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- PDB-4f15: Molecular basis of infectivity of 2009 pandemic H1N1 influenza A ... -

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Basic information

Entry
Database: PDB / ID: 4f15
TitleMolecular basis of infectivity of 2009 pandemic H1N1 influenza A viruses
Components
  • Fab fragment, heavy chain
  • Fab fragment, light chain
  • Hemagglutinin
KeywordsIMMUNE SYSTEM / 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2540 / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2540 / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Helix non-globular / Special / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.81 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: To be Published
Title: Molecular basis of infectivity of 2009 pandemic H1N1 influenza A viruses
Authors: Kim, K.H. / Cho, K.J. / Lee, J.H. / Park, Y.H. / Khan, T.G. / Lee, J.Y. / Kang, S.H. / Alam, I. / Hong, K.W. / Kim, S.H. / Unzai, S. / Park, S.Y. / Kim, C.J. / Lee, J.Y. / Khan, C. / Oh, H.B. / Chung, M.S.
History
DepositionMay 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Fab fragment, heavy chain
C: Fab fragment, light chain
D: Hemagglutinin
E: Fab fragment, heavy chain
F: Fab fragment, light chain
G: Hemagglutinin
H: Fab fragment, heavy chain
I: Fab fragment, light chain
J: Hemagglutinin
K: Fab fragment, heavy chain
L: Fab fragment, light chain


Theoretical massNumber of molelcules
Total (without water)421,06112
Polymers421,06112
Non-polymers00
Water2,072115
1
A: Hemagglutinin
B: Fab fragment, heavy chain
C: Fab fragment, light chain


Theoretical massNumber of molelcules
Total (without water)105,2653
Polymers105,2653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Hemagglutinin
E: Fab fragment, heavy chain
F: Fab fragment, light chain


Theoretical massNumber of molelcules
Total (without water)105,2653
Polymers105,2653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Hemagglutinin
H: Fab fragment, heavy chain
I: Fab fragment, light chain


Theoretical massNumber of molelcules
Total (without water)105,2653
Polymers105,2653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Hemagglutinin
K: Fab fragment, heavy chain
L: Fab fragment, light chain


Theoretical massNumber of molelcules
Total (without water)105,2653
Polymers105,2653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.698, 90.127, 238.179
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hemagglutinin


Mass: 58167.086 Da / Num. of mol.: 4 / Fragment: UNP residues 18-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Korea/01/2009(H1N1) / Gene: HA / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C5MQE6
#2: Antibody
Fab fragment, heavy chain


Mass: 23233.916 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody
Fab fragment, light chain


Mass: 23864.318 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.88 Å3/Da / Density % sol: 34.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 200mM potassium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.492
ReflectionResolution: 2.8→50 Å / Num. obs: 121633 / % possible obs: 81.4 %
Reflection shellResolution: 2.8→2.9 Å / % possible all: 71.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→49.681 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7386 / σ(F): 1.37 / Phase error: 32.24 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2895 3510 5.25 %
Rwork0.2329 --
obs0.2351 66880 87.51 %
all-76425 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.136 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 101.91 Å2 / Biso mean: 32.7383 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--0.9428 Å20 Å21.2654 Å2
2--13.1629 Å20 Å2
3----13.5792 Å2
Refinement stepCycle: LAST / Resolution: 2.81→49.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19785 0 0 115 19900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00920268
X-RAY DIFFRACTIONf_angle_d1.67227472
X-RAY DIFFRACTIONf_chiral_restr0.1133026
X-RAY DIFFRACTIONf_plane_restr0.0083520
X-RAY DIFFRACTIONf_dihedral_angle_d19.4987204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8098-2.85820.30521410.24652714285572
2.8582-2.91020.31181640.23932961312577
2.9102-2.96610.33881620.24362850301276
2.9661-3.02670.27431510.24372917306877
3.0267-3.09240.30311630.24032926308976
3.0924-3.16430.2951640.23562959312378
3.1643-3.24340.2951410.23592991313278
3.2434-3.33110.30771650.23122973313878
3.3311-3.4290.26351590.2332976313579
3.429-3.53960.32421850.23143087327280
3.5396-3.66610.26821580.2173117327583
3.6661-3.81270.26171500.2193204335485
3.8127-3.98610.26731710.22343271344285
3.9861-4.1960.29331770.21053270344786
4.196-4.45850.29521620.2023425358789
4.4585-4.80210.24751790.19963432361190
4.8021-5.28420.25931850.21383489367490
5.2842-6.04620.2971860.25383540372693
6.0462-7.60750.32292020.29963631383394
7.6075-37.96090.33232160.25543752396894

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