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- PDB-8sj9: Crystal structure of the H1 hemagglutinin COBRA X6 -

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Basic information

Entry
Database: PDB / ID: 8sj9
TitleCrystal structure of the H1 hemagglutinin COBRA X6
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / hemagglutinin / receptor binding / virus entry / fusion
Function / homology
Function and homology information


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
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsDzimianski, J.V. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00052 United States
CitationJournal: Structure / Year: 2024
Title: Structural basis for the broad antigenicity of the computationally optimized influenza hemagglutinin X6.
Authors: Kaito A Nagashima / John V Dzimianski / Meng Yang / Jan Abendroth / Giuseppe A Sautto / Ted M Ross / Rebecca M DuBois / Thomas E Edwards / Jarrod J Mousa /
Abstract: Influenza causes significant morbidity and mortality. As an alternative approach to current seasonal vaccines, the computationally optimized broadly reactive antigen (COBRA) platform has been ...Influenza causes significant morbidity and mortality. As an alternative approach to current seasonal vaccines, the computationally optimized broadly reactive antigen (COBRA) platform has been previously applied to hemagglutinin (HA). This approach integrates wild-type HA sequences into a single immunogen to expand the breadth of accessible antibody epitopes. Adding to previous studies of H1, H3, and H5 COBRA HAs, we define the structural features of another H1 subtype COBRA, X6, that incorporates HA sequences from before and after the 2009 H1N1 influenza pandemic. We determined structures of this antigen alone and in complex with COBRA-specific as well as broadly reactive and functional antibodies, analyzing its antigenicity. We found that X6 possesses features representing both historic and recent H1 HA strains, enabling binding to both head- and stem-reactive antibodies. Overall, these data confirm the integrity of broadly reactive antibody epitopes of X6 and contribute to design efforts for a next-generation vaccine.
History
DepositionApr 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references
Category: citation / citation_author / pdbx_related_exp_data_set
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,73021
Polymers172,6933
Non-polymers5,03718
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18230 Å2
ΔGint34 kcal/mol
Surface area61300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.504, 218.725, 68.572
Angle α, β, γ (deg.)90.000, 109.680, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Hemagglutinin


Mass: 57564.367 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Computationally designed / Source: (gene. exp.) Influenza A virus / Gene: HA / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0G2RXV5

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Sugars , 3 types, 15 molecules

#2: 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.: 3
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
#3: 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.: 2
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
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10 / Source method: obtained synthetically / 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 , 2 types, 3 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.4, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 29281 / % possible obs: 98.12 % / Redundancy: 3.5 % / Biso Wilson estimate: 107.08 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.143 / Net I/σ(I): 6
Reflection shellResolution: 3.25→3.45 Å / Rmerge(I) obs: 1.268 / Mean I/σ(I) obs: 1 / Num. unique obs: 2921 / CC1/2: 0.312 / % possible all: 98.35

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→44.43 Å / SU ML: 0.5533 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2763 1399 4.78 %
Rwork0.2212 27873 -
obs0.2239 29272 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 123.11 Å2
Refinement stepCycle: LAST / Resolution: 3.25→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11507 0 327 0 11834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001912121
X-RAY DIFFRACTIONf_angle_d0.452316434
X-RAY DIFFRACTIONf_chiral_restr0.05291819
X-RAY DIFFRACTIONf_plane_restr0.00382114
X-RAY DIFFRACTIONf_dihedral_angle_d4.17921726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.370.42171240.33752793X-RAY DIFFRACTION98.35
3.37-3.50.351290.32062760X-RAY DIFFRACTION98.1
3.5-3.660.36191540.29752779X-RAY DIFFRACTION97.9
3.66-3.850.36421700.26912785X-RAY DIFFRACTION98.66
3.85-4.090.29691530.23522767X-RAY DIFFRACTION98.28
4.09-4.410.2911180.2122807X-RAY DIFFRACTION98.39
4.41-4.850.22611510.17832784X-RAY DIFFRACTION98.23
4.85-5.550.23431390.18912785X-RAY DIFFRACTION97.99
5.56-6.990.3011260.22742817X-RAY DIFFRACTION98.43
7-44.430.22331350.19472796X-RAY DIFFRACTION97.28
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)
1-0.1998792382231.065188856471.22292500479.390504129977.269412945376.10956963516-0.1799603835590.4168896874460.120161031206-0.8564313299750.411668576902-0.882970216057-0.9434277879850.176188547743-0.2034664648920.876031767601-0.2378272474940.04302813340640.998871151041-0.08817694899640.911842477419-4.64048170748-31.5565293707-31.9616873954
27.595324959644.782870649514.543072408074.529795417063.853313886993.84484257032-0.8090238376581.77259863843-0.731798310811-1.6400298291.108212452-0.625377268249-1.347814444510.804234693764-0.3929553905131.10254642608-0.4172452202140.2729834335551.38279011904-0.2332645201321.00732221689-10.5979439013-58.9689591105-48.3477929639
35.634772529522.03623478833-0.1438040052736.43166832605-0.9869310131426.40659425-0.0699518038950.483752606879-0.544079459085-0.617614394350.0981249064622-0.2849836909210.321923644066-0.422565802824-0.08730411330840.61192747163-0.1614553469560.2300216919681.00453238477-0.2529923267620.768081965492-14.1377845439-77.2782264453-47.9044954768
48.71719924735-0.09245942486582.820883526765.281328671192.711742539826.47867049334-0.5566589546861.815723475130.100991222302-0.3010358578450.0140227005997-0.32875906342-0.837505734767-0.3094432395280.3115932536260.687030625225-0.2789692492840.3029144860341.33288068743-0.2343357857320.461749094004-19.8676812914-75.5164066518-46.1121851624
54.47358655063-3.21724167479-2.84017638228.155581673210.9340729283821.56775594021-0.218810701128-0.287595001771.0390920810.1843588833690.576488614082-0.773471062054-0.4649926577530.570385182423-0.4152335645420.616360101882-0.238248915002-0.1604253135541.21722562618-0.2038912130250.963084592768-4.06781147039-51.8066126376-40.0203035068
65.69584871960.3378388314352.555202449524.16032159733.652941578066.33780379745-0.122938792598-0.04524985580070.571271301517-0.685938470080.560315431846-0.623228577037-1.127791190420.382557719528-0.313430009920.8839321521-0.1548773470730.1189768449840.6606937201080.03221320956940.708735864307-4.42526775324-21.9598001841-21.4799387405
76.75855826616.646709273463.004457905139.23595689122.312093212345.757473387190.4712478633390.528906621970.542976518121.836586627440.0182174332974-1.41771167831-0.162755379428-0.390021253147-0.4599056626990.621229389280.02290256489640.1374964082510.729550775514-0.03003081448480.91769798926.66537134102-19.3968571756-15.7636911733
82.67485121423.192863790870.4879734582397.076624764131.343049234570.8578169719410.357630311426-0.008668201725960.6774352678491.26584581683-0.2178574411560.051866293991-0.1832584385920.0347332434133-0.205251073491.07052153623-0.121449527471-0.162979889630.6783521066870.02311025665170.883293242089-1.70348234313-18.9006146225-11.7710602796
91.63758038528-1.16676656795-0.7011886177091.048026812711.137897669890.0459635280090.260297515842-0.11223240885-0.3418392840690.0918424371883-0.115971001676-0.113702557778-0.813209708113-0.7794543233860.1630957142191.279092147410.0392220614272-0.3506506657050.815826334305-0.06009057520261.13022686469-35.3938514903-33.3269443618-9.17569723168
100.581243290487-0.253688096661-1.471282637981.05480226303-1.559909304878.51397395205-0.5017752545121.40675481001-1.41838068679-1.61348014989-1.269615528033.240432830911.13185515621-1.044701871941.181829204951.661564790170.30161668631-0.8827337544431.5504792247-0.7320905180352.26023946467-49.7624482635-49.5524729-29.1932657836
111.159663995470.3102014617730.3251534928525.504968698990.604624138355.87572814175-0.06015291705350.546299964345-0.292910014743-0.2967442323090.08128262929110.0752795191356-0.0204256488758-0.234190722353-0.01275364654490.457033754844-0.0992759245337-0.08773264840981.06193561278-0.06982240435050.846917142645-46.1703848269-69.0645812509-36.7542161377
128.896216956284.9450005848-4.53624664236.84165283051-1.552092479892.36678008227-0.8209874697980.0761984490207-0.287928273726-0.428902599602-0.5472387957380.00426162531449-0.53619266732-1.23166239731.220671998981.1911707324-0.0134930350169-0.2595647818830.693318987829-0.2391226164141.04118439833-42.3019688833-41.9926652119-19.0666738135
133.661855111593.479514466263.034989978375.211371567255.492607119997.72114564544-0.8496338005810.07148720629270.65087276233-0.5048710280930.2316340360210.965770215733-0.7482159557480.3096160754530.7168022171470.6871131217290.1181001409490.03383514922260.857532666007-0.08507883037360.797068541155-25.146615099-27.9785194546-4.11485781232
140.7212073225933.192704950332.598850033189.108254956267.071065572894.41228428692-0.142162131657-0.4518317689520.816758179131-2.41537986640.569129222287-0.0650660640609-2.31662581938-0.0201897330563-0.5518048666881.553829188390.115787857741-0.04742670994970.817690178193-0.231553768431.58346748391-23.4610263251-6.67274121805-3.07302877478
152.3003075172.056059752523.11309419963.617606474294.082745580114.988060053360.08400307282010.3265008232491.346632625150.406371748223-1.754247580911.55430035741-0.559611252575-1.488499323551.246671620130.7343633189370.329026317871-0.03174219315831.6934521416-0.03832810659621.42408388862-28.2238204449-52.1438176033-20.6493779343
160.888218919442-0.8007169629660.7205942825143.270364945641.954959874553.40851501476-0.654479408633-0.100005813270.6008906400670.1878622300280.826822192017-0.909883766349-1.095297597340.228859052811-0.08242031579041.549890705350.0954329373931-0.2268731533570.843324026155-0.3799802110231.33720156756-14.6453221897-10.4738862998-0.894513615972
171.807136307883.273115453951.350509418949.233792053142.242152747910.9151351787790.669761688767-0.382338290501-0.6727358270791.69141853883-0.0143189209654-2.179334327940.5459694458920.301802816619-0.6734047267441.13965694299-0.061200722643-0.1501856337580.991410987056-0.1655309183340.805479604587-2.82747089606-50.69150242320.844061868913
183.17307085005-4.74686747619-3.989035179079.546485888843.257972859478.25311774111-1.33861498454-4.66358543424-3.177640925865.293805609671.174500419111.380793896284.29069535694-0.4391576245470.4176981386113.49798491131-0.601634514352-0.1178253467492.161490237410.4763114562791.7590246049-15.947181031-83.6776651657-2.28334915793
195.859357123121.614938580982.211311666777.799056999413.841137013013.75468244088-0.3332565932040.5089584519970.09450120359810.555976145427-0.1112798961020.1163371968950.03022735024520.2562877519870.5474549031250.899666982189-0.08954317391630.22812947420.5126466839220.1094807752150.712617498153-16.5137150605-75.3949224909-12.9977011534
205.7831549451-2.90368750153-0.8441986940374.875641116863.741283815624.23033411892-0.181329471243-0.0601740386658-0.958209052350.6468340744650.0500285718881-0.3459322607730.802639102485-0.1020084726040.2629160817811.00118643549-0.2111453972510.04305241183460.6291424652840.02272985774810.699954948861-26.6781716782-92.1379949861-15.9383273325
217.935045050471.04901560725-2.350934251128.304963959351.882016626524.96518069984-0.1285481358040.671165369628-0.371302758266-0.254054842561-0.2143849384380.4778875629110.491526052241-0.2844327888380.1378577351780.779941969769-0.02517357054790.03672648556060.5944949191260.06299949029280.442114287612-27.5372283783-84.4629206438-21.4838764958
227.981990848550.4962136514632.132499450154.647232653185.429178926916.853633184190.893665730431-1.93822840486-0.2803895250192.93780117567-0.5006293572430.465261021214-0.4318105375750.773013783879-0.0512713760651.99528655749-0.33906398678-0.05651667466131.19478206856-0.03551954233540.56123664797-9.11648435432-63.2884522843-0.782245809846
232.47141898182.494558784572.134643945417.528232678455.553389739243.442764977960.184629088463-0.3455347506590.3015828858130.703221124022-0.161565984042-0.1384647556150.219853235125-0.194833229816-0.1491149307161.053766526580.0377376303062-0.1750494518090.63439348519-0.05010003649120.826258888913-2.6739094317-34.30119962745.93387257075
241.179602473172.12118870782.1138303963.751689364233.700756621745.496150083530.0319518146314-0.09030728683150.1857223266581.30862230211-0.202200911443-0.2352661561060.0919998273880.2800689516890.1236962570481.36800123228-0.128064659302-0.3672310760191.06302879688-0.2701410885480.990680384347-3.12633988013-24.91808709114.146324715
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 0:66)AA0 - 661 - 67
22(chain A and resid 67:94)AA67 - 9468 - 95
33(chain A and resid 95:211)AA95 - 21196 - 212
44(chain A and resid 212:250)AA212 - 250213 - 251
55(chain A and resid 251:287)AA251 - 287252 - 288
66(chain A and resid 288:349)AA288 - 349289 - 344
77(chain A and resid 350:390)AA350 - 390345 - 385
88(chain A and resid 391:490)AA391 - 490386 - 485
99(chain B and resid 1:67)BI1 - 671 - 67
1010(chain B and resid 68:80)BI68 - 8068 - 80
1111(chain B and resid 81:259)BI81 - 25981 - 259
1212(chain B and resid 260:286)BI260 - 286260 - 286
1313(chain B and resid 287:340)BI287 - 340287 - 334
1414(chain B and resid 341:383)BI341 - 383335 - 377
1515(chain B and resid 384:404)BI384 - 404378 - 398
1616(chain B and resid 405:490)BI405 - 490399 - 484
1717(chain C and resid 1:66)CQ1 - 661 - 66
1818(chain C and resid 67:73)CQ67 - 7367 - 73
1919(chain C and resid 74:106)CQ74 - 10674 - 106
2020(chain C and resid 107:193)CQ107 - 193107 - 193
2121(chain C and resid 194:260)CQ194 - 260194 - 260
2222(chain C and resid 261:288)CQ261 - 288261 - 288
2323(chain C and resid 289:394)CQ289 - 394289 - 389
2424(chain C and resid 395:491)CQ395 - 491390 - 486

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