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- PDB-6n5d: Broadly protective antibodies directed to a subdominant influenza... -

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Basic information

Entry
Database: PDB / ID: 6n5d
TitleBroadly protective antibodies directed to a subdominant influenza hemagglutinin epitope
Components
  • Hemagglutinin
  • antibody heavy chainImmunoglobulin heavy chain
  • antibody light chainImmunoglobulin light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / influenza / antibody / complex / hemagglutinin / immunogen design / glycan / 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 / 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 / membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBajic, G. / Schmidt, A.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI089618 United States
CitationJournal: Cell Host Microbe / Year: 2019
Title: Influenza Antigen Engineering Focuses Immune Responses to a Subdominant but Broadly Protective Viral Epitope.
Authors: Bajic, G. / Maron, M.J. / Adachi, Y. / Onodera, T. / McCarthy, K.R. / McGee, C.E. / Sempowski, G.D. / Takahashi, Y. / Kelsoe, G. / Kuraoka, M. / Schmidt, A.G.
History
DepositionNov 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: Hemagglutinin
C: antibody heavy chain
B: Hemagglutinin
E: antibody heavy chain
K: Hemagglutinin
L: antibody heavy chain
N: antibody light chain
F: antibody light chain
D: antibody light chain


Theoretical massNumber of molelcules
Total (without water)238,2249
Polymers238,2249
Non-polymers00
Water0
1
A: Hemagglutinin
C: antibody heavy chain
D: antibody light chain


Theoretical massNumber of molelcules
Total (without water)79,4083
Polymers79,4083
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-30 kcal/mol
Surface area32040 Å2
MethodPISA
2
B: Hemagglutinin
E: antibody heavy chain
F: antibody light chain


Theoretical massNumber of molelcules
Total (without water)79,4083
Polymers79,4083
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-31 kcal/mol
Surface area32010 Å2
MethodPISA
3
K: Hemagglutinin
L: antibody heavy chain
N: antibody light chain


Theoretical massNumber of molelcules
Total (without water)79,4083
Polymers79,4083
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-28 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.190, 153.190, 94.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Hemagglutinin /


Mass: 31150.033 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03437
#2: Antibody antibody heavy chain / Immunoglobulin heavy chain


Mass: 25338.352 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: HC / Production host: Homo sapiens (human)
#3: Antibody antibody light chain / Immunoglobulin light chain


Mass: 22919.457 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium bromide, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.46
ReflectionResolution: 3→44.369 Å / Num. obs: 49440 / % possible obs: 100 % / Redundancy: 6.437 % / Biso Wilson estimate: 51.897 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.255 / Rrim(I) all: 0.277 / Χ2: 0.914 / Net I/σ(I): 9.22 / Num. measured all: 318259 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3-3.36.451.1991.84122680.4551.304100
3.3-3.56.4430.6483.4260140.7090.705100
3.5-46.4310.3845.64103010.8720.417100
4-56.4010.16112.44102020.9790.175100
5-66.3340.14513.444770.9830.158100
6-106.5780.08421.548600.9970.091100
10-206.520.03247.311670.9990.035100
20-306.1540.03154.121170.9990.034100
30-505.2940.02353.03340.9990.02694.4
44.369-500

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1HA0, 6N5B, & 4HKX

1ha0

6n5b

4hkx


Resolution: 3→44.369 Å / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.82
RfactorNum. reflection% reflection
Rfree0.2444 2396 4.85 %
Rwork0.2173 --
obs0.2279 49440 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.15 Å2 / Biso mean: 55.5971 Å2 / Biso min: 26.59 Å2
Refinement stepCycle: final / Resolution: 3→44.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16356 0 0 0 16356
Num. residues----2148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.001-3.06220.35271480.30852742289095
3.0622-3.12870.3267980.28852812291097
3.1287-3.20140.32291580.28972743290195
3.2014-3.28140.2941600.28362739289994
3.2814-3.370.26911700.26312716288694
3.37-3.4690.2671200.25792805292596
3.469-3.58070.30621300.25332751288195
3.5807-3.70850.30451580.24212737289595
3.7085-3.85660.26341760.23642746292294
3.8566-4.03170.22711180.23042790290896
4.0317-4.24370.23361420.20882741288395
4.2437-4.50860.20951440.2012803294795
4.5086-4.85520.20771450.17692762290795
4.8552-5.34110.24621300.18632743287395
5.3411-6.10770.2331240.19432758288296
6.1077-7.67130.21271200.20362804292496
7.6713-28.99260.24431550.23452758291395

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