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- PDB-6d7u: The crystal structure of hemagglutinin from A/Guangdong/17SF003/2... -

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Basic information

Entry
Database: PDB / ID: 6d7u
TitleThe crystal structure of hemagglutinin from A/Guangdong/17SF003/2016 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 / 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
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: 2.7 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 25, 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)165,04315
Polymers163,0526
Non-polymers1,9919
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Trimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34700 Å2
ΔGint-144 kcal/mol
Surface area57490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.125, 117.046, 119.971
Angle α, β, γ (deg.)90.00, 124.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 34577.883 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Guangdong/17SF003/2016(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A1S6R2B6
#2: Protein Hemagglutinin HA2 chain


Mass: 19772.805 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Guangdong/17SF003/2016(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A2I7YV20
#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.: 9
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: 3.61 Å3/Da / Density % sol: 65.89 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2M Ammonium Formate, pH 6.6, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 62809 / % possible obs: 98.65 % / Redundancy: 3.2 % / Net I/σ(I): 22.27
Reflection shellResolution: 2.7→2.75 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: 2.7→37.998 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.97
RfactorNum. reflection% reflection
Rfree0.2575 3265 5.2 %
Rwork0.2211 --
obs0.223 62809 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→37.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11433 0 126 0 11559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911799
X-RAY DIFFRACTIONf_angle_d1.27115960
X-RAY DIFFRACTIONf_dihedral_angle_d9.2497026
X-RAY DIFFRACTIONf_chiral_restr0.0651734
X-RAY DIFFRACTIONf_plane_restr0.0062112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6999-2.74020.42091510.34972442X-RAY DIFFRACTION94
2.7402-2.7830.34931570.33622617X-RAY DIFFRACTION100
2.783-2.82870.34561380.30042563X-RAY DIFFRACTION100
2.8287-2.87740.29911280.28432630X-RAY DIFFRACTION100
2.8774-2.92970.3261830.26362604X-RAY DIFFRACTION100
2.9297-2.9860.35441330.28012579X-RAY DIFFRACTION99
2.986-3.0470.27991400.26212576X-RAY DIFFRACTION99
3.047-3.11320.36171340.26352599X-RAY DIFFRACTION100
3.1132-3.18560.34161120.27512620X-RAY DIFFRACTION99
3.1856-3.26520.32891390.28692635X-RAY DIFFRACTION99
3.2652-3.35340.33651620.25732612X-RAY DIFFRACTION99
3.3534-3.45210.28721440.25442545X-RAY DIFFRACTION99
3.4521-3.56340.29281640.22862597X-RAY DIFFRACTION99
3.5634-3.69070.26691520.21682557X-RAY DIFFRACTION99
3.6907-3.83830.2681180.23192624X-RAY DIFFRACTION99
3.8383-4.01280.2134960.20962654X-RAY DIFFRACTION99
4.0128-4.22410.2493930.20652618X-RAY DIFFRACTION99
4.2241-4.48840.21851440.18192593X-RAY DIFFRACTION99
4.4884-4.83430.21011810.18582568X-RAY DIFFRACTION98
4.8343-5.31960.24021360.18572587X-RAY DIFFRACTION98
5.3196-6.08660.24921440.2032575X-RAY DIFFRACTION98
6.0866-7.65820.2171850.20972542X-RAY DIFFRACTION98
7.6582-38.00170.18921310.18172607X-RAY DIFFRACTION96

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