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- PDB-7wvg: Crystal structure of H18 complexed with SIA28 -

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Basic information

Entry
Database: PDB / ID: 7wvg
TitleCrystal structure of H18 complexed with SIA28
Components
  • (Hemagglutinin) x 2
  • Heavy chain of SIA28
  • Light chain of SIA28
KeywordsVIRUS / Influenza Virus / Hemagglutinin / Monoclonal antibody
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
Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, Y. / Qi, J. / Gao, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for a human broadly neutralizing influenza A hemagglutinin stem-specific antibody including H17/18 subtypes.
Authors: Chen, Y. / Wang, F. / Yin, L. / Jiang, H. / Lu, X. / Bi, Y. / Zhang, W. / Shi, Y. / Burioni, R. / Tong, Z. / Song, H. / Qi, J. / Gao, G.F.
History
DepositionFeb 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 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
B: Hemagglutinin
C: Heavy chain of SIA28
D: Light chain of SIA28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6289
Polymers80,4834
Non-polymers2,1455
Water4,017223
1
A: Hemagglutinin
B: Hemagglutinin
C: Heavy chain of SIA28
D: Light chain of SIA28
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
C: Heavy chain of SIA28
D: Light chain of SIA28
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
C: Heavy chain of SIA28
D: Light chain of SIA28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,88327
Polymers241,44812
Non-polymers6,43515
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area47560 Å2
ΔGint-139 kcal/mol
Surface area89010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.427, 140.427, 195.734
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 36019.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus
Strain: A/dark fruit-eating bat/Bolivia/PBV780-781/2011(H18N11)
Gene: HA / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A1W5II89
#2: Protein Hemagglutinin


Mass: 19591.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A455KJU7

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Antibody , 2 types, 2 molecules CD

#3: Antibody Heavy chain of SIA28


Mass: 13501.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody Light chain of SIA28


Mass: 11370.739 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Sugars , 4 types, 5 molecules

#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: 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.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 1 types, 223 molecules

#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 6.92 Å3/Da / Density % sol: 82.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis Tris 25 % w/v PEG 3350(pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 66862 / % possible obs: 99.9 % / Redundancy: 16.5 % / Biso Wilson estimate: 41.66 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.8
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 6653 / CC1/2: 0.586

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eyj

3eyj


Resolution: 2.6→45.97 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1776
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2239 3258 5.17 %
Rwork0.212 59701 -
obs0.2126 62959 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.66 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5661 0 141 223 6025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00525941
X-RAY DIFFRACTIONf_angle_d0.848066
X-RAY DIFFRACTIONf_chiral_restr0.0588918
X-RAY DIFFRACTIONf_plane_restr0.00651028
X-RAY DIFFRACTIONf_dihedral_angle_d14.10012172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.3579670.32591341X-RAY DIFFRACTION48.69
2.64-2.680.3945850.32641563X-RAY DIFFRACTION57.28
2.68-2.730.31231180.30851998X-RAY DIFFRACTION72.97
2.73-2.770.35081360.29852511X-RAY DIFFRACTION91.02
2.77-2.820.29581410.28672709X-RAY DIFFRACTION98.38
2.82-2.880.3451580.29142738X-RAY DIFFRACTION99.45
2.88-2.940.27461600.28282753X-RAY DIFFRACTION99.93
2.94-30.28431220.26742788X-RAY DIFFRACTION99.9
3-3.070.27931590.25912710X-RAY DIFFRACTION99.9
3.07-3.150.26571600.26852734X-RAY DIFFRACTION100
3.15-3.230.26061590.26452773X-RAY DIFFRACTION99.93
3.23-3.330.27441740.25062729X-RAY DIFFRACTION99.97
3.33-3.430.23541270.22662787X-RAY DIFFRACTION99.97
3.43-3.560.2311410.20742724X-RAY DIFFRACTION99.97
3.56-3.70.19261480.20882790X-RAY DIFFRACTION100
3.7-3.870.22891600.20132726X-RAY DIFFRACTION100
3.87-4.070.2081280.19242790X-RAY DIFFRACTION100
4.07-4.330.19111430.15872762X-RAY DIFFRACTION100
4.33-4.660.16671640.15332759X-RAY DIFFRACTION100
4.66-5.130.17981440.16062774X-RAY DIFFRACTION100
5.13-5.870.17561570.18032762X-RAY DIFFRACTION99.97
5.87-7.390.19081560.1982785X-RAY DIFFRACTION100
7.4-45.970.17861510.18272695X-RAY DIFFRACTION96.31
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)
10.258510373901-0.0109256145455-0.01610234125310.359968396486-0.3302098746262.358405205380.01903580181520.06345063248620.108771707236-0.02895096719380.0222572863544-0.0324768986425-0.309643310193-0.0147706999643-0.06317681939130.30732573993-0.003389928680780.01913482882170.2102755926230.0203584867210.35096898852270.1162044835-20.2403562068-20.9953520381
20.4678913594180.111918163962-0.02848611387420.4826477337830.6763251986475.065149278410.0787109875589-0.2092951006170.09071226501980.2036657790950.0293293627470.000574939404391-0.26626022440.00467679248289-0.1089350539530.3438844659490.0146140162510.02003257907050.251539268756-0.03917892773460.30602607966668.2010612409-28.536534360530.5674901232
31.399714828360.7804940528250.6924322466373.943019103261.468374232011.98847287566-0.0799188344419-0.06828310551730.241402561383-0.26879249980.0410072731796-0.019472437269-0.3131382981120.1284362083010.04243762115270.609795240437-0.01697782416140.08366708621480.381934002013-0.09547373150.40840892638774.67102176911.758130321136.0469762167
43.53099869725-0.120483256222-0.1045330021392.81187549922-0.4047250572373.402423451340.1007296457520.6109544211670.109169745228-0.9460313515760.126971411478-0.469102045701-0.5330980880780.500488759996-0.2038965589710.820595869043-0.1031464366810.2035192738180.562903002132-0.1773663106920.47928779616585.1516678321-6.0502780838218.4560747106
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA11 - 8081
22chain BBB5 - 7011
33chain CCC31 - 1541 - 124
44chain DDD43 - 1491 - 107

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