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- PDB-4hkx: Influenza hemagglutinin in complex with CH67 Fab -

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Basic information

Entry
Database: PDB / ID: 4hkx
TitleInfluenza hemagglutinin in complex with CH67 Fab
Components
  • CH67 heavy chain
  • CH67 light chain
  • Hemagglutinin HA1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Fab fragment / VIRAL PROTEIN-IMMUNE SYSTEM complex
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
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSchmidt, A.G. / Harrison, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody.
Authors: Schmidt, A.G. / Xu, H. / Khan, A.R. / O'Donnell, T. / Khurana, S. / King, L.R. / Manischewitz, J. / Golding, H. / Suphaphiphat, P. / Carfi, A. / Settembre, E.C. / Dormitzer, P.R. / Kepler, T. ...Authors: Schmidt, A.G. / Xu, H. / Khan, A.R. / O'Donnell, T. / Khurana, S. / King, L.R. / Manischewitz, J. / Golding, H. / Suphaphiphat, P. / Carfi, A. / Settembre, E.C. / Dormitzer, P.R. / Kepler, T.B. / Zhang, R. / Moody, M.A. / Haynes, B.F. / Liao, H.X. / Shaw, D.E. / Harrison, S.C.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Sep 25, 2013Group: Structure summary
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Hemagglutinin HA1
A: CH67 heavy chain
B: CH67 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0375
Polymers72,5953
Non-polymers4422
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.099, 69.815, 80.343
Angle α, β, γ (deg.)90.00, 107.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Hemagglutinin HA1


Mass: 24890.701 Da / Num. of mol.: 1 / Fragment: UNP residues 65-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA1 / Plasmid: pFastBac / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A7UPX0
#2: Antibody CH67 heavy chain


Mass: 24903.875 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Antibody CH67 light chain


Mass: 22800.078 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3.34 Å3/Da / Density % sol: 63.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 46% PEG400, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2012
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 65129 / Num. obs: 60500 / % possible obs: 91.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 41.26 Å2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.111 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8353 / SU ML: 0.29 / σ(F): 1.37 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 1735 5.21 %
Rwork0.1866 --
obs0.1883 33323 99.89 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.528 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 152.56 Å2 / Biso mean: 46.5448 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--12.6628 Å20 Å2-0.3653 Å2
2--20.5738 Å20 Å2
3----7.911 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4919 0 28 252 5199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085087
X-RAY DIFFRACTIONf_angle_d1.0876932
X-RAY DIFFRACTIONf_chiral_restr0.07764
X-RAY DIFFRACTIONf_plane_restr0.005891
X-RAY DIFFRACTIONf_dihedral_angle_d14.261813
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.57360.32771410.235126032744100
2.5736-2.65660.24561510.214926102761100
2.6566-2.75150.26511460.20226192765100
2.7515-2.86170.25211520.198225992751100
2.8617-2.99180.26471570.206926022759100
2.9918-3.14950.25311340.199226502784100
3.1495-3.34660.25591270.195426502777100
3.3466-3.60480.22011450.183826052750100
3.6048-3.96710.19011560.17626332789100
3.9671-4.54010.19371330.154226522785100
4.5401-5.71610.17881370.168626782815100
5.7161-35.11480.20661560.20422687284399

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