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- PDB-6xq4: Human antibody S8V2-47 in complex with the influenza hemagglutini... -

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Basic information

Entry
Database: PDB / ID: 6xq4
TitleHuman antibody S8V2-47 in complex with the influenza hemagglutinin head domain of A/Beijing/262/1995(H1N1)
Components
  • Hemagglutinin
  • antibody S8V2-47 heavy chain
  • antibody S8V2-47 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody antigen complex / hemagglutinin / virus / influenza / 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
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.347 Å
AuthorsMcCarthy, K.R. / Harrison, S.C.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089618 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI117892 United States
CitationJournal: Mbio / Year: 2021
Title: A Prevalent Focused Human Antibody Response to the Influenza Virus Hemagglutinin Head Interface.
Authors: McCarthy, K.R. / Lee, J. / Watanabe, A. / Kuraoka, M. / Robinson-McCarthy, L.R. / Georgiou, G. / Kelsoe, G. / Harrison, S.C.
History
DepositionJul 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 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: Hemagglutinin
D: Hemagglutinin
B: antibody S8V2-47 light chain
F: antibody S8V2-47 light chain
C: antibody S8V2-47 heavy chain
E: antibody S8V2-47 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,2838
Polymers149,2726
Non-polymers1,0112
Water00
1
A: Hemagglutinin
B: antibody S8V2-47 light chain
C: antibody S8V2-47 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0604
Polymers74,6363
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Hemagglutinin
F: antibody S8V2-47 light chain
E: antibody S8V2-47 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2234
Polymers74,6363
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.090, 66.470, 135.180
Angle α, β, γ (deg.)90.000, 101.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemagglutinin


Mass: 25338.191 Da / Num. of mol.: 2 / Fragment: head domain (UNP residues 65-280)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Beijing/262/1995(H1N1))
Strain: A/Beijing/262/1995(H1N1) / Gene: HA / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B4UPF7
#2: Antibody antibody S8V2-47 light chain


Mass: 24193.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody antibody S8V2-47 heavy chain


Mass: 25103.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#4: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 1
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
Has ligand of interestN
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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium chloride, 12% w/v PEG4000 , 0.1 M trisodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 23, 2018
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.347→49.475 Å / Num. obs: 23648 / % possible obs: 96.6 % / Redundancy: 2 % / Biso Wilson estimate: 97.09 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05192 / Rpim(I) all: 0.05192 / Rrim(I) all: 0.07343 / Net I/σ(I): 9.38
Reflection shellResolution: 3.347→3.467 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3033 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2357 / CC1/2: 0.765 / CC star: 0.931 / Rpim(I) all: 0.3033 / Rrim(I) all: 0.4289 / % possible all: 97.92

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 6Q0E, 4TSB, 6B5L, & 6E4X

6q0e

4tsb

6b5l

6e4x


Resolution: 3.347→49.475 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2793 1142 4.83 %
Rwork0.2381 22493 -
obs0.2401 23635 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 234.54 Å2 / Biso mean: 102.3972 Å2 / Biso min: 45.96 Å2
Refinement stepCycle: final / Resolution: 3.347→49.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10122 0 67 0 10189
Biso mean--150.94 --
Num. residues----1303
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3472-3.49950.42911340.3317281697
3.4995-3.6840.35251550.2984280598
3.684-3.91470.33081320.2855280797
3.9147-4.21680.3461400.2662274795
4.2168-4.64090.26811390.2242283598
4.6409-5.31170.2441400.2133275095
5.3117-6.68960.24721430.2322288999
6.6896-49.4750.23411590.1988284495

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