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- PDB-6lxi: Crystal structure of Z2B3 Fab in complex with influenza virus neu... -

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Basic information

Entry
Database: PDB / ID: 6lxi
TitleCrystal structure of Z2B3 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1)
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 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / 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: 2.5 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 (MoST, China)2018ZX10733403 China
Chinese Academy of SciencesXDB37030204 China
Ministry of Science and Technology (MoST, 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 / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
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

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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 Fab
L: Light chain of Z2B3 Fab
B: Neuraminidase
C: Heavy chain of Z2B3 Fab
D: Light chain of Z2B3 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,70312
Polymers198,7536
Non-polymers1,9506
Water10,178565
1
A: Neuraminidase
H: Heavy chain of Z2B3 Fab
L: Light chain of Z2B3 Fab
hetero molecules

A: Neuraminidase
H: Heavy chain of Z2B3 Fab
L: Light chain of Z2B3 Fab
hetero molecules

A: Neuraminidase
H: Heavy chain of Z2B3 Fab
L: Light chain of Z2B3 Fab
hetero molecules

A: Neuraminidase
H: Heavy chain of Z2B3 Fab
L: Light chain of Z2B3 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,40624
Polymers397,50612
Non-polymers3,90012
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
Buried area38850 Å2
ΔGint-170 kcal/mol
Surface area117250 Å2
MethodPISA
2
B: Neuraminidase
C: Heavy chain of Z2B3 Fab
D: Light chain of Z2B3 Fab
hetero molecules

B: Neuraminidase
C: Heavy chain of Z2B3 Fab
D: Light chain of Z2B3 Fab
hetero molecules

B: Neuraminidase
C: Heavy chain of Z2B3 Fab
D: Light chain of Z2B3 Fab
hetero molecules

B: Neuraminidase
C: Heavy chain of Z2B3 Fab
D: Light chain of Z2B3 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,40624
Polymers397,50612
Non-polymers3,90012
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
Buried area39100 Å2
ΔGint-171 kcal/mol
Surface area113660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.130, 163.130, 190.757
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab

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Components

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Antibody , 2 types, 4 molecules HCLD

#2: Antibody Heavy chain of Z2B3 Fab


Mass: 25133.088 Da / Num. of mol.: 2
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.: 2
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 / Sugars , 2 types, 4 molecules AB

#1: Protein Neuraminidase /


Mass: 51447.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)
Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IGQ6, exo-alpha-sialidase
#4: 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 569 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O

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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: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4% Tacsimate pH 7.0, 20% 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: 2.499→50 Å / Num. obs: 88386 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 38.09 Å2 / CC1/2: 0.998 / Net I/σ(I): 18
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 0.18 / Num. unique obs: 83916

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BEQ, 5W0D

3beq

5w0d


Resolution: 2.5→47.93 Å / SU ML: 0.2377 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.0504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2116 4442 5.03 %
Rwork0.1834 83944 -
obs0.1848 88386 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12308 0 124 565 12997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011612740
X-RAY DIFFRACTIONf_angle_d1.015317347
X-RAY DIFFRACTIONf_chiral_restr0.06681933
X-RAY DIFFRACTIONf_plane_restr0.00712218
X-RAY DIFFRACTIONf_dihedral_angle_d17.06274549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.27291170.23622531X-RAY DIFFRACTION91.03
2.53-2.560.2911430.22762652X-RAY DIFFRACTION94.3
2.56-2.590.27481660.24212671X-RAY DIFFRACTION95.88
2.59-2.620.29361380.22352709X-RAY DIFFRACTION97.57
2.62-2.660.29281360.23432744X-RAY DIFFRACTION98.7
2.66-2.690.27061370.2232767X-RAY DIFFRACTION98.91
2.69-2.730.27641320.22552791X-RAY DIFFRACTION99.39
2.73-2.770.28891550.22632785X-RAY DIFFRACTION99.9
2.77-2.810.26371540.2152790X-RAY DIFFRACTION99.97
2.81-2.860.27641480.20752794X-RAY DIFFRACTION100
2.86-2.910.24681480.222792X-RAY DIFFRACTION100
2.91-2.960.22621620.212808X-RAY DIFFRACTION99.97
2.96-3.020.2421550.21212789X-RAY DIFFRACTION100
3.02-3.080.23421160.2092811X-RAY DIFFRACTION100
3.08-3.150.22431590.20752801X-RAY DIFFRACTION100
3.15-3.220.27041500.20512811X-RAY DIFFRACTION99.97
3.22-3.30.2171660.20412782X-RAY DIFFRACTION100
3.3-3.390.22121290.19412853X-RAY DIFFRACTION100
3.39-3.490.2141450.18632808X-RAY DIFFRACTION100
3.49-3.60.21651410.18232835X-RAY DIFFRACTION100
3.6-3.730.23071410.18762818X-RAY DIFFRACTION99.93
3.73-3.880.21221650.17622835X-RAY DIFFRACTION100
3.88-4.060.18751380.16372834X-RAY DIFFRACTION100
4.06-4.270.16261590.14512835X-RAY DIFFRACTION100
4.27-4.540.14021550.13492851X-RAY DIFFRACTION99.97
4.54-4.890.1681600.13252842X-RAY DIFFRACTION99.97
4.89-5.380.14931630.14792856X-RAY DIFFRACTION99.8
5.38-6.160.20751530.17532894X-RAY DIFFRACTION99.84
6.16-7.750.2011610.17732920X-RAY DIFFRACTION99.26
7.76-47.930.19561500.1852935X-RAY DIFFRACTION94.54
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)
10.4833511587020.06492597419850.02182653581990.315619341652-0.02027292701910.2281970640410.02288349263310.00912733118189-0.0223488087628-0.00435241539304-0.00517315622566-0.02125680158110.02946669421910.01943347249011.62062929987E-100.1634673444840.0102251274361-0.002329926306210.161933042448-0.004318061821320.161909143426-60.6907006222-18.5731972749104.856956411
20.095490699363-0.0163353036901-0.1389873194480.0209629477241-0.05214798548020.3380637582150.00650793168488-0.00133723818242-0.0486813764154-0.0651924699669-0.007893928298830.04525036338520.0136881118647-0.00300110411437-2.60757651821E-100.2888281607220.02898870283530.00734441676180.222209513427-0.0192191037510.259427904016-39.751870976-17.182691422557.859520866
30.284235468047-0.2436492067820.2729094695190.415271366421-0.3886826368830.3688248931860.0495182318619-0.0395808237319-0.022838071518-0.0929667183816-0.0810120614348-0.01998283678910.2269805544760.129632557539-0.009252002399410.2883238247590.06502431917230.01715325505330.206343782211-0.008308100442320.20502101383-28.2442841033-31.016053111159.4517463808
40.356828190023-0.018755685198-0.03634283315580.2699786672470.01855525699180.178550394317-0.01608353468250.0200224593556-0.0487446518621-0.014705114537-0.00493652184621-0.01557355528420.04036335665290.0399745043334-4.07207624509E-100.1817751214270.01837177079240.01726372483020.1730605810630.002145778207510.17777236315-65.2693053823-22.6757651825-14.7985089326
50.3789481941220.171580317209-0.1934495287020.131143392867-0.04588186436760.1281878607530.00887429920439-0.174736686983-0.0766542667094-0.0628726983056-0.0699436313422-0.0952484047211-0.02363648658220.0872271300872-0.02036354528610.2275388718080.00171009111870.008106490380410.3210543227060.05572866502070.285450138361-70.9669575117-42.051178904130.4559577966
60.346543211638-0.0334889414538-0.02870781335080.4217522585250.104915774480.4837989529440.00489470929187-0.110264614428-0.309503534654-0.02653690330740.0284888822463-0.03189190445090.02099784829630.1741200586220.1480712603710.2425583005330.106848054685-0.008118392194550.3688565329480.1085512924860.378187130927-55.6016248515-52.402668836331.5501860708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1'chain A' or 'chain E'
2X-RAY DIFFRACTION2chain H
3X-RAY DIFFRACTION3chain L
4X-RAY DIFFRACTION4'chain B' or 'chain F'
5X-RAY DIFFRACTION5chain C
6X-RAY DIFFRACTION6chain D

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