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- PDB-6iut: Crystal structure of influenza A virus H5 hemagglutinin globular ... -

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Basic information

Entry
Database: PDB / ID: 6iut
TitleCrystal structure of influenza A virus H5 hemagglutinin globular head in complex with the Fab of antibody AVFluIgG01
Components
  • AVFluIgG01 Heavy Chain
  • AVFluIgG01 Light Chain
  • Hemagglutinin
KeywordsIMMUNE SYSTEM / influenza virus / HPAI / H5N1 / neutralizing antibody / epitope / major vulnerable site / vaccine development
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 (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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, P. / Zuo, Y. / Sun, J. / Zhang, L. / Wang, X.
Funding support China, 10items
OrganizationGrant numberCountry
National Natural Science Foundation of China81530065 China
National Natural Science Foundation of China81661128042 China
National Natural Science Foundation of China31470751 China
National Natural Science Foundation of ChinaU1405228 China
Ministry of Science and Technology (China)2016YFD0500307 China
Ministry of Science and Technology (China)2012ZX10001-004 China
Ministry of Science and Technology (China)2012ZX10001-006 China
Ministry of Science and Technology (China)2012ZX10001-009 China
Ministry of Science and Technology (China)2017ZX10201-101 China
Ministry of Science and Technology (China)2014CB542500-03 China
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Structural and functional definition of a vulnerable site on the hemagglutinin of highly pathogenic avian influenza A virus H5N1.
Authors: Wang, P. / Zuo, Y. / Sun, J. / Zuo, T. / Zhang, S. / Guo, S. / Shi, X. / Liang, M. / Zhou, P. / Zhang, L. / Wang, X.
History
DepositionNov 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
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
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: AVFluIgG01 Heavy Chain
L: AVFluIgG01 Light Chain
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4785
Polymers72,6863
Non-polymers7922
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-12 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.101, 150.046, 107.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11L-349-

HOH

21L-353-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody AVFluIgG01 Heavy Chain


Mass: 23132.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody AVFluIgG01 Light Chain


Mass: 23300.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 152 molecules A

#3: Protein Hemagglutinin /


Mass: 26252.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Anhui/1/2005(H5N1))
Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q1WDM0
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}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.: 1
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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 25% w/v Polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 39949 / % possible obs: 99 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.8
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.957 / Num. unique obs: 3508

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DUT

5dut


Resolution: 2.3→42.066 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.08
RfactorNum. reflection% reflection
Rfree0.2552 2035 5.09 %
Rwork0.205 --
obs0.2075 39942 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 0 52 151 5133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095125
X-RAY DIFFRACTIONf_angle_d1.1016995
X-RAY DIFFRACTIONf_dihedral_angle_d6.2883776
X-RAY DIFFRACTIONf_chiral_restr0.061787
X-RAY DIFFRACTIONf_plane_restr0.007888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2969-2.35030.33171120.27662018X-RAY DIFFRACTION79
2.3503-2.40910.32231450.26772512X-RAY DIFFRACTION100
2.4091-2.47420.32911270.27832548X-RAY DIFFRACTION100
2.4742-2.5470.33531510.25512559X-RAY DIFFRACTION100
2.547-2.62920.30621470.25672525X-RAY DIFFRACTION99
2.6292-2.72320.33391130.25412569X-RAY DIFFRACTION99
2.7232-2.83220.27531430.24612556X-RAY DIFFRACTION99
2.8322-2.96110.30491570.23612488X-RAY DIFFRACTION99
2.9611-3.11710.32051310.23362568X-RAY DIFFRACTION99
3.1171-3.31240.2391400.22742533X-RAY DIFFRACTION99
3.3124-3.5680.29141480.20992542X-RAY DIFFRACTION99
3.568-3.92680.23881350.19862582X-RAY DIFFRACTION99
3.9268-4.49450.19311100.17432636X-RAY DIFFRACTION100
4.4945-5.66040.2111510.15912611X-RAY DIFFRACTION100
5.6604-42.07310.22541250.18382660X-RAY DIFFRACTION96

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