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- PDB-8gv5: Crystal structure of PN-SIA28 in complex with influenza hemagglut... -

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Basic information

Entry
Database: PDB / ID: 8gv5
TitleCrystal structure of PN-SIA28 in complex with influenza hemagglutinin A/swine/Guangdong/104/2013 (H1N1)
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
  • PN-SIA28 Heavy chain
  • PN-SIA28 Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / influenza / hemagglutinin / antibody / broadly neutralizing / ANTIVIRAL 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
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: PN-SIA28 Heavy chain
D: PN-SIA28 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3235
Polymers82,1024
Non-polymers2211
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.797, 85.797, 231.289
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

#1: Protein Hemagglutinin HA1 chain


Mass: 37049.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/swine/Guangdong/104/2013(H1N1))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A0A0D3LZV1
#2: Protein Hemagglutinin HA2 chain


Mass: 19936.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/swine/Guangdong/104/2013(H1N1))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A0A0D3LZV1
#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)
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / 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
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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M magnesium acetate, 0.1M sodium acetate, 8% w/v PEG 8000 (pH 4.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 15923 / % possible obs: 73.2 % / Redundancy: 12.6 % / Biso Wilson estimate: 54.76 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 15.3
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 2.4 / Mean I/σ(I) obs: 1 / Num. unique obs: 1571

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX1.20_4459refinement
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJS

5gjs


Resolution: 3.2→45.63 Å / SU ML: 0.4456 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.0492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3082 653 5.61 %
Rwork0.2673 10980 -
obs0.2697 11633 73.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.87 Å2
Refinement stepCycle: LAST / Resolution: 3.2→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 14 0 5504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00535636
X-RAY DIFFRACTIONf_angle_d0.96577650
X-RAY DIFFRACTIONf_chiral_restr0.0661833
X-RAY DIFFRACTIONf_plane_restr0.0059986
X-RAY DIFFRACTIONf_dihedral_angle_d11.39682003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.440.4262300.3548689X-RAY DIFFRACTION22.77
3.45-3.790.3412820.31751411X-RAY DIFFRACTION47.16
3.79-4.340.32351580.28242866X-RAY DIFFRACTION95.64
4.34-5.460.27791840.24472992X-RAY DIFFRACTION100
5.47-45.630.30581990.25133022X-RAY DIFFRACTION99.88
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)
11.058912586570.142522925335-0.04574708988880.4938648225110.1370657757472.86931689462-0.01925963627790.507048981199-0.0716626207197-0.4482330707420.1277966842040.356195818452-0.327291125958-1.22142712478-0.1181164977680.338438276899-0.0874453041407-0.2511084165320.7006205851740.1068700413480.34973437065222.84056452-28.5895560343-57.6806070019
21.95333718495-0.0466528209275-0.6848962154891.5804416234-0.1173223070451.99216032389-0.0753664471921-0.723485773963-0.1273902167940.5952528062110.05690330606530.450258722473-0.0969670409049-0.1705517827160.01731988504620.137483168193-0.08194868305730.1346653732580.4360891058280.1739022624940.17901039637330.5252889176-28.1940873589-8.63422170118
34.30094170884-1.201489920010.02138461626450.505096202227-0.1280666452171.11188849159-0.0531533792803-0.96864779488-0.867139951140.3109586347140.19674842081.788685160330.155426287577-0.649581397898-0.1416660690690.7429727552830.0448619442550.2444042360631.012747693130.3382669736861.71961554869-0.388761944004-25.4062239837-3.66414063786
42.30293596692-0.860860282341-0.2932265362912.3179387553-0.4759746259942.097422542880.4157099591750.6320372267780.397025663814-0.689986261906-0.01936045198170.587043681427-0.911552736015-0.737970967297-0.3935952058410.8644747726540.1751449531140.1044744273050.8620940551420.2610723410941.159844265418.63934997799-14.57061081-20.5969524254
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA1 - 3231 - 321
22chain BBB331 - 4871 - 157
33chain CCC31 - 1541 - 124
44chain DDD43 - 1491 - 107

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