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- PDB-4yy0: The structure of hemagglutinin from a H6N1 influenza virus (A/chi... -

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Basic information

Entry
Database: PDB / ID: 4yy0
TitleThe structure of hemagglutinin from a H6N1 influenza virus (A/chicken/Taiwan/A2837/2013)
Components
  • HA1
  • HA2
KeywordsIMMUNE SYSTEM / Hemagglutinin
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / 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 / membrane
Similarity search - Function
Haemagglutinin, influenzavirus 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 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 HA2 chain / Hemagglutinin
Similarity search - Component
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsWang, F. / Qi, J. / Bi, Y. / Zhang, W. / Wang, M. / Wang, M. / Liu, J. / Yan, J. / Shi, Y. / Gao, G.F.
Funding support China, 5items
OrganizationGrant numberCountry
China Ministry of Science and Technology National 973 Project2011CB504703 China
Intramural Special Grant for Influenza Virus Research from the Chinese Academy of SciencesKJZD-EW-L09 China
Intramural Special Grant for Strategic Priority Research Program of the Chinese Academy of SciencesXDB08020100 China
National Natural Science Foundation of China31402196 China
China National Grand S&T Special Project2014ZX10004002 China
CitationJournal: To Be Published
Title: Structure of hemagglutinin from a H6N1 influenza virus (A/chicken/Taiwan/A2837/2013)
Authors: Wang, F. / Qi, J. / Bi, Y. / Zhang, W. / Wang, M. / Wang, M. / Liu, J. / Yan, J. / Shi, Y. / Gao, G.F.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Non-polymer description
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HA1
B: HA2
C: HA1
D: HA2
E: HA1
F: HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,41213
Polymers163,8636
Non-polymers1,5487
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30200 Å2
ΔGint-132 kcal/mol
Surface area58720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.610, 106.257, 125.277
Angle α, β, γ (deg.)90.00, 102.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HA1


Mass: 36474.211 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: A0A0J9X268*PLUS
#2: Protein HA2


Mass: 18146.955 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: A0A0J9X267*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.: 7 / Source method: obtained synthetically / 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.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium thiocyanate, 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 53268 / % possible obs: 99.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 12.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data processing
PHASERphasing
Cootmodel building
PHENIX1.8.4_1496refinement
SCALAdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→41.37 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 2711 5.09 %
Rwork0.22 --
obs0.223 53268 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11514 0 98 69 11681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811931
X-RAY DIFFRACTIONf_angle_d1.48916173
X-RAY DIFFRACTIONf_dihedral_angle_d15.4964323
X-RAY DIFFRACTIONf_chiral_restr0.0731758
X-RAY DIFFRACTIONf_plane_restr0.0062100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5929-2.640.41021170.34882505X-RAY DIFFRACTION94
2.64-2.69080.40181510.32572695X-RAY DIFFRACTION100
2.6908-2.74570.34411270.31952657X-RAY DIFFRACTION100
2.7457-2.80540.351260.31052696X-RAY DIFFRACTION100
2.8054-2.87070.3141420.29252670X-RAY DIFFRACTION100
2.8707-2.94240.36661620.28972660X-RAY DIFFRACTION100
2.9424-3.0220.35791500.27872612X-RAY DIFFRACTION100
3.022-3.11090.3061360.2622675X-RAY DIFFRACTION100
3.1109-3.21120.32731740.24882686X-RAY DIFFRACTION100
3.2112-3.3260.31381650.23982619X-RAY DIFFRACTION100
3.326-3.45910.30481480.24492654X-RAY DIFFRACTION100
3.4591-3.61640.28461280.23512690X-RAY DIFFRACTION100
3.6164-3.80690.29631500.222687X-RAY DIFFRACTION100
3.8069-4.04530.28141310.20222666X-RAY DIFFRACTION100
4.0453-4.35730.23251380.18262655X-RAY DIFFRACTION99
4.3573-4.79520.20121460.17422646X-RAY DIFFRACTION98
4.7952-5.48770.21971590.18192652X-RAY DIFFRACTION99
5.4877-6.90870.2261260.20682706X-RAY DIFFRACTION99
6.9087-41.37690.221350.17432726X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -35.3913 Å / Origin y: -32.4471 Å / Origin z: 24.1701 Å
111213212223313233
T0.4048 Å2-0.0023 Å2-0.0351 Å2-0.335 Å2-0.0252 Å2--0.3151 Å2
L0.1085 °20.033 °20.0042 °2-0.7512 °2-0.095 °2--0.3398 °2
S-0.008 Å °0.0399 Å °-0.0205 Å °-0.3061 Å °0.033 Å °0.0928 Å °0.0762 Å °-0.0102 Å °-0.0002 Å °
Refinement TLS groupSelection details: ALL

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