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- PDB-5xl4: The structure of hemagglutinin from an avian-origin H4N6 influenz... -

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Basic information

Entry
Database: PDB / ID: 5xl4
TitleThe structure of hemagglutinin from an avian-origin H4N6 influenza virus in complex with human receptor analog Lstc
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 / 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 / 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
N-acetyl-alpha-neuraminic acid / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,12110
Polymers112,6184
Non-polymers1,5036
Water14,088782
1
A: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0615
Polymers56,3092
Non-polymers7523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-30 kcal/mol
Surface area23850 Å2
MethodPISA
2
B: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0615
Polymers56,3092
Non-polymers7523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-30 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.307, 100.307, 685.399
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
11C-743-

HOH

21C-758-

HOH

31C-765-

HOH

41C-766-

HOH

51C-769-

HOH

61C-772-

HOH

71D-776-

HOH

81D-777-

HOH

91D-782-

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 / N-Acetylglucosamine


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: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 782 / 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: 2.95 Å3/Da / Density % sol: 58.25 %
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: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 78082 / % possible obs: 99.9 % / Redundancy: 11.8 % / Net I/σ(I): 25.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 10.5 / Rsym value: 0.304 / % possible all: 100

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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: 2.102→48.987 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.12
RfactorNum. reflection% reflection
Rfree0.2231 3930 5.03 %
Rwork0.1878 --
obs0.1896 78082 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.102→48.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7722 0 98 782 8602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067992
X-RAY DIFFRACTIONf_angle_d1.0210830
X-RAY DIFFRACTIONf_dihedral_angle_d14.5382938
X-RAY DIFFRACTIONf_chiral_restr0.0441192
X-RAY DIFFRACTIONf_plane_restr0.0051436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1018-2.12750.24191310.19942418X-RAY DIFFRACTION92
2.1275-2.15440.31041260.19792619X-RAY DIFFRACTION100
2.1544-2.18270.21211450.19392668X-RAY DIFFRACTION100
2.1827-2.21260.24941620.19942550X-RAY DIFFRACTION100
2.2126-2.24430.22331490.18912608X-RAY DIFFRACTION100
2.2443-2.27780.21141330.18942646X-RAY DIFFRACTION100
2.2778-2.31330.23161340.18532610X-RAY DIFFRACTION100
2.3133-2.35130.20211360.1842641X-RAY DIFFRACTION100
2.3513-2.39180.24491310.19772656X-RAY DIFFRACTION100
2.3918-2.43530.27091210.19682639X-RAY DIFFRACTION100
2.4353-2.48210.27071480.19892625X-RAY DIFFRACTION100
2.4821-2.53280.22871200.19852634X-RAY DIFFRACTION100
2.5328-2.58790.2381260.19322659X-RAY DIFFRACTION100
2.5879-2.64810.2491550.19292620X-RAY DIFFRACTION100
2.6481-2.71430.2311460.19962644X-RAY DIFFRACTION100
2.7143-2.78770.19691310.19772658X-RAY DIFFRACTION100
2.7877-2.86970.22361540.20042624X-RAY DIFFRACTION100
2.8697-2.96230.24251470.19522623X-RAY DIFFRACTION100
2.9623-3.06820.22051450.19872636X-RAY DIFFRACTION100
3.0682-3.1910.25151410.20022664X-RAY DIFFRACTION100
3.191-3.33620.21391310.19222690X-RAY DIFFRACTION100
3.3362-3.5120.24071480.18552649X-RAY DIFFRACTION100
3.512-3.7320.23221420.18132682X-RAY DIFFRACTION100
3.732-4.020.20651310.17012713X-RAY DIFFRACTION100
4.02-4.42430.19041420.15932682X-RAY DIFFRACTION100
4.4243-5.0640.19811510.15812708X-RAY DIFFRACTION100
5.064-6.37790.19341520.19082747X-RAY DIFFRACTION100
6.3779-49.00030.21311520.20612839X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -105.1419 Å / Origin y: 202.467 Å / Origin z: 61.4368 Å
111213212223313233
T0.0989 Å2-0.0024 Å20.0051 Å2-0.0714 Å2-0.0134 Å2--0.1001 Å2
L0.0371 °20.0046 °2-0.0174 °2-0.0841 °2-0.0861 °2--0.0307 °2
S-0.0048 Å °0.0244 Å °-0.0029 Å °-0.0406 Å °-0.0054 Å °0.0056 Å °0.0277 Å °0.0016 Å °-0.0083 Å °
Refinement TLS groupSelection details: all

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