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- PDB-5xl2: The structure of hemagglutininfrom a swine-origin H4N6 influenza virus -

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Basic information

Entry
Database: PDB / ID: 5xl2
TitleThe structure of hemagglutininfrom a swine-origin H4N6 influenza virus
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / H4 hemagglutinin / influenza virus / receptor binding
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSong, H. / Qi, J. / Gao, G.F.
CitationJournal: Cell Rep / Year: 2017
Title: Avian-to-Human Receptor-Binding Adaptation by Influenza A Virus Hemagglutinin H4
Authors: Song, H. / Qi, J. / Xiao, H. / Bi, Y. / Zhang, W. / Xu, Y. / Wang, F. / Shi, Y. / Gao, G.F.
History
DepositionMay 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Feb 7, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 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
Revision 1.5Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)170,6569
Polymers169,3283
Non-polymers1,3276
Water13,097727
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14620 Å2
ΔGint-16 kcal/mol
Surface area58470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.419, 120.559, 132.278
Angle α, β, γ (deg.)90.00, 92.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemagglutinin /


Mass: 56442.820 Da / Num. of mol.: 3 / Fragment: UNP residues 17-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/swine/Ontario/01911-1/99 (H4N6))
Strain: A/swine/Ontario/01911-1/99 (H4N6) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9E148
#2: 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.: 6
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 727 / Source method: isolated from a natural source / Formula: H2O

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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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2% (v/v) Tacsimate (pH 8.0), 0.1 M Tris (pH 8.5), and 16% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 91122 / % possible obs: 99.8 % / Redundancy: 5.8 % / Net I/σ(I): 17.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 5.8 / Rsym value: 0.331 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HA0

1ha0


Resolution: 2.3→35.57 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.89
RfactorNum. reflection% reflection
Rfree0.2134 4559 5.01 %
Rwork0.1842 --
obs0.1857 91064 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11514 0 84 727 12325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611868
X-RAY DIFFRACTIONf_angle_d1.03916091
X-RAY DIFFRACTIONf_dihedral_angle_d15.5174344
X-RAY DIFFRACTIONf_chiral_restr0.0431768
X-RAY DIFFRACTIONf_plane_restr0.0052128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2959-2.3220.27771640.21872701X-RAY DIFFRACTION93
2.322-2.34930.24061580.2072861X-RAY DIFFRACTION100
2.3493-2.3780.28721470.21292848X-RAY DIFFRACTION99
2.378-2.40810.26911550.20822889X-RAY DIFFRACTION100
2.4081-2.43970.25921590.21112863X-RAY DIFFRACTION100
2.4397-2.47310.22391270.20612881X-RAY DIFFRACTION100
2.4731-2.50850.25431530.21032905X-RAY DIFFRACTION100
2.5085-2.54590.24881280.20042904X-RAY DIFFRACTION100
2.5459-2.58570.26491230.2072891X-RAY DIFFRACTION100
2.5857-2.62810.22741630.19932873X-RAY DIFFRACTION100
2.6281-2.67340.25241500.20632876X-RAY DIFFRACTION100
2.6734-2.72190.23911490.20682892X-RAY DIFFRACTION100
2.7219-2.77430.23641610.19922848X-RAY DIFFRACTION100
2.7743-2.83090.24661470.19712901X-RAY DIFFRACTION100
2.8309-2.89240.22931480.19992863X-RAY DIFFRACTION100
2.8924-2.95970.2271500.20032931X-RAY DIFFRACTION100
2.9597-3.03360.24531430.1952875X-RAY DIFFRACTION100
3.0336-3.11560.21571780.22907X-RAY DIFFRACTION100
3.1156-3.20720.22381420.19742860X-RAY DIFFRACTION100
3.2072-3.31070.24621430.20382931X-RAY DIFFRACTION100
3.3107-3.42890.231240.1912934X-RAY DIFFRACTION100
3.4289-3.56610.2151600.18642861X-RAY DIFFRACTION100
3.5661-3.72820.21111540.17972886X-RAY DIFFRACTION100
3.7282-3.92460.21011620.17532879X-RAY DIFFRACTION100
3.9246-4.17010.18291710.16062902X-RAY DIFFRACTION100
4.1701-4.49150.1771700.14422874X-RAY DIFFRACTION100
4.4915-4.94240.16431700.14252899X-RAY DIFFRACTION100
4.9424-5.65510.15541440.15452907X-RAY DIFFRACTION100
5.6551-7.11550.19931540.1782920X-RAY DIFFRACTION99
7.1155-35.57390.18481620.18092943X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 4.6691 Å / Origin y: -24.9762 Å / Origin z: -36.3175 Å
111213212223313233
T0.1685 Å20.0114 Å2-0.0044 Å2-0.1729 Å2-0.0045 Å2--0.1657 Å2
L0.2388 °2-0.0263 °2-0.1448 °2-0.1108 °20.1119 °2--0.1751 °2
S-0.0165 Å °-0.1013 Å °-0.0076 Å °0.0406 Å °0.0281 Å °0.0063 Å °0.0578 Å °0.1026 Å °0.0059 Å °
Refinement TLS groupSelection details: all

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