RAY DIFFRACTION19chain 'B' and (resid 73 through 96 )B73 - 96
20X-RAY DIFFRACTION20chain 'B' and (resid 97 through 106 )B97 - 106
21X-RAY DIFFRACTION21chain 'B' and (resid 107 through 228 )B107 - 228

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