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- PDB-6xpy: Human antibody S1V2-58 in complex with the influenza hemagglutini... -

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Basic information

Entry
Database: PDB / ID: 6xpy
TitleHuman antibody S1V2-58 in complex with the influenza hemagglutinin head domain of A/Texas/50/2012(H3N2)
Components
  • Fab heavy chain
  • Fab light chain
  • Hemagglutinin
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 / 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: 3.603 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: Fab light chain
B: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7085
Polymers81,5353
Non-polymers1,1732
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.070, 158.190, 137.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hemagglutinin


Mass: 32618.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Texas/50/2012(H3N2) / Gene: HA, L998_47834gpHA / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4L1D1
#2: Antibody Fab light chain


Mass: 23493.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: antibody kappa chain / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody Fab heavy chain


Mass: 25423.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: antibody heavy chain / Cell line (production host): 293F / Production host: Homo sapiens (human)
#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.: 2
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

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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: 3.97 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 10.5 / Details: 30% (v/v) PEG 400, 0.1M CAPS, pH 10.5

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.603→48.214 Å / Num. obs: 15283 / % possible obs: 99.49 % / Redundancy: 7.4 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.04303 / Rrim(I) all: 0.1184 / Net I/σ(I): 13.82
Reflection shellResolution: 3.603→3.732 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.8952 / Num. unique obs: 11109 / CC1/2: 0.867 / CC star: 0.964 / Rpim(I) all: 0.3439 / Rrim(I) all: 0.9602 / % possible all: 98.24

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W08, 6E4X

5w08

6e4x


Resolution: 3.603→48.214 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3037 722 4.73 %
Rwork0.2557 14533 -
obs0.2581 15255 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 320.56 Å2 / Biso mean: 163.2586 Å2 / Biso min: 70.33 Å2
Refinement stepCycle: final / Resolution: 3.603→48.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 78 0 5568
Biso mean--176.6 --
Num. residues----711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035717
X-RAY DIFFRACTIONf_angle_d0.6547798
X-RAY DIFFRACTIONf_dihedral_angle_d4.0133408
X-RAY DIFFRACTIONf_chiral_restr0.044885
X-RAY DIFFRACTIONf_plane_restr0.005992
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.6033-3.88140.37081310.3469284099
3.8814-4.27180.32091490.28882872100
4.2718-4.88940.30641540.25642879100
4.8894-6.15810.3081480.26982902100
6.1581-48.2140.27841400.22023040100
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)
11.9754-0.26562.92140.0455-0.50424.8418-2.50370.94030.9595-1.41863.5145-0.76540.26240.74770.95022.2773-0.0247-0.11441.42430.78051.294319.0535-44.6122-45.8
23.3624-0.16290.86591.7276-3.14878.2736-0.14150.38530.1145-0.40440.23040.40440.071-1.0741-0.16371.3383-0.0458-0.02481.3429-0.04131.099117.5988-64.1668-28.4873
38.515-4.5037-2.57624.34064.00056.19631.81393.016-1.5372-1.3152-0.7611.46280.2788-2.32550.50111.458-0.2414-0.23651.5856-0.30021.3328.2675-71.2384-21.6784
45.92450.3696-2.0464.4013-1.9226.33170.99760.55820.19760.0633-0.10010.24-0.64220.47060.31961.5751-0.0146-0.04490.9997-0.10561.315424.0164-81.3658-18.7143
51.93251.96221.22254.4523-1.00965.06570.2214-0.55520.26860.52870.270.36290.8302-0.6986-0.07451.05370.036-0.10830.71510.09431.056318.7571-71.0973-12.0466
68.24653.0557-5.60795.082-4.31455.2413-0.58261.6316-1.39980.35850.6993-0.81590.5302-1.4253-0.29881.2190.1997-0.15141.2779-0.12391.327230.2241-72.8535-12.368
73.4718-5.74143.15379.9974-2.74996.6188-0.69120.4139-0.85132.07960.70820.8306-0.9883-1.54850.34121.78780.3226-0.01981.7994-0.04481.211511.4193-61.7199-7.9283
85.7702-0.07170.46115.7539-3.74827.0593-0.1523-0.1392-0.1202-1.36550.4119-0.17140.3479-0.88740.44920.9329-0.06980.05890.5806-0.07510.750426.4437-72.0604-21.8139
93.44982.69331.77893.8892-1.26155.01-0.42491.85281.5677-0.5736-0.4708-0.563-1.622-1.1750.62011.850.0532-0.1331.84790.11071.023820.5428-51.9036-41.5563
107.81662.1806-1.31992.2176-1.53491.0249-1.6843-0.37333.39990.25742.94682.818-3.96590.88060.00342.7361-0.3516-0.22131.59710.46921.548124.4125-39.9992-44.8785
114.98144.0279-1.1698.75081.12911.5226-0.4085-0.4279-0.6578-0.77041.62631.05071.6419-2.1545-0.07471.7486-0.0980.50072.38320.90782.326328.9654-40.4753-40.5517
120.42030.7566-0.0912.14732.9515.1812-0.8680.6030.1396-1.5572-0.19361.9548-1.791-2.88081.48741.93990.7702-0.41242.2507-0.43632.5395-2.2433-36.5743-9.7613
135.30480.1869-3.24247.4187-0.10627.2687-1.7517-1.26991.4288-0.0414-1.0668-1.418-1.0087-0.54140.76181.661.0315-0.0592.0306-0.1521.15665.9357-41.6855-12.7104
143.7495-1.0156-1.35444.52022.96194.41410.73641.61670.4825-1.3139-0.84710.1639-0.4014-0.9240.31891.45460.4918-0.45552.0539-0.28031.22160.9664-48.5044-9.0661
150.842-1.2075-1.66142.57632.44361.9659-0.26362.26022.0711-1.0754-0.06381.3253-0.5602-0.80270.33361.64790.372-0.32172.0086-0.43211.3147-2.1108-40.6873-4.2399
167.3075-0.6992-3.8296.19594.46336.89760.16620.3225-1.5458-0.29770.05360.58520.7584-0.06-0.60471.16290.2646-0.36730.8672-0.1011.2509-15.9108-28.006520.3889
177.7318-2.3526-0.01254.196-2.41433.21780.85791.3348-0.8604-0.6218-0.2243-0.00780.6770.162-0.11510.94440.1069-0.31.2671-0.15050.9342-15.2788-25.226318.4257
187.57620.8984.11890.3902-1.102810.0083-0.57760.2136-0.6304-0.7578-0.0795-0.2002-0.20381.1385-0.25851.2092-0.1167-0.04030.9402-0.12791.1456-25.8342-25.574918.1532
195.8702-1.64690.99619.1899-0.53047.68380.445-0.55260.02690.038-0.2293-0.05550.5811-0.64710.02411.45170.0692-0.07381.2531-0.1041.274217.9633-43.19375.9214
206.2582-3.6044-2.53584.82133.87494.72560.12310.03870.4922-0.1794-0.0118-0.70810.43070.27140.18651.2190.146-0.08961.228-0.01520.97216.3124-43.7074.8584
218.74074.75570.33565.9841-0.11677.15410.971-0.3655-2.095-0.1339-0.40310.00780.7790.7413-0.45121.38450.2916-0.51121.1188-0.19181.6809-8.7836-36.273923.5274
220.517-1.355-0.09842.29390.23763.69620.65570.1664-1.5117-0.345-0.1384-0.01920.86641.4016-0.50721.1357-0.0219-0.56471.0658-0.03441.832-9.069-41.098228.6317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 60 )A41 - 60
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 132 )A61 - 132
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 153 )A133 - 153
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 174 )A154 - 174
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 195 )A175 - 195
6X-RAY DIFFRACTION6chain 'A' and (resid 196 through 214 )A196 - 214
7X-RAY DIFFRACTION7chain 'A' and (resid 215 through 228 )A215 - 228
8X-RAY DIFFRACTION8chain 'A' and (resid 229 through 260 )A229 - 260
9X-RAY DIFFRACTION9chain 'A' and (resid 261 through 280 )A261 - 280
10X-RAY DIFFRACTION10chain 'A' and (resid 281 through 298 )A281 - 298
11X-RAY DIFFRACTION11chain 'A' and (resid 299 through 311 )A299 - 311
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 18 )C1 - 18
13X-RAY DIFFRACTION13chain 'C' and (resid 19 through 38 )C19 - 38
14X-RAY DIFFRACTION14chain 'C' and (resid 39 through 75 )C39 - 75
15X-RAY DIFFRACTION15chain 'C' and (resid 76 through 113 )C76 - 113
16X-RAY DIFFRACTION16chain 'C' and (resid 114 through 150 )C114 - 150
17X-RAY DIFFRACTION17chain 'C' and (resid 151 through 198 )C151 - 198
18X-RAY DIFFRACTION18chain 'C' and (resid 199 through 212 )C199 - 212
19X-RAY DIFFRACTION19chain 'B' and (resid 1 through 66 )B1 - 66
20X-RAY DIFFRACTION20chain 'B' and (resid 67 through 133 )B67 - 133
21X-RAY DIFFRACTION21chain 'B' and (resid 134 through 189 )B134 - 189
22X-RAY DIFFRACTION22chain 'B' and (resid 190 through 228 )B190 - 228

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