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- PDB-5xl6: The structure of hemagglutinin Q226L mutant from a avian-origin H... -

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Basic information

Entry
Database: PDB / ID: 5xl6
TitleThe structure of hemagglutinin Q226L mutant from a 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
N-acetyl-alpha-neuraminic acid / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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
Revision 1.4Nov 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 1.5Oct 9, 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
A: Hemagglutinin
C: Hemagglutinin
B: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7829
Polymers112,5884
Non-polymers1,1945
Water4,792266
1
A: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0465
Polymers56,2942
Non-polymers7523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-29 kcal/mol
Surface area23970 Å2
MethodPISA
2
B: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7364
Polymers56,2942
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-29 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.688, 100.688, 686.416
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hemagglutinin


Mass: 35951.488 Da / Num. of mol.: 2 / Fragment: UNP residues 17-343 / Mutation: Q226L
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: Trichobaicalia (invertebrata) / 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: Trichobaicalia (invertebrata) / 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: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
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


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 0.2 M Trimethylamine N-oxide dehydrate, 0.1 M Tris (pH 8.4), and 18% 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 S 6M / Detector: PIXEL / Date: Jan 13, 2015
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.406→50 Å / Num. obs: 52838 / % possible obs: 99.9 % / Redundancy: 10.5 % / Net I/σ(I): 20.5
Reflection shellResolution: 2.41→2.49 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.855 / % possible all: 99.9

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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: 2.41→49.168 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.46
RfactorNum. reflection% reflection
Rfree0.2519 2688 5.09 %
Rwork0.2096 --
obs0.2118 52838 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.41→49.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7724 0 77 266 8067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097973
X-RAY DIFFRACTIONf_angle_d1.2510803
X-RAY DIFFRACTIONf_dihedral_angle_d15.4912927
X-RAY DIFFRACTIONf_chiral_restr0.0521190
X-RAY DIFFRACTIONf_plane_restr0.0061432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4063-2.450.32031580.27212575X-RAY DIFFRACTION99
2.45-2.49720.28741280.26992594X-RAY DIFFRACTION100
2.4972-2.54810.35051330.24822608X-RAY DIFFRACTION100
2.5481-2.60350.27661500.2462587X-RAY DIFFRACTION100
2.6035-2.66410.28111300.23562616X-RAY DIFFRACTION100
2.6641-2.73070.30121470.2422632X-RAY DIFFRACTION100
2.7307-2.80450.34161470.24522598X-RAY DIFFRACTION100
2.8045-2.88710.2991410.2392619X-RAY DIFFRACTION100
2.8871-2.98020.26371490.24142579X-RAY DIFFRACTION100
2.9802-3.08670.3141360.24182605X-RAY DIFFRACTION100
3.0867-3.21030.26721430.22512643X-RAY DIFFRACTION100
3.2103-3.35640.29771310.22282672X-RAY DIFFRACTION100
3.3564-3.53330.26631500.21682583X-RAY DIFFRACTION100
3.5333-3.75460.25771360.20872679X-RAY DIFFRACTION100
3.7546-4.04430.22051450.19562655X-RAY DIFFRACTION100
4.0443-4.45110.2181320.18592668X-RAY DIFFRACTION100
4.4511-5.09460.22991280.16432713X-RAY DIFFRACTION100
5.0946-6.41640.21191630.18892702X-RAY DIFFRACTION100
6.4164-49.17810.19821410.19422822X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -206.3446 Å / Origin y: -145.479 Å / Origin z: 747.4017 Å
111213212223313233
T0.2345 Å2-0.0076 Å20.0027 Å2-0.2284 Å2-0.0209 Å2--0.2785 Å2
L0.0661 °2-0.0005 °2-0.0297 °2-0.1943 °2-0.1758 °2--0.4273 °2
S-0.0171 Å °0.0577 Å °-0.0014 Å °-0.0799 Å °-0.0085 Å °-0.0087 Å °0.0269 Å °-0.0351 Å °0 Å °
Refinement TLS groupSelection details: all

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