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- PDB-8eqc: Crystal structure of human anti-N1 neuraminidase 3H03 Fab -

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Basic information

Entry
Database: PDB / ID: 8eqc
TitleCrystal structure of human anti-N1 neuraminidase 3H03 Fab
Components
  • 3H03 Fab heavy chain
  • 3H03 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / neuraminidase / H1N1 / broad protection / pandemic
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: 3H03 Fab light chain
H: 3H03 Fab heavy chain
A: 3H03 Fab light chain
B: 3H03 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7875
Polymers95,6924
Non-polymers951
Water7,945441
1
L: 3H03 Fab light chain
H: 3H03 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9413
Polymers47,8462
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area19480 Å2
MethodPISA
2
A: 3H03 Fab light chain
B: 3H03 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,8462
Polymers47,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-28 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.299, 117.721, 136.145
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 3H03 Fab light chain


Mass: 23361.855 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 3H03 Fab heavy chain


Mass: 24484.332 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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M (NH4)2PO4, 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: 2.2→46.41 Å / Num. obs: 61480 / % possible obs: 98.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.979 / Rpim(I) all: 0.07 / Rsym value: 0.16 / Net I/σ(I): 11.1
Reflection shellResolution: 2.2→2.24 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2759 / CC1/2: 0.547 / Rpim(I) all: 0.5 / Rsym value: 0.8

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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: 4KMT, 6OBZ

4kmt

6obz


Resolution: 2.2→46.41 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 3012 4.91 %
Rwork0.1791 58370 -
obs0.181 61382 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.24 Å2 / Biso mean: 46.8673 Å2 / Biso min: 25.6 Å2
Refinement stepCycle: final / Resolution: 2.2→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6608 0 5 441 7054
Biso mean--45.49 49.21 -
Num. residues----868
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.3277900.31932134222479
2.23-2.270.35611350.30932448258393
2.27-2.310.3021320.27232542267496
2.31-2.350.2861220.25222633275598
2.35-2.390.30351460.24732622276899
2.39-2.440.28221300.239826672797100
2.44-2.50.30571270.230826662793100
2.5-2.550.27351470.224526482795100
2.55-2.620.26641470.233326752822100
2.62-2.690.3241330.23526982831100
2.69-2.770.32531290.238826592788100
2.77-2.860.24671450.217126812826100
2.86-2.960.23361440.200326742818100
2.96-3.080.24371420.191726782820100
3.08-3.220.2411340.19726972831100
3.22-3.390.22091280.197627102838100
3.39-3.60.2221300.172527332863100
3.6-3.880.17171380.154526952833100
3.88-4.270.20081340.139427462880100
4.27-4.880.13391420.115927432885100
4.88-6.150.17611720.133527422914100
6.15-46.410.18611650.16862879304499
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)
10.9047-0.6029-0.33883.3572-0.39471.5559-0.1772-0.0427-0.0083-0.34980.2289-0.11680.147-0.005-0.06420.3523-0.02180.00120.35980.03490.354430.2232-38.3342-30.1466
21.39620.9039-0.05621.4596-0.63612.4625-0.0697-0.05380.0796-0.16260.01660.17980.0188-0.1310.03110.3326-0.0230.01230.32750.00390.332121.6567-41.3457-21.6879
31.45120.08130.69992.877-0.80431.3487-0.14830.0285-0.0331-0.23560.1437-0.02120.0082-0.22-0.10170.369-0.00410.03120.35310.02930.300824.1748-38.0761-27.5033
40.30680.27690.32951.12750.2930.4595-0.1437-0.07780.1097-0.060.10350.0609-0.10730.0184-0.00270.34020.0086-0.01340.3549-0.00950.351534.2984-21.0734-17.5265
51.85340.36621.74581.47920.62851.97180.03060.1148-0.1539-0.12910.02250.01350.12480.0007-0.0680.35890.0333-0.02860.3377-0.00940.331239.3896-11.4541-20.4071
62.36890.93851.78512.009-0.30812.4511-0.26250.15060.4156-0.14380.00650.1091-0.25860.07470.25520.4163-0.0033-0.03840.3251-0.00270.418444.8422-1.401-16.8456
72.6020.4686-0.47142.63730.04010.5604-0.12540.05690.43570.0701-0.03520.1855-0.0543-0.05080.19630.311-0.0039-0.01760.36930.01760.292125.3915-39.4650.0493
82.28390.16720.24472.77360.33332.35660.0182-0.28330.0497-0.0717-0.1068-0.2868-0.04730.18980.0710.2570.0178-0.00130.24890.00370.320630.2478-43.4704-8.7041
96.71271.2887-2.14983.3075-0.6374.12720.4267-0.1394-0.72680.3746-0.232-0.24760.16570.3261-0.14810.29710.03340.05560.2919-0.01970.418229.4072-53.4307-4.9977
101.28161.00320.20461.57590.10421.3165-0.0648-0.093-0.05420.1237-0.0391-0.0644-0.0480.03520.11490.30710.01060.01870.32130.02490.339827.6099-44.5182-4.8685
112.313-0.2650.94951.9997-0.13251.8141-0.0093-0.2650.25990.1151-0.03050.1717-0.2131-0.3370.00270.32360.02070.01530.4476-0.01090.396332.0282-11.8779-4.8713
122.297-0.50990.92990.9818-0.38891.71120.0392-0.08430.0632-0.05240.04890.050.0136-0.0744-0.09450.4572-0.0232-0.03220.3869-0.01670.378828.9019-32.1389-41.4152
130.5036-0.3218-0.46882.7205-0.04952.84350.01650.2193-0.3426-0.2291-0.0087-0.02010.362-0.116-0.05020.3822-0.0544-0.02510.3451-0.00820.373331.5358-35.9214-53.0111
141.92530.0420.16231.2946-0.41281.1499-0.04450.2139-0.1074-0.11710.0220.0330.2193-0.08880.01350.4008-0.0587-0.00380.3715-0.02520.323629.6009-33.5421-48.448
151.71560.32371.05791.34870.78840.92370.03190.0391-0.07810.01780.0635-0.17340.03770.1245-0.16850.38560.00320.01720.3910.03260.329358.357-20.8976-36.9759
163.15282.25070.11265.35360.25390.66-0.025-0.22450.28110.42160.02130.29770.0655-0.158-0.00030.39550.0182-0.00180.3730.00840.359556.9567-18.1108-31.7566
170.83890.78420.40481.62941.05311.74860.1078-0.2742-0.03750.71550.1337-0.2107-0.33140.1515-0.15390.612-0.00870.00010.5634-0.05480.4457.4145-8.9507-30.4852
182.81760.78270.28813.1754-0.03871.61130.0842-0.16450.14560.3459-0.0335-0.1665-0.07540.2922-0.02690.3743-0.0484-0.01740.4644-0.01810.350561.7426-16.4449-31.7969
192.51751.58330.57272.42681.06761.30930.16060.391-0.4199-0.4606-0.0299-0.5315-0.079-0.0331-0.20030.487-0.0314-0.00210.4046-0.04820.399240.761-21.9033-67.9547
204.03280.42590.93082.1282-1.10042.8635-0.17090.0553-0.0954-0.03860.10840.0099-0.54810.082-0.05060.42090.0052-0.02780.3281-0.01640.328332.6789-22.1625-60.7785
211.4440.77950.76842.7636-0.05073.41850.0170.2788-0.0247-0.2724-0.04260.02580.1106-0.14850.06430.3655-0.0222-0.01770.3825-0.03160.298932.8194-21.5889-66.174
220.48530.1003-0.07941.3146-0.05760.6046-0.0793-0.0524-0.0522-0.00350.10080.0720.15740.16080.0110.38770.02210.03940.3789-0.01120.340858.2433-16.1474-48.8717
231.5338-0.4662-0.06113.3465-0.38212.5595-0.1691-0.1237-0.2278-0.08050.1966-0.27790.07020.4661-0.03870.37980.04120.06240.4687-0.03270.430566.4117-21.1867-49.7583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 25 )L1 - 25
2X-RAY DIFFRACTION2chain 'L' and (resid 26 through 61 )L26 - 61
3X-RAY DIFFRACTION3chain 'L' and (resid 62 through 90 )L62 - 90
4X-RAY DIFFRACTION4chain 'L' and (resid 91 through 128 )L91 - 128
5X-RAY DIFFRACTION5chain 'L' and (resid 129 through 174 )L129 - 174
6X-RAY DIFFRACTION6chain 'L' and (resid 175 through 214 )L175 - 214
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 33 )H1 - 33
8X-RAY DIFFRACTION8chain 'H' and (resid 34 through 51 )H34 - 51
9X-RAY DIFFRACTION9chain 'H' and (resid 52 through 63 )H52 - 63
10X-RAY DIFFRACTION10chain 'H' and (resid 64 through 109 )H64 - 109
11X-RAY DIFFRACTION11chain 'H' and (resid 110 through 228 )H110 - 228
12X-RAY DIFFRACTION12chain 'A' and (resid 1 through 25 )A1 - 25
13X-RAY DIFFRACTION13chain 'A' and (resid 26 through 61 )A26 - 61
14X-RAY DIFFRACTION14chain 'A' and (resid 62 through 101 )A62 - 101
15X-RAY DIFFRACTION15chain 'A' and (resid 102 through 128 )A102 - 128
16X-RAY DIFFRACTION16chain 'A' and (resid 129 through 150 )A129 - 150
17X-RAY DIFFRACTION17chain 'A' and (resid 151 through 163 )A151 - 163
18X-RAY DIFFRACTION18chain 'A' and (resid 164 through 214 )A164 - 214
19X-RAY DIFFRACTION19chain 'B' and (resid 1 through 33 )B1 - 33
20X-RAY DIFFRACTION20chain 'B' and (resid 34 through 51 )B34 - 51
21X-RAY DIFFRACTION21chain 'B' and (resid 52 through 106 )B52 - 106
22X-RAY DIFFRACTION22chain 'B' and (resid 107 through 184 )B107 - 184
23X-RAY DIFFRACTION23chain 'B' and (resid 185 through 228 )B185 - 228

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