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- PDB-5xl1: The structure of hemagglutinin from an avian-origin H4N6 influenz... -

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Basic information

Entry
Database: PDB / ID: 5xl1
TitleThe structure of hemagglutinin from an avian-origin H4N6 influenza virus
Components(Hemagglutinin) x 2
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 / host cell surface receptor binding / 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 / membrane
Similarity search - Function
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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSong, H. / Qi, J. / Gao, F.G.
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 1.2Jul 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 1.3Nov 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,5038
Polymers112,6184
Non-polymers8854
Water7,963442
1
B: Hemagglutinin
C: Hemagglutinin
hetero molecules

B: Hemagglutinin
C: Hemagglutinin
hetero molecules

B: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,25412
Polymers168,9276
Non-polymers1,3276
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_785-y+2,x-y+3,z1
crystal symmetry operation3_475-x+y-1,-x+2,z1
Buried area33710 Å2
ΔGint-130 kcal/mol
Surface area56000 Å2
MethodPISA
2
A: Hemagglutinin
D: Hemagglutinin
hetero molecules

A: Hemagglutinin
D: Hemagglutinin
hetero molecules

A: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,25412
Polymers168,9276
Non-polymers1,3276
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_795-y+2,x-y+4,z1
crystal symmetry operation3_375-x+y-2,-x+2,z1
Buried area33610 Å2
ΔGint-131 kcal/mol
Surface area56400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.476, 100.476, 685.126
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11D-704-

HOH

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Components

#1: Protein Hemagglutinin


Mass: 35966.461 Da / Num. of mol.: 2 / Fragment: UNP residues 17-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6)
Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3KF09, UniProt: P19696*PLUS
#2: Protein Hemagglutinin


Mass: 20342.391 Da / Num. of mol.: 2 / Fragment: UNP residues 344-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6)
Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3KF09, UniProt: P19696*PLUS
#3: 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.: 4
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Trimethylamine N-oxide dehydrate, 0.1 M Tris (pH 8.0), and 20% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2014
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: 60221 / % possible obs: 100 % / Redundancy: 9 % / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.686 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HA0

1ha0


Resolution: 2.3→43.42 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6
RfactorNum. reflection% reflection
Rfree0.2296 3037 5.05 %
Rwork0.1891 --
obs0.1912 60176 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7722 0 56 442 8220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067950
X-RAY DIFFRACTIONf_angle_d1.01610768
X-RAY DIFFRACTIONf_dihedral_angle_d14.2832916
X-RAY DIFFRACTIONf_chiral_restr0.0411180
X-RAY DIFFRACTIONf_plane_restr0.0041432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3003-2.33620.27411470.23322555X-RAY DIFFRACTION99
2.3362-2.37450.29311260.23442550X-RAY DIFFRACTION100
2.3745-2.41550.28241480.23772567X-RAY DIFFRACTION100
2.4155-2.45940.2861160.2172557X-RAY DIFFRACTION100
2.4594-2.50670.25671440.22172594X-RAY DIFFRACTION100
2.5067-2.55790.2411360.20822543X-RAY DIFFRACTION100
2.5579-2.61350.25261450.20992519X-RAY DIFFRACTION100
2.6135-2.67430.25141320.20742601X-RAY DIFFRACTION100
2.6743-2.74110.24821340.2092584X-RAY DIFFRACTION100
2.7411-2.81520.27061370.22262571X-RAY DIFFRACTION100
2.8152-2.89810.26631340.21882570X-RAY DIFFRACTION100
2.8981-2.99160.28261510.21282564X-RAY DIFFRACTION100
2.9916-3.09850.27271560.2042568X-RAY DIFFRACTION100
3.0985-3.22250.24721610.20052565X-RAY DIFFRACTION100
3.2225-3.36910.23111580.1922585X-RAY DIFFRACTION100
3.3691-3.54660.21461230.19092602X-RAY DIFFRACTION100
3.5466-3.76870.21211310.17722614X-RAY DIFFRACTION100
3.7687-4.05950.19641240.16532630X-RAY DIFFRACTION100
4.0595-4.46770.21981410.16132627X-RAY DIFFRACTION100
4.4677-5.11330.17851080.1472688X-RAY DIFFRACTION100
5.1133-6.43880.19241560.17932670X-RAY DIFFRACTION100
6.4388-43.42760.20611290.18572815X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -73.1146 Å / Origin y: 163.8395 Å / Origin z: 61.5862 Å
111213212223313233
T0.1825 Å20.0146 Å2-0.0233 Å2-0.1861 Å20.003 Å2--0.1966 Å2
L0.078 °2-0.0235 °2-0.0878 °2-0.0569 °20.0705 °2--0.0713 °2
S0.0004 Å °0.0624 Å °0.0129 Å °-0.0514 Å °-0.0157 Å °0.0056 Å °-0.0351 Å °-0.0283 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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