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- PDB-6lxk: Crystal structure of Z2B3 D102R Fab in complex with influenza vir... -

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Basic information

Entry
Database: PDB / ID: 6lxk
TitleCrystal structure of Z2B3 D102R Fab in complex with influenza virus neuraminidase from A/Serbia/NS-601/2014 (H1N1)
Components
  • Heavy chain of Z2B3-D102R Fab
  • Light chain of Z2B3-D102R Fab
  • Neuraminidase
KeywordsHYDROLASE/IMMUNE SYSTEM / antibody / antigen / complex / IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neuraminidase / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.608 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 1.1Dec 9, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Nov 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
Revision 1.3Oct 23, 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: Neuraminidase
H: Heavy chain of Z2B3-D102R Fab
L: Light chain of Z2B3-D102R Fab
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
E: Heavy chain of Z2B3-D102R Fab
F: Light chain of Z2B3-D102R Fab
J: Heavy chain of Z2B3-D102R Fab
K: Light chain of Z2B3-D102R Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,69922
Polymers350,03210
Non-polymers2,66712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31460 Å2
ΔGint-159 kcal/mol
Surface area100820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.442, 214.442, 168.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Neuraminidase


Mass: 51529.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NA / Variant: A/Serbia/NS-601/2014(H1N1) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: X2L845, UniProt: A0A5P1N996*PLUS, exo-alpha-sialidase
#2: Antibody Heavy chain of Z2B3-D102R Fab


Mass: 25175.193 Da / Num. of mol.: 3
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-D102R Fab


Mass: 22796.049 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY
Sequence detailsSequence reference for Neuraminidase from Influenza A virus (A/Serbia/NS-601/2014(H1N1)) was not ...Sequence reference for Neuraminidase from Influenza A virus (A/Serbia/NS-601/2014(H1N1)) was not yet available at UNIPROT at the time of data processing. Thus, X2L845_9INFA, which was derived from Influenza A virus (A/Czech Republic/2/2014(H1N1)), was used as the sequence reference.

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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: 3.2 Å3/Da / Density % sol: 61.55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M magnesium acetate, 0.1M MES pH 6.5, 10% (w/v) PEG 10000

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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: Jul 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 51355 / % possible obs: 100 % / Redundancy: 8.3 % / CC1/2: 0.998 / Net I/σ(I): 6.4
Reflection shellResolution: 3.6→3.73 Å / Num. unique obs: 51355 / CC1/2: 0.998

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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: 3BEQ, 5W0D

3beq

5w0d


Resolution: 3.608→25.459 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.16
RfactorNum. reflection% reflection
Rfree0.2488 2511 4.89 %
Rwork0.2147 --
obs0.2164 51355 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 550.28 Å2 / Biso mean: 97.1993 Å2 / Biso min: 19.39 Å2
Refinement stepCycle: final / Resolution: 3.608→25.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21823 0 164 0 21987
Biso mean--128.74 --
Num. residues----2877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322544
X-RAY DIFFRACTIONf_angle_d0.63430685
X-RAY DIFFRACTIONf_dihedral_angle_d16.7618173
X-RAY DIFFRACTIONf_chiral_restr0.0473361
X-RAY DIFFRACTIONf_plane_restr0.0043949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6083-3.67750.331830.26872526X-RAY DIFFRACTION92
3.6775-3.75240.28311450.2672696X-RAY DIFFRACTION99
3.7524-3.83370.27571180.26072717X-RAY DIFFRACTION100
3.8337-3.92260.31951410.26362690X-RAY DIFFRACTION100
3.9226-4.02030.32781370.23912698X-RAY DIFFRACTION100
4.0203-4.12860.2821270.22442737X-RAY DIFFRACTION100
4.1286-4.24950.27521320.2112697X-RAY DIFFRACTION100
4.2495-4.3860.21261290.19882721X-RAY DIFFRACTION100
4.386-4.54190.22461360.22702X-RAY DIFFRACTION100
4.5419-4.72270.21631520.18052686X-RAY DIFFRACTION100
4.7227-4.93610.23591340.18392750X-RAY DIFFRACTION100
4.9361-5.19430.23081340.18352708X-RAY DIFFRACTION100
5.1943-5.51660.24281550.20312728X-RAY DIFFRACTION100
5.5166-5.93760.22891450.19912731X-RAY DIFFRACTION100
5.9376-6.5260.24491670.20472711X-RAY DIFFRACTION100
6.526-7.44950.24461820.20542716X-RAY DIFFRACTION100
7.4495-9.30870.2151490.1992790X-RAY DIFFRACTION100
9.3087-25.45930.23621450.23132840X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -53.3555 Å / Origin y: 55.853 Å / Origin z: 14.369 Å
111213212223313233
T0.2252 Å2-0.0346 Å20.0196 Å2-0.3303 Å20.0192 Å2--0.3175 Å2
L0.1956 °20.1752 °20.0316 °2-0.3505 °2-0.0467 °2--0.1159 °2
S0.0221 Å °0.0012 Å °-0.1584 Å °-0.0381 Å °-0.059 Å °-0.1527 Å °0.024 Å °0.0856 Å °-0.0003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA83 - 469
2X-RAY DIFFRACTION1allA583 - 696
3X-RAY DIFFRACTION1allH1 - 232
4X-RAY DIFFRACTION1allL2 - 212
5X-RAY DIFFRACTION1allB83 - 469
6X-RAY DIFFRACTION1allB583 - 696
7X-RAY DIFFRACTION1allC83 - 469
8X-RAY DIFFRACTION1allC583 - 696
9X-RAY DIFFRACTION1allD83 - 469
10X-RAY DIFFRACTION1allD583 - 696
11X-RAY DIFFRACTION1allE1 - 232
12X-RAY DIFFRACTION1allF2 - 212
13X-RAY DIFFRACTION1allJ1 - 232
14X-RAY DIFFRACTION1allK2 - 212

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