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- PDB-3eyj: Structure of Influenza Haemagglutinin in complex with an inhibito... -

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Basic information

Entry
Database: PDB / ID: 3eyj
TitleStructure of Influenza Haemagglutinin in complex with an inhibitor of membrane fusion
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Influenza / hemagglutinin / inhibitor / Envelope protein / Fusion protein / Glycoprotein / Lipoprotein / Membrane / Palmitate / Transmembrane / Virion
Function / homology
Function and homology information


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 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRussell, R.J. / Kerry, P.S. / Stevens, D.J. / Steinahuer, D.A. / Martin, S.R. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structure of influenza hemagglutinin in complex with an inhibitor of membrane fusion
Authors: Russell, R.J. / Kerry, P.S. / Stevens, D.J. / Steinhauer, D.A. / Martin, S.R. / Gamblin, S.J. / Skehel, J.J.
History
DepositionOct 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain


Theoretical massNumber of molelcules
Total (without water)55,2032
Polymers55,2032
Non-polymers00
Water6,557364
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain


Theoretical massNumber of molelcules
Total (without water)165,6086
Polymers165,6086
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area33140 Å2
ΔGint-145 kcal/mol
Surface area55420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.765, 138.765, 138.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 35279.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / References: UniProt: P26137
#2: Protein Hemagglutinin HA2 chain


Mass: 19922.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / References: UniProt: P26137
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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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: 4.03 Å3/Da / Density % sol: 69.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris, PEG8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 27599 / Num. obs: 27461 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.69 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.585 Å / SU ML: 0.38 / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 1381 5.03 %Random
Rwork0.1933 ---
obs0.1959 27461 51.75 %-
all-27599 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.534 Å2 / ksol: 0.311 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→29.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 0 364 4210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69310.31751380.23912567X-RAY DIFFRACTION51
2.6931-2.80080.32971480.22532565X-RAY DIFFRACTION51
2.8008-2.92820.30131320.20862619X-RAY DIFFRACTION51
2.9282-3.08240.24171420.1912552X-RAY DIFFRACTION51
3.0824-3.27530.25881400.17292593X-RAY DIFFRACTION51
3.2753-3.52780.23021210.18162581X-RAY DIFFRACTION51
3.5278-3.88220.21751300.16372598X-RAY DIFFRACTION51
3.8822-4.44230.17261310.14882633X-RAY DIFFRACTION52
4.4423-5.59060.20451480.15852638X-RAY DIFFRACTION53
5.5906-29.58670.23911510.23412734X-RAY DIFFRACTION54

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