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- PDB-5xl8: The structure of hemagglutinin G228S mutant from a avian-origin H... -

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Basic information

Entry
Database: PDB / ID: 5xl8
TitleThe structure of hemagglutinin G228S mutant from a avian-origin H4N6 influenza virus (A/duck/Czech/1956)
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 / 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 (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: 2.001 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 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)170,2909
Polymers168,9623
Non-polymers1,3276
Water20,9331162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-16 kcal/mol
Surface area57680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.203, 115.974, 132.336
Angle α, β, γ (deg.)90.00, 102.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemagglutinin


Mass: 56320.773 Da / Num. of mol.: 3 / Fragment: UNP residues 17-519 / Mutation: G228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3KF09, UniProt: P19696*PLUS
#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


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


Mass: 18.015 Da / Num. of mol.: 1162 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris (pH 6.5) and 20% (w/v) PEG 1,500

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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: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 128888 / % possible obs: 99.8 % / Redundancy: 5.1 % / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.495 / % possible all: 99.7

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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: 2.001→43.161 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2
RfactorNum. reflection% reflection
Rfree0.2137 6484 5.03 %
Rwork0.1864 --
obs0.1878 128888 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.001→43.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11499 0 84 1162 12745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811838
X-RAY DIFFRACTIONf_angle_d1.14716038
X-RAY DIFFRACTIONf_dihedral_angle_d14.6794353
X-RAY DIFFRACTIONf_chiral_restr0.051764
X-RAY DIFFRACTIONf_plane_restr0.0052130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.02370.28391950.24033838X-RAY DIFFRACTION93
2.0237-2.04760.27012110.23224075X-RAY DIFFRACTION100
2.0476-2.07250.28052260.22584060X-RAY DIFFRACTION100
2.0725-2.09880.25052020.21444126X-RAY DIFFRACTION100
2.0988-2.12640.23282100.2064000X-RAY DIFFRACTION100
2.1264-2.15550.21022210.20154075X-RAY DIFFRACTION100
2.1555-2.18630.22182290.20444061X-RAY DIFFRACTION99
2.1863-2.21890.24222060.20554095X-RAY DIFFRACTION100
2.2189-2.25360.21742170.19384096X-RAY DIFFRACTION100
2.2536-2.29050.22962080.24037X-RAY DIFFRACTION100
2.2905-2.330.21952370.19384092X-RAY DIFFRACTION100
2.33-2.37240.23142270.19324015X-RAY DIFFRACTION100
2.3724-2.4180.22112200.19784123X-RAY DIFFRACTION100
2.418-2.46740.20262020.19194064X-RAY DIFFRACTION100
2.4674-2.5210.21181980.1924097X-RAY DIFFRACTION100
2.521-2.57970.23152090.18714065X-RAY DIFFRACTION100
2.5797-2.64420.21672200.18324113X-RAY DIFFRACTION100
2.6442-2.71570.22392170.19834089X-RAY DIFFRACTION100
2.7157-2.79550.24612210.1914044X-RAY DIFFRACTION100
2.7955-2.88580.23062170.19274096X-RAY DIFFRACTION100
2.8858-2.98890.21892170.18934111X-RAY DIFFRACTION100
2.9889-3.10850.21812310.18854098X-RAY DIFFRACTION100
3.1085-3.24990.20162140.19164103X-RAY DIFFRACTION100
3.2499-3.42120.19792180.18434085X-RAY DIFFRACTION100
3.4212-3.63550.21552270.17784106X-RAY DIFFRACTION100
3.6355-3.9160.19012000.17114108X-RAY DIFFRACTION100
3.916-4.30980.19612350.16414099X-RAY DIFFRACTION100
4.3098-4.93260.15812130.15014120X-RAY DIFFRACTION100
4.9326-6.21160.23222190.17694125X-RAY DIFFRACTION100
6.2116-43.17110.20672170.19534188X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 145.8598 Å / Origin y: 114.4143 Å / Origin z: 23.7814 Å
111213212223313233
T0.1334 Å2-0.0103 Å20.003 Å2-0.1164 Å2-0.0093 Å2--0.1176 Å2
L0.2898 °20.0351 °20.0325 °2-0.2479 °2-0.0164 °2--0.1431 °2
S0.0168 Å °-0.0648 Å °0.0085 Å °0.082 Å °-0.0165 Å °-0.0083 Å °-0.0116 Å °-0.0441 Å °0.0005 Å °
Refinement TLS groupSelection details: all

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