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- PDB-4xkd: Crystal structure of hemagglutinin from Taiwan (2013) H6N1 influe... -

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Basic information

Entry
Database: PDB / ID: 4xkd
TitleCrystal structure of hemagglutinin from Taiwan (2013) H6N1 influenza virus
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN
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 speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.482 Å
AuthorsTzarum, N. / Zhu, X. / Wilson, I.A.
CitationJournal: Cell Host Microbe / Year: 2015
Title: Structure and Receptor Binding of the Hemagglutinin from a Human H6N1 Influenza Virus.
Authors: Tzarum, N. / de Vries, R.P. / Zhu, X. / Yu, W. / McBride, R. / Paulson, J.C. / Wilson, I.A.
History
DepositionJan 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 31, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 27, 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 1.5Jan 10, 2024Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.6Nov 20, 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)175,21612
Polymers173,8896
Non-polymers1,3276
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30220 Å2
ΔGint-135 kcal/mol
Surface area60610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.446, 98.963, 132.863
Angle α, β, γ (deg.)90.000, 126.120, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 37331.152 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Taiwan/2/2013 (H6N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A0A0J9X268*PLUS
#2: Protein Hemagglutinin HA2 chain


Mass: 20631.859 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Taiwan/2/2013 (H6N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / 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.: 6 / 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.: 247 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10mM NiCl2, 0.1M Tris pH 8.5, 20% (w/v) MPEG 2000 and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.482→50 Å / Num. obs: 66521 / % possible obs: 98.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.056 / Rrim(I) all: 0.11 / Χ2: 1.017 / Net I/av σ(I): 11.938 / Net I/σ(I): 4.7 / Num. measured all: 240934
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.482-2.543.20.44831860.7850.2780.530.42194.4
2.54-2.593.40.43131940.8010.2660.510.41396.6
2.59-2.643.50.39532960.8510.2410.4650.42997.7
2.64-2.693.50.38533240.6860.2370.4540.72898.2
2.69-2.753.60.31633060.9040.1920.3710.45298
2.75-2.823.30.26232240.9260.1630.3110.47196.2
2.82-2.893.60.23633150.940.1420.2770.50598.8
2.89-2.963.80.21433540.9540.1250.2480.50799.6
2.96-3.053.80.1833320.9610.1050.2090.53799.6
3.05-3.153.80.15733840.9740.0910.1820.5899.2
3.15-3.263.80.13633530.9770.0790.1580.61499.2
3.26-3.393.70.1233440.9820.070.140.69799.2
3.39-3.553.70.11333260.9770.0670.1320.88798.3
3.55-3.733.30.09432850.9680.0580.1111.37797.2
3.73-3.973.90.09533750.9420.0550.111.25199.6
3.97-4.273.80.07533790.9890.0440.0871.59999.7
4.27-4.73.80.06633530.9920.0380.0771.24799.2
4.7-5.383.50.06333370.9890.0380.0741.61598.1
5.38-6.783.70.06233940.9910.0370.0731.41699.1
6.78-503.70.05234600.9890.0310.064.13198.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data scaling
PHENIXmodel building
HKL-2000705bdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M4Y

4m4y


Resolution: 2.482→49.481 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 3354 5.04 %
Rwork0.2066 --
obs0.2091 66484 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.04 Å2 / Biso mean: 40.9529 Å2 / Biso min: 9.73 Å2
Refinement stepCycle: final / Resolution: 2.482→49.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11897 0 84 247 12228
Biso mean--79.3 40.69 -
Num. residues----1498

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