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- PDB-6lxj: Crystal structure of human Z2B3 Fab in complex with influenza vir... -

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Basic information

Entry
Database: PDB / ID: 6lxj
TitleCrystal structure of human Z2B3 Fab in complex with influenza virus neuraminidase from A/Anhui/1/2013 (H7N9)
Components
  • Heavy chain of Z2B3 Fab
  • Light chain of Z2B3 Fab
  • Neuraminidase
KeywordsHYDROLASE/IMMUNE SYSTEM / antibody / antigen / complex / IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.903 Å
AuthorsJiang, H. / Peng, W. / Qi, J. / Chai, Y. / Song, H. / Shi, Y. / Gao, G.F. / Wu, Y.
Funding support China, 5items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010202 China
Ministry of Science and Technology (China)2018ZX10733403 China
Chinese Academy of SciencesXDB37030204 China
Ministry of Science and Technology (China)2018ZX10101004-001 China
Chinese Academy of Sciences2016086 China
CitationJournal: Mbio / Year: 2020
Title: Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus.
Authors: Jiang, H. / Peng, W. / Qi, J. / Chai, Y. / Song, H. / Bi, Y. / Rijal, P. / Wang, H. / Oladejo, B.O. / Liu, J. / Shi, Y. / Gao, G.F. / Townsend, A.R. / Wu, Y.
History
DepositionFeb 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 2.0Dec 9, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num ..._atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _struct_conn.ptnr2_auth_seq_id
Revision 2.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
H: Heavy chain of Z2B3 Fab
L: Light chain of Z2B3 Fab
E: Heavy chain of Z2B3 Fab
F: Light chain of Z2B3 Fab
J: Heavy chain of Z2B3 Fab
K: Light chain of Z2B3 Fab
M: Heavy chain of Z2B3 Fab
N: Light chain of Z2B3 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)376,37028
Polymers365,93112
Non-polymers10,44016
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49820 Å2
ΔGint44 kcal/mol
Surface area118240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.307, 207.514, 207.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

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Antibody , 2 types, 8 molecules HEJMLFKN

#2: Antibody
Heavy chain of Z2B3 Fab


Mass: 25133.088 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody
Light chain of Z2B3 Fab


Mass: 22796.049 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Protein / Non-polymers , 2 types, 8 molecules ABCD

#1: Protein
Neuraminidase


Mass: 43553.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Anhui/1-BALF_RG44/2013(H7N9))
Strain: A/Anhui/1-BALF_RG44/2013(H7N9) / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A024E1X5, exo-alpha-sialidase
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Sugars , 4 types, 12 molecules

#4: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1559.386 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 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: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: May 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 94896 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 16.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.7 % / Num. unique obs: 94896 / CC1/2: 0.998 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MWJ, 5W0D

4mwj

5w0d


Resolution: 2.903→48.911 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2412 4742 5 %
Rwork0.1932 --
obs0.1956 94896 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.25 Å2 / Biso mean: 39.882 Å2 / Biso min: 10.29 Å2
Refinement stepCycle: final / Resolution: 2.903→48.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24832 0 691 0 25523
Biso mean--48.38 --
Num. residues----3238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01226251
X-RAY DIFFRACTIONf_angle_d1.22335888
X-RAY DIFFRACTIONf_dihedral_angle_d15.3569738
X-RAY DIFFRACTIONf_chiral_restr0.074089
X-RAY DIFFRACTIONf_plane_restr0.0094493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9034-2.93640.371510.28612845X-RAY DIFFRACTION95
2.9364-2.9710.35691350.27712930X-RAY DIFFRACTION97
2.971-3.00720.34841540.26492933X-RAY DIFFRACTION98
3.0072-3.04520.29591240.26272998X-RAY DIFFRACTION98
3.0452-3.08530.35451600.25822934X-RAY DIFFRACTION98
3.0853-3.12760.30851620.24982966X-RAY DIFFRACTION99
3.1276-3.17220.32351820.24712926X-RAY DIFFRACTION99
3.1722-3.21960.33921670.24662982X-RAY DIFFRACTION99
3.2196-3.26990.29211700.24372977X-RAY DIFFRACTION99
3.2699-3.32350.29521560.24142955X-RAY DIFFRACTION99
3.3235-3.38080.32021730.23792976X-RAY DIFFRACTION99
3.3808-3.44220.2681840.23062950X-RAY DIFFRACTION99
3.4422-3.50840.25061830.20662966X-RAY DIFFRACTION99
3.5084-3.580.23811610.2042968X-RAY DIFFRACTION99
3.58-3.65780.24141430.20573007X-RAY DIFFRACTION99
3.6578-3.74290.23751520.18593005X-RAY DIFFRACTION100
3.7429-3.83650.25371570.19053023X-RAY DIFFRACTION100
3.8365-3.94010.26911380.19513024X-RAY DIFFRACTION100
3.9401-4.0560.25331760.18172996X-RAY DIFFRACTION100
4.056-4.18690.21171500.16033073X-RAY DIFFRACTION100
4.1869-4.33640.18391470.15843016X-RAY DIFFRACTION100
4.3364-4.50990.1911490.1563080X-RAY DIFFRACTION100
4.5099-4.7150.17721520.14523014X-RAY DIFFRACTION100
4.715-4.96340.18861720.14963052X-RAY DIFFRACTION100
4.9634-5.2740.19361840.15973016X-RAY DIFFRACTION100
5.274-5.68070.23451570.16463045X-RAY DIFFRACTION100
5.6807-6.25130.20881430.18053112X-RAY DIFFRACTION100
6.2513-7.15350.22311270.18023105X-RAY DIFFRACTION100
7.1535-9.00340.2081570.17383123X-RAY DIFFRACTION100
9.0034-48.91830.22271760.19733157X-RAY DIFFRACTION98

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