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- PDB-6ii8: Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in comp... -

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Basic information

Entry
Database: PDB / ID: 6ii8
TitleCrystal structure of H7 hemagglutinin from A/Anhui/1/2013 in complex with a human neutralizing antibody L4B-18
Components
  • (Hemagglutinin) x 2
  • Heavy chain of L4B-18 Fab
  • Light chain of L4B-18 Fab
KeywordsIMMUNE SYSTEM / H7 haemagglutinin / receptor binding site / neutralizing antibody / protection in vivo
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; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / 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 / Resolution: 3.32 Å
AuthorsJiang, H.H. / Shi, Y. / Qi, J. / Gao, G.F.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China81621091 China
National Natural Science Foundation of China81622031 China
Chinese Academy of SciencesXDB29010000 China
CitationJournal: Nat Microbiol / Year: 2019
Title: Structure-function analysis of neutralizing antibodies to H7N9 influenza from naturally infected humans.
Authors: Huang, K.A. / Rijal, P. / Jiang, H. / Wang, B. / Schimanski, L. / Dong, T. / Liu, Y.M. / Chang, P. / Iqbal, M. / Wang, M.C. / Chen, Z. / Song, R. / Huang, C.C. / Yang, J.H. / Qi, J. / Lin, T. ...Authors: Huang, K.A. / Rijal, P. / Jiang, H. / Wang, B. / Schimanski, L. / Dong, T. / Liu, Y.M. / Chang, P. / Iqbal, M. / Wang, M.C. / Chen, Z. / Song, R. / Huang, C.C. / Yang, J.H. / Qi, J. / Lin, T.Y. / Li, A. / Powell, T.J. / Jan, J.T. / Ma, C. / Gao, G.F. / Shi, Y. / Townsend, A.R.
History
DepositionOct 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
J: Heavy chain of L4B-18 Fab
K: Light chain of L4B-18 Fab
G: Heavy chain of L4B-18 Fab
H: Heavy chain of L4B-18 Fab
I: Light chain of L4B-18 Fab
L: Light chain of L4B-18 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,13921
Polymers302,14812
Non-polymers1,9919
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47780 Å2
ΔGint-215 kcal/mol
Surface area102110 Å2
Unit cell
Length a, b, c (Å)203.409, 116.062, 185.207
Angle α, β, γ (deg.)90.00, 108.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemagglutinin / / H7 Hemagglutinin


Mass: 34439.859 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A024CX39
#2: Protein Hemagglutinin / / H7 Hemagglutinin


Mass: 19888.789 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0K1LUI9
#3: Antibody Heavy chain of L4B-18 Fab


Mass: 23596.410 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Antibody Light chain of L4B-18 Fab


Mass: 22790.965 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.64 %
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 7 / Details: 35% v/v TacsimateTM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 59498 / % possible obs: 98.8 % / Redundancy: 4.4 % / CC1/2: 0.994 / Rpim(I) all: 0.113 / Net I/σ(I): 6.5
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.9 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.32→49.486 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.57
RfactorNum. reflection% reflection
Rfree0.2507 2839 4.98 %
Rwork0.2033 --
obs0.2058 57029 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.32→49.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19573 0 126 0 19699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820137
X-RAY DIFFRACTIONf_angle_d0.79727310
X-RAY DIFFRACTIONf_dihedral_angle_d18.9717373
X-RAY DIFFRACTIONf_chiral_restr0.0523006
X-RAY DIFFRACTIONf_plane_restr0.0053559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.37720.35921020.26372006X-RAY DIFFRACTION70
3.3772-3.43860.3141150.24682307X-RAY DIFFRACTION80
3.4386-3.50480.29321290.24442335X-RAY DIFFRACTION83
3.5048-3.57630.32271210.22782519X-RAY DIFFRACTION88
3.5763-3.6540.2771210.21882617X-RAY DIFFRACTION90
3.654-3.7390.2791440.2232665X-RAY DIFFRACTION94
3.739-3.83250.24311510.22382756X-RAY DIFFRACTION97
3.8325-3.9360.27561570.22382779X-RAY DIFFRACTION98
3.936-4.05180.27041290.19882821X-RAY DIFFRACTION98
4.0518-4.18250.24921560.19352798X-RAY DIFFRACTION98
4.1825-4.33190.21641400.1832809X-RAY DIFFRACTION98
4.3319-4.50530.24321530.17932836X-RAY DIFFRACTION98
4.5053-4.71020.22791220.17972836X-RAY DIFFRACTION98
4.7102-4.95830.21581500.17832809X-RAY DIFFRACTION99
4.9583-5.26860.23991640.18452860X-RAY DIFFRACTION100
5.2686-5.67490.2331710.19742827X-RAY DIFFRACTION100
5.6749-6.24490.28361400.21372911X-RAY DIFFRACTION100
6.2449-7.14630.28361360.21382883X-RAY DIFFRACTION100
7.1463-8.99470.2221590.19832905X-RAY DIFFRACTION99
8.9947-49.49170.22511790.20342911X-RAY DIFFRACTION99

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