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- PDB-6xpx: Human antibody S1V2-51 in complex with the influenza hemagglutini... -

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Basic information

Entry
Database: PDB / ID: 6xpx
TitleHuman antibody S1V2-51 in complex with the influenza hemagglutinin head domain of A/Aichi/2/1968 (X-31)(H3N2)
Components
  • Hemagglutinin
  • S1V2-51 Fab heavy chain
  • S1V2-51 Fab light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / antibody antigen complex / hemagglutinin / virus / influenza / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN 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
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 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 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
C: S1V2-51 Fab light chain
B: S1V2-51 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,53316
Polymers80,2953
Non-polymers2,23813
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-28 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.420, 101.560, 77.410
Angle α, β, γ (deg.)90.000, 108.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hemagglutinin /


Mass: 31936.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Aichi/2/1968 (X-31)(H3N2) / Gene: 41857 / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03437

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Antibody , 2 types, 2 molecules CB

#2: Antibody S1V2-51 Fab light chain


Mass: 24198.760 Da / Num. of mol.: 1
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 S1V2-51 Fab heavy chain


Mass: 24159.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)

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Sugars , 2 types, 3 molecules

#4: 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
#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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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 , 4 types, 26 molecules

#6: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 61.39 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.3 M Magnesium chloride, 25% (w/v) PEG 2000, 15% (w/v) Glycerol, 0.1 M BICINE, pH 9.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.598→42.65 Å / Num. obs: 30757 / % possible obs: 98.84 % / Redundancy: 3.8 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.06237 / Rpim(I) all: 0.03622 / Rrim(I) all: 0.07237 / Net I/σ(I): 12.78
Reflection shellResolution: 2.598→2.691 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.7997 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 2992 / CC1/2: 0.583 / CC star: 0.858 / Rpim(I) all: 0.4695 / Rrim(I) all: 0.931 / % possible all: 96.86

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E56, 5I18, 6E4X

6e56

5i18

6e4x


Resolution: 2.598→42.646 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2154 1579 5.13 %
Rwork0.1853 29173 -
obs0.187 30752 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.15 Å2 / Biso mean: 80.1681 Å2 / Biso min: 34.58 Å2
Refinement stepCycle: final / Resolution: 2.598→42.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5372 0 147 16 5535
Biso mean--116.89 61.06 -
Num. residues----702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145647
X-RAY DIFFRACTIONf_angle_d1.4067667
X-RAY DIFFRACTIONf_dihedral_angle_d6.5963338
X-RAY DIFFRACTIONf_chiral_restr0.07859
X-RAY DIFFRACTIONf_plane_restr0.008976
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5984-2.68220.35571390.2965256597
2.6822-2.77810.2941330.26282668100
2.7781-2.88930.33311150.2586267099
2.8893-3.02070.31831400.2384260498
3.0207-3.17990.29581340.2136268999
3.1799-3.37910.25671510.20422659100
3.3791-3.63990.24351480.19912655100
3.6399-4.00590.21291520.1856265999
4.0059-4.5850.17281520.1558263398
4.585-5.77430.19311640.15292662100
5.7743-42.6460.18541510.1747270999
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)
12.58091.00472.22661.25780.23882.26340.1809-0.1247-0.08510.0052-0.0295-0.11810.10210.0943-0.15790.71860.07010.09080.7116-0.05870.68191.0242-4.1956-8.2913
23.20110.32781.64832.91531.0613.84010.1073-0.05660.3003-0.0428-0.09230.4373-0.0269-0.5448-0.0310.4830.02120.05540.67860.08680.6111-17.2164-8.0623-22.6415
32.65041.35131.81721.18920.3881.9437-0.08430.25270.5435-0.0318-0.05980.0505-0.170.39640.10860.72760.03170.05620.7276-0.05040.73517.71033.9043-10.2939
43.1594-2.32840.11066.6709-0.39632.5994-0.3089-0.2716-0.23810.31820.4160.1597-0.242-0.0057-0.09760.6212-0.10450.02080.59160.04190.5651-0.5886-40.4497-9.2624
52.5455-1.3516-0.3211.1232-0.08770.9424-0.1158-0.2993-0.13420.11540.119-0.00790.10850.28040.00090.6762-0.0183-0.01440.6445-0.01210.570519.6491-50.932-13.5216
63.4226-1.72061.83842.63740.73483.8021-0.25450.437-0.3022-1.17290.1494-0.7933-0.32820.20620.10550.89840.06530.20520.62420.06450.824114.9179-34.0234-35.1746
72.6648-0.4246-0.91354.17460.48392.48380.22840.31360.1931-0.6983-0.278-0.16-0.0351-0.01570.02960.63230.00480.05840.58890.07170.56194.4527-30.3416-29.8453
84.7077-0.35920.76063.72590.00985.03890.3680.48320.5809-0.8197-0.394-0.638-0.72340.02770.08780.97820.02970.07840.63910.02830.72368.5626-25.2393-32.1248
92.3107-1.5451-0.88151.59751.21870.9233-0.04630.30980.1988-0.346-0.0345-0.2052-0.03910.05340.07530.7879-0.05270.03850.59320.11230.731614.822-35.2764-28.7494
104.98841.6392-1.27095.394-0.52832.3675-0.02310.08770.0150.22280.19820.17830.36380.0643-0.0910.61380.0264-0.00270.6279-0.0520.588131.6735-55.8808-24.9834
114.1911.2455-1.57757.3174-3.07764.5197-0.16550.3527-0.6633-0.54110.3772-0.4150.8344-0.0348-0.31760.76890.0105-0.08470.7713-0.13460.809635.5494-60.9439-32.0468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 104 )A41 - 104
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 249 )A105 - 249
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 311 )A250 - 311
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 38 )C1 - 38
5X-RAY DIFFRACTION5chain 'C' and (resid 39 through 218 )C39 - 218
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 17 )B1 - 17
7X-RAY DIFFRACTION7chain 'B' and (resid 18 through 60 )B18 - 60
8X-RAY DIFFRACTION8chain 'B' and (resid 61 through 83 )B61 - 83
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 122 )B84 - 122
10X-RAY DIFFRACTION10chain 'B' and (resid 123 through 188 )B123 - 188
11X-RAY DIFFRACTION11chain 'B' and (resid 189 through 216 )B189 - 216

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