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- PDB-4nkj: Structure of influenza B virus hemagglutinin at membrane fusion pH -

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Basic information

Entry
Database: PDB / ID: 4nkj
TitleStructure of influenza B virus hemagglutinin at membrane fusion pH
ComponentsHemagglutinin HA2
KeywordsVIRAL PROTEIN / HA
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus B / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4535 Å
AuthorsNi, F. / Chen, X. / Shen, J. / Wang, Q.
CitationJournal: Biochemistry / Year: 2014
Title: Structural insights into the membrane fusion mechanism mediated by influenza virus hemagglutinin.
Authors: Ni, F. / Chen, X. / Shen, J. / Wang, Q.
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin HA2


Theoretical massNumber of molelcules
Total (without water)17,2111
Polymers17,2111
Non-polymers00
Water48627
1
A: Hemagglutinin HA2

A: Hemagglutinin HA2

A: Hemagglutinin HA2


Theoretical massNumber of molelcules
Total (without water)51,6343
Polymers51,6343
Non-polymers00
Water543
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 area12510 Å2
ΔGint-107 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.180, 48.180, 354.895
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

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Components

#1: Protein Hemagglutinin HA2


Mass: 17211.225 Da / Num. of mol.: 1 / Fragment: Hemagglutinin HA2 (UNP Residues 392-541)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Gene: HA / Production host: Escherichia coli (E. coli) / References: UniProt: S5DRP1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.3 Å3/Da / Density % sol: 46.59 %

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.45→37.76 Å / Num. all: 6281 / Num. obs: 5617 / % possible obs: 89.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.21 / Num. unique all: 615 / % possible all: 94.96

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4535→37.758 Å / SU ML: 0.27 / σ(F): 1.94 / Phase error: 32.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 264 4.71 %random
Rwork0.2549 ---
obs0.2556 5609 89.3 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.41 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2278 Å20 Å20 Å2
2--3.2278 Å20 Å2
3----6.4555 Å2
Refinement stepCycle: LAST / Resolution: 2.4535→37.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 0 27 1111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151169
X-RAY DIFFRACTIONf_angle_d0.811472
X-RAY DIFFRACTIONf_dihedral_angle_d12.832412
X-RAY DIFFRACTIONf_chiral_restr0.05179
X-RAY DIFFRACTIONf_plane_restr0.002193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4535-3.09090.2951320.24672737X-RAY DIFFRACTION94
3.0909-37.76260.25771320.25822608X-RAY DIFFRACTION85

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