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- PDB-5dup: Influenza A virus H5 hemagglutinin globular head in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5dup
TitleInfluenza A virus H5 hemagglutinin globular head in complex with antibody AVFluIgG03
Components
  • AVFluIgG03 Heavy Chain
  • AVFluIgG03 Light Chain
  • Hemagglutinin
KeywordsIMMUNE SYSTEM / Influenza virus / Antibody / Complex / Neutralize
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / 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 / Resolution: 3.052 Å
AuthorsZuo, T. / Sun, J. / Wang, G. / Zhou, P. / Wang, X. / Zhang, L.
CitationJournal: Nat Commun / Year: 2015
Title: Comprehensive analysis of antibody recognition in convalescent humans from highly pathogenic avian influenza H5N1 infection
Authors: Zuo, T. / Sun, J. / Wang, G. / Jiang, L. / Zuo, Y. / Li, D. / Shi, X. / Liu, X. / Fan, S. / Ren, H. / Hu, H. / Sun, L. / Zhou, B. / Liang, M. / Zhou, P. / Wang, X. / Zhang, L.
History
DepositionSep 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin
H: AVFluIgG03 Heavy Chain
L: AVFluIgG03 Light Chain


Theoretical massNumber of molelcules
Total (without water)74,1793
Polymers74,1793
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-27 kcal/mol
Surface area27820 Å2
Unit cell
Length a, b, c (Å)132.664, 132.664, 87.957
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Hemagglutinin


Mass: 26535.771 Da / Num. of mol.: 1 / Fragment: globular head, UNP residues 61-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Anhui/1/2005(H5N1))
Strain: A/Anhui/1/2005(H5N1) / Gene: HA / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q1WDM0
#2: Antibody AVFluIgG03 Heavy Chain


Mass: 24784.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#3: Antibody AVFluIgG03 Light Chain


Mass: 22859.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
Has protein modificationY

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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: 3.01 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→38.94 Å / Num. obs: 16857 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.052→38.938 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.72 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.257 837 4.97 %
Rwork0.199 --
obs0.2073 16853 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.052→38.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 0 0 4703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094822
X-RAY DIFFRACTIONf_angle_d1.3526547
X-RAY DIFFRACTIONf_dihedral_angle_d18.9351718
X-RAY DIFFRACTIONf_chiral_restr0.052719
X-RAY DIFFRACTIONf_plane_restr0.008845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0536-3.24480.39241330.3462644X-RAY DIFFRACTION94
3.2448-3.49510.31121500.25652637X-RAY DIFFRACTION95
3.4951-3.84640.25191370.22622648X-RAY DIFFRACTION95
3.8464-4.40210.26561330.18942677X-RAY DIFFRACTION95
4.4021-5.54260.22931550.15632650X-RAY DIFFRACTION94
5.5426-34.92230.23051290.18662750X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8968-0.21520.71271.0509-0.39170.59990.1370.1603-0.1371-0.0643-0.2841-0.04250.36430.2208-0.00020.50750.03940.0470.66760.0050.592293.527739.1812.6077
20.9311-0.17670.22250.3925-0.34870.9366-0.1354-0.0001-0.07310.20710.0316-0.0942-0.350.0817-0.00020.5144-0.05790.02140.4667-0.02220.626283.075652.926322.0091
32.4583-0.5265-0.34262.0217-0.12871.98990.37690.58040.09870.0215-0.3558-0.0165-0.6148-0.4033-0.00010.66780.0942-0.00110.82720.11440.574269.382471.2305-18.4556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L
2X-RAY DIFFRACTION2chain H
3X-RAY DIFFRACTION3chain A

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