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- PDB-4lvh: Insight into highly conserved H1 subtype-specific epitopes in inf... -

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Basic information

Entry
Database: PDB / ID: 4lvh
TitleInsight into highly conserved H1 subtype-specific epitopes in influenza virus hemagglutinin
Components
  • Hemagglutinin
  • MONOCLONAL ANTIBODY H-CHAIN
  • MONOCLONAL ANTIBODY L-CHAIN
KeywordsIMMUNE SYSTEM / influenza virus / hemagglutinin / 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 (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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...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 / 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: 2.8 Å
AuthorsKim, K.H. / Cho, K.J. / Kim, S. / Seok, J.H. / Lee, J.-H.
CitationJournal: Plos One / Year: 2014
Title: Insight into highly conserved h1 subtype-specific epitopes in influenza virus hemagglutinin
Authors: Cho, K.J. / Hong, K.W. / Kim, S.H. / Seok, J.H. / Kim, S. / Lee, J.-H. / Saelens, X. / Kim, K.H.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Mar 4, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: MONOCLONAL ANTIBODY H-CHAIN
C: MONOCLONAL ANTIBODY L-CHAIN
D: Hemagglutinin
E: MONOCLONAL ANTIBODY H-CHAIN
F: MONOCLONAL ANTIBODY L-CHAIN
G: Hemagglutinin
H: MONOCLONAL ANTIBODY H-CHAIN
I: MONOCLONAL ANTIBODY L-CHAIN
J: Hemagglutinin
K: MONOCLONAL ANTIBODY H-CHAIN
L: MONOCLONAL ANTIBODY L-CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)419,57216
Polymers419,41212
Non-polymers1604
Water19811
1
A: Hemagglutinin
B: MONOCLONAL ANTIBODY H-CHAIN
C: MONOCLONAL ANTIBODY L-CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8934
Polymers104,8533
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Hemagglutinin
E: MONOCLONAL ANTIBODY H-CHAIN
F: MONOCLONAL ANTIBODY L-CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8934
Polymers104,8533
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Hemagglutinin
H: MONOCLONAL ANTIBODY H-CHAIN
I: MONOCLONAL ANTIBODY L-CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8934
Polymers104,8533
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Hemagglutinin
K: MONOCLONAL ANTIBODY H-CHAIN
L: MONOCLONAL ANTIBODY L-CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8934
Polymers104,8533
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.751, 237.814, 94.230
Angle α, β, γ (deg.)90.000, 110.310, 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
MONOCLONAL ANTIBODY H-CHAIN


Mass: 23670.512 Da / Num. of mol.: 4 / Fragment: Fab fragment, heavy chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody
MONOCLONAL ANTIBODY L-CHAIN


Mass: 23015.395 Da / Num. of mol.: 4 / Fragment: Fab fragment, light chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 1.82 Å3/Da / Density % sol: 32.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 3350, 200mM potassium iodide, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.844
11-H, -K, H+L20.156
ReflectionResolution: 2.8→50 Å / Num. all: 73117 / Num. obs: 63466 / % possible obs: 86.8 %
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1 / % possible all: 81.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F15

4f15


Resolution: 2.8→43.49 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.812 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.334 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 3244 5.1 %RANDOM
Rwork0.2317 ---
obs0.2338 63442 76.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.71 Å2 / Biso mean: 22.1224 Å2 / Biso min: 3.41 Å2
Baniso -1Baniso -2Baniso -3
1--4.04 Å20 Å2-2.64 Å2
2---11.06 Å2-0 Å2
3---15.1 Å2
Refinement stepCycle: LAST / Resolution: 2.8→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20059 0 4 11 20074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0220626
X-RAY DIFFRACTIONr_angle_refined_deg2.2421.94228044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.4452603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.96524.065856
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.666153259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1551592
X-RAY DIFFRACTIONr_chiral_restr0.1490.23045
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02115716
LS refinement shellResolution: 2.804→2.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 221 -
Rwork0.153 4053 -
obs--79.77 %

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