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- PDB-5xl5: The structure of hemagglutinin Q226L mutant from an avian-origin ... -

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Basic information

Entry
Database: PDB / ID: 5xl5
TitleThe structure of hemagglutinin Q226L mutant 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 / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
Revision 1.6Oct 23, 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)113,4738
Polymers112,5884
Non-polymers8854
Water8,827490
1
A: Hemagglutinin
C: 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 area6140 Å2
ΔGint-29 kcal/mol
Surface area23990 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 area6150 Å2
ΔGint-28 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.549, 100.549, 685.737
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-723-

HOH

21D-840-

HOH

31D-841-

HOH

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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: 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.: 490 / 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: 2.96 Å3/Da / Density % sol: 58.48 %
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 6M / Detector: PIXEL / Date: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 69076 / % possible obs: 99.9 % / Redundancy: 9.1 % / Net I/σ(I): 18.8
Reflection shellResolution: 2.21→2.27 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 3 / Rsym value: 0.812 / % 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: 2.2→33.82 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.38
RfactorNum. reflection% reflection
Rfree0.227 3494 5.06 %
Rwork0.201 --
obs0.202 69076 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→33.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7724 0 56 490 8270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097952
X-RAY DIFFRACTIONf_angle_d1.23410772
X-RAY DIFFRACTIONf_dihedral_angle_d15.1172916
X-RAY DIFFRACTIONf_chiral_restr0.0641184
X-RAY DIFFRACTIONf_plane_restr0.0061430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1953-2.22530.30981420.25922480X-RAY DIFFRACTION96
2.2253-2.25710.30241450.24522587X-RAY DIFFRACTION100
2.2571-2.29080.27111210.24032628X-RAY DIFFRACTION100
2.2908-2.32660.28761390.22852538X-RAY DIFFRACTION100
2.3266-2.36470.27941260.22982616X-RAY DIFFRACTION100
2.3647-2.40550.30031390.23672605X-RAY DIFFRACTION100
2.4055-2.44920.29141360.23062611X-RAY DIFFRACTION100
2.4492-2.49630.24461610.23452545X-RAY DIFFRACTION100
2.4963-2.54730.28771210.21772618X-RAY DIFFRACTION100
2.5473-2.60260.29051290.2182631X-RAY DIFFRACTION100
2.6026-2.66310.21351420.21522604X-RAY DIFFRACTION100
2.6631-2.72970.25181350.21562604X-RAY DIFFRACTION100
2.7297-2.80350.23631390.21392609X-RAY DIFFRACTION100
2.8035-2.88590.24431400.20632600X-RAY DIFFRACTION100
2.8859-2.9790.22861430.21132615X-RAY DIFFRACTION100
2.979-3.08540.28091430.22182591X-RAY DIFFRACTION100
3.0854-3.20890.25871300.21722646X-RAY DIFFRACTION100
3.2089-3.35480.22851230.20712678X-RAY DIFFRACTION100
3.3548-3.53150.21581310.19982614X-RAY DIFFRACTION100
3.5315-3.75250.19161570.19012631X-RAY DIFFRACTION100
3.7525-4.04180.20571620.182643X-RAY DIFFRACTION100
4.0418-4.44770.18461450.16742659X-RAY DIFFRACTION100
4.4477-5.08940.18221540.16072671X-RAY DIFFRACTION100
5.0894-6.4050.21921480.19342716X-RAY DIFFRACTION100
6.405-33.8270.20911430.1972842X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -206.0123 Å / Origin y: 202.9539 Å / Origin z: -624.2327 Å
111213212223313233
T0.2398 Å2-0.007 Å20.0015 Å2-0.2225 Å2-0.0257 Å2--0.2651 Å2
L0.0889 °20.0024 °2-0.0377 °2-0.1936 °2-0.1767 °2--0.3263 °2
S-0.009 Å °0.059 Å °-0.01 Å °-0.0939 Å °-0.0017 Å °-0.001 Å °0.0469 Å °-0.0274 Å °-0.0001 Å °
Refinement TLS groupSelection details: ALL

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