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- PDB-4edb: Structures of monomeric hemagglutinin and its complex with an Fab... -

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Basic information

Entry
Database: PDB / ID: 4edb
TitleStructures of monomeric hemagglutinin and its complex with an Fab fragment of a neutralizing antibody that binds to H1 subtype influenza viruses: molecular basis of infectivity of 2009 pandemic H1N1 influenza A viruses
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / influenza virus / haemagglutinin / conformation / antibody
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion membrane
Similarity search - Function
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 ...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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKim, K.H. / Cho, K.J. / Lee, J.H. / Park, Y.H. / Khan, T.G. / Lee, J.Y. / Kang, S.H. / Alam, I.
CitationJournal: J.Gen.Virol. / Year: 2013
Title: Insight into structural diversity of influenza virus haemagglutinin
Authors: Cho, K.J. / Lee, J.H. / Hong, K.W. / Kim, S.H. / Park, Y. / Lee, J.Y. / Kang, S. / Kim, S. / Yang, J.H. / Kim, E.K. / Seok, J.H. / Unzai, S. / Park, S.Y. / Saelens, X. / Kim, C.J. / Lee, J.Y. ...Authors: Cho, K.J. / Lee, J.H. / Hong, K.W. / Kim, S.H. / Park, Y. / Lee, J.Y. / Kang, S. / Kim, S. / Yang, J.H. / Kim, E.K. / Seok, J.H. / Unzai, S. / Park, S.Y. / Saelens, X. / Kim, C.J. / Lee, J.Y. / Kang, C. / Oh, H.B. / Chung, M.S. / Kim, K.H.
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)172,5106
Polymers172,5106
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32010 Å2
ΔGint-190 kcal/mol
Surface area58260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.115, 217.115, 266.016
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hemagglutinin


Mass: 36680.176 Da / Num. of mol.: 3 / Fragment: HA1 SUBUNIT, UNP residues 18-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Thailand/CU44/2006 / Gene: HA / Plasmid: pAcGP67A / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7LI25
#2: Protein Hemagglutinin


Mass: 20823.184 Da / Num. of mol.: 3 / Fragment: HA2 SUBUNIT, UNP residues 344-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Thailand/CU44/2006 / Gene: HA / Plasmid: pAcGP67A / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7LI25
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.5 Å3/Da / Density % sol: 64.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Tris-HCl, 20% PEG 3350, 200mM calcium acetate, 8% 1,3-butanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.249
11-2/3H-1/3K+2/3L, -1/3H-2/3K-2/3L, 2/3H-2/3K+1/20.25
11-1/3H+1/3K-2/3L, -K, -4/3H-2/3K+1/3L30.247
11-H, 1/3H-1/3K+2/3L, 2/3H+4/3K+1/3L40.254
ReflectionResolution: 2.5→50 Å / Num. all: 83089 / Num. obs: 83089 / % possible obs: 100 %
Reflection shellResolution: 2.5→2.6 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→44.34 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.848 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.002 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2743 4113 5 %RANDOM
Rwork0.2393 ---
obs0.241 83087 99.76 %-
all-83089 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.95 Å2 / Biso mean: 47.9836 Å2 / Biso min: 12.56 Å2
Baniso -1Baniso -2Baniso -3
1-3.18 Å20 Å20 Å2
2--3.18 Å20 Å2
3----6.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11433 0 0 16 11449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211734
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.93915922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85551443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54625.079573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.382151954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9411545
X-RAY DIFFRACTIONr_chiral_restr0.0810.21689
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219063
LS refinement shellResolution: 2.497→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 234 -
Rwork0.233 5740 -
all-5974 -
obs--97.25 %

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