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- PDB-5vag: Crystal structure of H7-specific antibody m826 in complex with th... -

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Basic information

Entry
Database: PDB / ID: 5vag
TitleCrystal structure of H7-specific antibody m826 in complex with the HA1 domain of hemagglutinin from H7N9 influenza virus
Components
  • Heavy chain of antibody m826
  • Hemagglutinin
  • Light chain of antibody m826
KeywordsIMMUNE SYSTEM / hemagglutinin / H7N9
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 / metal ion binding
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
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSong, H. / Ying, T. / Ji, X.
CitationJournal: Cell Host Microbe / Year: 2017
Title: A Potent Germline-like Human Monoclonal Antibody Targets a pH-Sensitive Epitope on H7N9 Influenza Hemagglutinin.
Authors: Yu, F. / Song, H. / Wu, Y. / Chang, S.Y. / Wang, L. / Li, W. / Hong, B. / Xia, S. / Wang, C. / Khurana, S. / Feng, Y. / Wang, Y. / Sun, Z. / He, B. / Hou, D. / Manischewitz, J. / King, L.R. ...Authors: Yu, F. / Song, H. / Wu, Y. / Chang, S.Y. / Wang, L. / Li, W. / Hong, B. / Xia, S. / Wang, C. / Khurana, S. / Feng, Y. / Wang, Y. / Sun, Z. / He, B. / Hou, D. / Manischewitz, J. / King, L.R. / Song, Y. / Min, J.Y. / Golding, H. / Ji, X. / Lu, L. / Jiang, S. / Dimitrov, D.S. / Ying, T.
History
DepositionMar 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Light chain of antibody m826
C: Heavy chain of antibody m826
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,34913
Polymers84,7293
Non-polymers62110
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-1 kcal/mol
Surface area26580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.334, 101.334, 136.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

21B-452-

HOH

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Components

#1: Protein Hemagglutinin


Mass: 35050.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/02/2013(H7N9) / Gene: HA / Production host: Escherichia coli (E. coli) / References: UniProt: R4NN21
#2: Antibody Light chain of antibody m826


Mass: 23382.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Heavy chain of antibody m826


Mass: 26295.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium fluoride, 20% (v/v) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 12, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→37.72 Å / Num. obs: 54391 / % possible obs: 97.1 % / Redundancy: 23.6 % / Net I/σ(I): 29.75
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 7.5 / % possible all: 77.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LN6

4ln6


Resolution: 1.9→37.72 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.83
RfactorNum. reflection% reflection
Rfree0.227 999 1.84 %
Rwork0.1911 --
obs0.1918 54391 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4890 0 40 410 5340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085169
X-RAY DIFFRACTIONf_angle_d1.0747032
X-RAY DIFFRACTIONf_dihedral_angle_d12.8473138
X-RAY DIFFRACTIONf_chiral_restr0.064781
X-RAY DIFFRACTIONf_plane_restr0.006908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9002-2.00030.34181130.31996035X-RAY DIFFRACTION78
2.0003-2.12560.27641410.26977584X-RAY DIFFRACTION97
2.1256-2.28970.2711460.22467798X-RAY DIFFRACTION100
2.2897-2.52010.23831470.21377852X-RAY DIFFRACTION100
2.5201-2.88470.28671480.21457867X-RAY DIFFRACTION100
2.8847-3.63390.22511490.19437970X-RAY DIFFRACTION100
3.6339-37.72790.19381550.15978286X-RAY DIFFRACTION100

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