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- PDB-4yy9: The structure of hemagglutinin from a H6N1 influenza virus (A/Tai... -

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Basic information

Entry
Database: PDB / ID: 4yy9
TitleThe structure of hemagglutinin from a H6N1 influenza virus (A/Taiwan/2/2013)
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 / 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
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: 2.601 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/Taiwan/2/2013) at 2.6 Angstroms resolution
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 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HA1
B: HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1145
Polymers55,0852
Non-polymers1,0293
Water3,387188
1
A: HA1
B: HA2
hetero molecules

A: HA1
B: HA2
hetero molecules

A: HA1
B: HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,34115
Polymers165,2546
Non-polymers3,0879
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area31850 Å2
ΔGint-128 kcal/mol
Surface area59940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.898, 113.898, 163.842
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-804-

HOH

21B-658-

HOH

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Components

#1: Protein HA1


Mass: 36548.293 Da / Num. of mol.: 1
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: 18536.426 Da / Num. of mol.: 1
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: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
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: 5.57 Å3/Da / Density % sol: 77.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium acetate, 0.1M sodium acetate pH4.0, 15%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.07138 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07138 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 36901 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 5.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data processing
PHASERphasing
Cootmodel building
PHENIX1.8.3_1479refinement
SCALAdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.601→47.226 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 1844 5 %
Rwork0.1914 --
obs0.1931 36901 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.601→47.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 0 188 4126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074038
X-RAY DIFFRACTIONf_angle_d1.0475477
X-RAY DIFFRACTIONf_dihedral_angle_d14.0011466
X-RAY DIFFRACTIONf_chiral_restr0.044601
X-RAY DIFFRACTIONf_plane_restr0.004706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6011-2.67140.26241380.21872662X-RAY DIFFRACTION99
2.6714-2.750.23321240.20122710X-RAY DIFFRACTION100
2.75-2.83880.24581360.20552701X-RAY DIFFRACTION100
2.8388-2.94020.26541290.20442702X-RAY DIFFRACTION100
2.9402-3.05790.23541300.19442694X-RAY DIFFRACTION100
3.0579-3.19710.20531520.18842678X-RAY DIFFRACTION100
3.1971-3.36560.21821300.19452719X-RAY DIFFRACTION100
3.3656-3.57640.26351410.19522709X-RAY DIFFRACTION100
3.5764-3.85240.24391320.18312698X-RAY DIFFRACTION100
3.8524-4.23990.21061580.16592695X-RAY DIFFRACTION100
4.2399-4.85280.18061660.16042673X-RAY DIFFRACTION100
4.8528-6.1120.19471420.19212706X-RAY DIFFRACTION100
6.112-47.23380.25531660.22662710X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -40.7218 Å / Origin y: 39.6464 Å / Origin z: -8.5359 Å
111213212223313233
T0.1628 Å2-0.0275 Å2-0.0219 Å2-0.245 Å20.0125 Å2--0.2604 Å2
L0.2149 °2-0.0193 °2-0.0681 °2-0.224 °20.0394 °2--0.9112 °2
S-0.0208 Å °-0.0404 Å °0.009 Å °0.0559 Å °0.0012 Å °-0.0653 Å °-0.0244 Å °0.2047 Å °0 Å °
Refinement TLS groupSelection details: all

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