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- PDB-8gv7: Crystal structure of PN-SIA28 in complex with influenza hemagglut... -

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Basic information

Entry
Database: PDB / ID: 8gv7
TitleCrystal structure of PN-SIA28 in complex with influenza hemagglutinin H18 A/flat-faced bat/Peru/033/2010
Components
  • (Hemagglutinin H18- ...) x 2
  • PN-SIA28 heavy chain
  • PN-SIA28 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Influenza / hemagglutinin / antibody / broadly neutralizing / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, Y. / Song, H. / Qi, J. / Gao, G.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for a human broadly neutralizing influenza A hemagglutinin stem-specific antibody including H17/18 subtypes.
Authors: Chen, Y. / Wang, F. / Yin, L. / Jiang, H. / Lu, X. / Bi, Y. / Zhang, W. / Shi, Y. / Burioni, R. / Tong, Z. / Song, H. / Qi, J. / Gao, G.F.
History
DepositionSep 14, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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

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Assembly

Deposited unit
A: Hemagglutinin H18-HA1
B: Hemagglutinin H18-HA2
C: PN-SIA28 heavy chain
D: PN-SIA28 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7909
Polymers81,6454
Non-polymers2,1455
Water4,017223
1
A: Hemagglutinin H18-HA1
B: Hemagglutinin H18-HA2
C: PN-SIA28 heavy chain
D: PN-SIA28 light chain
hetero molecules

A: Hemagglutinin H18-HA1
B: Hemagglutinin H18-HA2
C: PN-SIA28 heavy chain
D: PN-SIA28 light chain
hetero molecules

A: Hemagglutinin H18-HA1
B: Hemagglutinin H18-HA2
C: PN-SIA28 heavy chain
D: PN-SIA28 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,37027
Polymers244,93512
Non-polymers6,43515
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area47750 Å2
ΔGint-140 kcal/mol
Surface area88660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.427, 140.427, 195.734
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

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Hemagglutinin H18- ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin H18-HA1


Mass: 36406.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/flat-faced bat/Peru/033/2010(H18N11))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: U5N1D3
#2: Protein Hemagglutinin H18-HA2


Mass: 20122.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/flat-faced bat/Peru/033/2010(H18N11))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: U5N1D3

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Antibody , 2 types, 2 molecules CD

#3: Antibody PN-SIA28 heavy chain


Mass: 13588.259 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody PN-SIA28 light chain


Mass: 11527.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Sugars , 4 types, 5 molecules

#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#8: 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.: 2 / Source method: obtained synthetically / 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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Non-polymers , 1 types, 223 molecules

#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 6.82 Å3/Da / Density % sol: 81.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis Tris 25 % w/v PEG 3350(pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 66862 / % possible obs: 94.1 % / Redundancy: 16.5 % / Biso Wilson estimate: 41.66 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 19.83
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 1.68 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 6653

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data collection
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJS

5gjs


Resolution: 2.6→45.97 Å / SU ML: 0.2955 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.7349
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2217 3057 4.86 %
Rwork0.2089 59904 -
obs0.2095 62961 94.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.41 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5661 0 141 223 6025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225941
X-RAY DIFFRACTIONf_angle_d0.4968066
X-RAY DIFFRACTIONf_chiral_restr0.0409918
X-RAY DIFFRACTIONf_plane_restr0.00441028
X-RAY DIFFRACTIONf_dihedral_angle_d5.0075855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.3918630.30191425X-RAY DIFFRACTION48.95
2.64-2.690.3374700.3151655X-RAY DIFFRACTION57.73
2.69-2.730.27061010.29822204X-RAY DIFFRACTION75.43
2.73-2.780.31061290.28412705X-RAY DIFFRACTION93.81
2.78-2.840.28971600.27742835X-RAY DIFFRACTION98.62
2.84-2.890.29191110.2772900X-RAY DIFFRACTION99.6
2.89-2.960.28461400.2682882X-RAY DIFFRACTION99.97
2.96-3.020.2451730.26062849X-RAY DIFFRACTION99.9
3.03-3.10.29611530.24512894X-RAY DIFFRACTION99.9
3.1-3.180.2871520.26062878X-RAY DIFFRACTION99.93
3.18-3.280.25341630.24792877X-RAY DIFFRACTION99.97
3.28-3.380.25251510.23462892X-RAY DIFFRACTION99.97
3.38-3.50.28331500.20932889X-RAY DIFFRACTION99.97
3.5-3.640.24051480.20462876X-RAY DIFFRACTION100
3.65-3.810.20581560.20272888X-RAY DIFFRACTION100
3.81-4.010.20771370.1962909X-RAY DIFFRACTION100
4.01-4.260.1781580.16712890X-RAY DIFFRACTION100
4.26-4.590.17351530.15432885X-RAY DIFFRACTION100
4.59-5.050.16051400.16092912X-RAY DIFFRACTION100
5.05-5.780.20471500.17692897X-RAY DIFFRACTION99.97
5.78-7.280.18551460.19762923X-RAY DIFFRACTION100
7.28-45.970.17161530.18572839X-RAY DIFFRACTION96.55

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