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- PDB-6d8b: The crystal structure of hemagglutinin from A/Hong Kong/125/2017 ... -

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Basic information

Entry
Database: PDB / ID: 6d8b
TitleThe crystal structure of hemagglutinin from A/Hong Kong/125/2017 H7N9 influenza virus
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Influenza / H7N9
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; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsYang, H. / Stevens, J.
CitationJournal: J. Virol. / Year: 2018
Title: Structural and Molecular Characterization of the Hemagglutinin from the Fifth-Epidemic-Wave A(H7N9) Influenza Viruses.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Stevens, J.
History
DepositionApr 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
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 1.4Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 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 HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,33012
Polymers181,0026
Non-polymers1,3276
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, trimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34320 Å2
ΔGint-144 kcal/mol
Surface area56340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.642, 116.891, 119.628
Angle α, β, γ (deg.)90.00, 124.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 35032.613 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/125/2017(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A2I7YV81
#2: Protein Hemagglutinin HA2 chain


Mass: 25301.508 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/125/2017(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A218MY65
#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.: 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
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: 3.24 Å3/Da / Density % sol: 62.02 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2M Magnesium Acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 48207 / % possible obs: 98.89 % / Redundancy: 3.7 % / Net I/σ(I): 18.39
Reflection shellResolution: 2.95→3.06 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LN6

4ln6


Resolution: 2.95→39.154 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.24
RfactorNum. reflection% reflection
Rfree0.2787 2675 5.55 %
Rwork0.2341 --
obs0.2366 48207 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.95→39.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11415 0 84 0 11499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811733
X-RAY DIFFRACTIONf_angle_d1.33415864
X-RAY DIFFRACTIONf_dihedral_angle_d9.1696984
X-RAY DIFFRACTIONf_chiral_restr0.0751725
X-RAY DIFFRACTIONf_plane_restr0.0072094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9498-3.00340.30451020.29922087X-RAY DIFFRACTION85
3.0034-3.06120.38561720.3042367X-RAY DIFFRACTION100
3.0612-3.12360.3571800.30262338X-RAY DIFFRACTION100
3.1236-3.19150.3871330.29082425X-RAY DIFFRACTION100
3.1915-3.26570.37631430.29062428X-RAY DIFFRACTION100
3.2657-3.34740.33561670.28412397X-RAY DIFFRACTION100
3.3474-3.43780.36231200.28212419X-RAY DIFFRACTION100
3.4378-3.53890.30311170.27922438X-RAY DIFFRACTION100
3.5389-3.65310.37851620.25672403X-RAY DIFFRACTION100
3.6531-3.78350.33631540.26032377X-RAY DIFFRACTION100
3.7835-3.93490.30911230.2352416X-RAY DIFFRACTION100
3.9349-4.11380.259930.22812459X-RAY DIFFRACTION100
4.1138-4.33040.25221300.22282431X-RAY DIFFRACTION100
4.3304-4.60130.25551400.19792401X-RAY DIFFRACTION99
4.6013-4.9560.26851250.20432437X-RAY DIFFRACTION100
4.956-5.45350.27151540.20522414X-RAY DIFFRACTION100
5.4535-6.23990.26511480.21962416X-RAY DIFFRACTION100
6.2399-7.85120.22941480.23012445X-RAY DIFFRACTION100
7.8512-39.15750.22191640.21122434X-RAY DIFFRACTION98

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