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- PDB-6pzg: Crystal structure of human NA-80 Fab -

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Basic information

Entry
Database: PDB / ID: 6pzg
TitleCrystal structure of human NA-80 Fab
Components
  • NA-80 Fab heavy chain
  • NA-80 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / inhibition mechanism
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400024C United States
CitationJournal: Cell Host Microbe / Year: 2019
Title: Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies.
Authors: Xueyong Zhu / Hannah L Turner / Shanshan Lang / Ryan McBride / Sandhya Bangaru / Iuliia M Gilchuk / Wenli Yu / James C Paulson / James E Crowe / Andrew B Ward / Ian A Wilson /
Abstract: Influenza virus neuraminidase (NA) is a major target for small-molecule antiviral drugs. Antibodies targeting the NA surface antigen could also inhibit virus entry and egress to provide host ...Influenza virus neuraminidase (NA) is a major target for small-molecule antiviral drugs. Antibodies targeting the NA surface antigen could also inhibit virus entry and egress to provide host protection. However, our understanding of the nature and range of target epitopes is limited because of a lack of human antibody structures with influenza neuraminidase. Here, we describe crystal and cryogenic electron microscopy (cryo-EM) structures of NAs from human-infecting avian H7N9 viruses in complex with five human anti-N9 antibodies, systematically defining several antigenic sites and antibody epitope footprints. These antibodies either fully or partially block the NA active site or bind to epitopes distant from the active site while still showing neuraminidase inhibition. The inhibition of antibodies to NAs was further analyzed by glycan array and solution-based NA activity assays. Together, these structural studies provide insights into protection by anti-NA antibodies and templates for the development of NA-based influenza virus vaccines and therapeutics.
History
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: NA-80 Fab light chain
H: NA-80 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,1382
Polymers48,1382
Non-polymers00
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-25 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.770, 102.770, 80.359
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11L-534-

HOH

21H-365-

HOH

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Components

#1: Antibody NA-80 Fab light chain


Mass: 23344.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody NA-80 Fab heavy chain


Mass: 24793.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1 M sodium citrate, pH 5.6, 40% PEG600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.59→44.5 Å / Num. obs: 66498 / % possible obs: 99.9 % / Redundancy: 18.1 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rsym value: 0.08 / Net I/σ(I): 58
Reflection shellResolution: 1.59→1.62 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3234 / CC1/2: 0.63 / Rpim(I) all: 0.35 / Rsym value: 0.9 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4kmt, 5aze

4kmt

5aze


Resolution: 1.59→44.5 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.78
RfactorNum. reflection% reflection
Rfree0.2036 3374 5.08 %
Rwork0.1684 --
obs0.1702 66460 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.59→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 0 446 3743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013468
X-RAY DIFFRACTIONf_angle_d1.0614754
X-RAY DIFFRACTIONf_dihedral_angle_d11.1742111
X-RAY DIFFRACTIONf_chiral_restr0.063539
X-RAY DIFFRACTIONf_plane_restr0.007611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5856-1.60830.32721240.27772547X-RAY DIFFRACTION96
1.6083-1.63230.29291270.24442596X-RAY DIFFRACTION100
1.6323-1.65780.25351480.22682596X-RAY DIFFRACTION100
1.6578-1.6850.25221490.21292593X-RAY DIFFRACTION100
1.685-1.7140.25251600.20472620X-RAY DIFFRACTION100
1.714-1.74520.21811360.19712592X-RAY DIFFRACTION100
1.7452-1.77870.20341170.20022614X-RAY DIFFRACTION100
1.7787-1.81510.24791480.19792604X-RAY DIFFRACTION100
1.8151-1.85450.21211450.19982610X-RAY DIFFRACTION100
1.8545-1.89770.21861340.19652623X-RAY DIFFRACTION100
1.8977-1.94510.21831530.18792608X-RAY DIFFRACTION100
1.9451-1.99770.23161570.18282596X-RAY DIFFRACTION100
1.9977-2.05650.21911400.18122631X-RAY DIFFRACTION100
2.0565-2.12290.23611440.18012610X-RAY DIFFRACTION100
2.1229-2.19870.1981340.17512615X-RAY DIFFRACTION100
2.1987-2.28680.2091200.17362682X-RAY DIFFRACTION100
2.2868-2.39080.18821440.17272595X-RAY DIFFRACTION100
2.3908-2.51690.20441470.17582650X-RAY DIFFRACTION100
2.5169-2.67460.19481530.16822627X-RAY DIFFRACTION100
2.6746-2.8810.20671490.17032628X-RAY DIFFRACTION100
2.881-3.17090.19891440.17342650X-RAY DIFFRACTION100
3.1709-3.62950.2311180.15772722X-RAY DIFFRACTION100
3.6295-4.57210.17971500.13242666X-RAY DIFFRACTION100
4.5721-44.51820.16981330.15462811X-RAY DIFFRACTION100
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)
17.49265.5059-7.11614.1233-5.13167.02240.4466-0.47060.60090.3191-0.13630.2093-0.34350.3381-0.3450.2232-0.0141-0.00390.2524-0.06340.253437.0948-20.670419.6321
24.8470.7741-1.70452.9249-1.0873.0878-0.0247-0.275-0.2130.0699-0.0875-0.20860.15350.21980.08810.17690.0328-0.01770.1831-0.00070.183136.576-29.032416.4339
32.90233.743-4.31144.9832-5.70886.6313-0.1623-0.1699-0.3941-0.0993-0.1875-0.43730.17060.27130.36280.1638-0.0063-0.0020.2246-0.02910.203644.2669-9.84547.224
43.2715-0.17612.33852.21170.03133.16260.02360.36260.3228-1.26870.12760.58170.2919-0.31120.21030.4445-0.1241-0.27810.31630.14540.330723.7545.4214-9.929
57.1475-4.25880.8574.75-1.09891.5456-0.046-0.0964-0.1466-0.08340.20850.2154-0.02280.0004-0.110.1537-0.0563-0.00250.16590.02930.180431.69171.12182.4252
64.5942-2.6414-0.13736.13990.63761.0640.0155-0.0097-0.3923-0.0543-0.00180.26810.0048-0.0099-0.04230.1555-0.03680.00940.17870.03080.110831.898-3.14012.2664
75.6395-0.93081.29564.8431-0.51772.4805-0.2624-0.13570.3626-0.2350.21930.8518-0.3201-0.3-0.00230.18770.0047-0.0520.21550.03810.303722.39278.6291-0.7424
88.1169-3.34423.60895.4775-1.43094.1682-0.5288-0.0370.84160.12560.1984-0.3022-0.54850.00350.18880.1698-0.04850.0020.1858-0.00570.186434.8749.48441.6265
98.2412-5.5973-0.6394.50690.04093.98530.20590.6315-0.3189-0.2531-0.26710.30250.0440.20430.08560.1655-0.0469-0.04730.2018-0.01660.240717.8489-30.5575-1.341
103.5697-1.30270.38243.1733-0.17071.4075-0.09890.0902-0.31210.26820.01040.29420.1573-0.1580.0780.20030.00530.03950.1883-0.02480.210918.3321-36.9788.7576
115.7983-1.47351.76624.8605-1.75752.3963-0.13610.18370.18910.19540.06690.2464-0.0725-0.14650.1690.12960.00620.02080.1709-0.03040.145716.7723-27.36596.6627
121.12940.41460.40241.61680.39290.1896-0.17690.14860.0244-0.19910.14560.02690.04060.0396-0.05750.1628-0.01570.01680.2725-0.00890.157525.1759-18.4099-0.6433
134.79322.33040.06542.0633-0.78810.501-0.97541.1973-0.4194-0.92510.7552-0.1680.2195-0.0470.05320.4616-0.2380.04370.451-0.12070.213627.5168-6.8031-13.3987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN L AND RESID 0:25 )L0 - 25
2X-RAY DIFFRACTION2( CHAIN L AND RESID 26:101 )L26 - 101
3X-RAY DIFFRACTION3( CHAIN L AND RESID 102:113 )L102 - 113
4X-RAY DIFFRACTION4( CHAIN L AND RESID 114:128 )L114 - 128
5X-RAY DIFFRACTION5( CHAIN L AND RESID 129:150 )L129 - 150
6X-RAY DIFFRACTION6( CHAIN L AND RESID 151:174 )L151 - 174
7X-RAY DIFFRACTION7( CHAIN L AND RESID 175:197 )L175 - 197
8X-RAY DIFFRACTION8( CHAIN L AND RESID 198:213 )L198 - 213
9X-RAY DIFFRACTION9( CHAIN H AND RESID 1:17 )H1 - 17
10X-RAY DIFFRACTION10( CHAIN H AND RESID 18:82 )H18 - 82
11X-RAY DIFFRACTION11( CHAIN H AND RESID 83:95 )H83 - 95
12X-RAY DIFFRACTION12( CHAIN H AND RESID 96:136 )H96 - 136
13X-RAY DIFFRACTION13( CHAIN H AND RESID 137:228 )H137 - 228

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