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- PDB-5dum: Crystal structure of influenza A virus H5 hemagglutinin globular ... -

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Basic information

Entry
Database: PDB / ID: 5dum
TitleCrystal structure of influenza A virus H5 hemagglutinin globular head in complex with the Fab of antibody 65C6
Components
  • 65C6 Heavy Chain
  • 65C6 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 speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.003 Å
AuthorsSun, J. / Zuo, T. / Wang, G. / Zhou, P. / Zhang, L. / Wang, X.
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 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 65C6 Heavy Chain
L: 65C6 Light Chain
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1075
Polymers75,6653
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-21 kcal/mol
Surface area28770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.539, 92.981, 134.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody 65C6 Heavy Chain


Mass: 25716.766 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)
#2: Antibody 65C6 Light Chain


Mass: 23412.010 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: Protein Hemagglutinin


Mass: 26535.771 Da / Num. of mol.: 1
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
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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
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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 2% w/v Polyethylene glycol 400, 0.1M Imidazole pH7.0, 24% w/v Polyethylene glycol monomethyl ether 5000

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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: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 16304 / % possible obs: 99.8 % / Redundancy: 5.8 % / Net I/σ(I): 13.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.003→36.13 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2687 796 4.88 %
Rwork0.2154 --
obs0.218 16304 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.003→36.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4887 0 28 0 4915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115060
X-RAY DIFFRACTIONf_angle_d1.3836885
X-RAY DIFFRACTIONf_dihedral_angle_d15.0191801
X-RAY DIFFRACTIONf_chiral_restr0.052764
X-RAY DIFFRACTIONf_plane_restr0.006874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0033-3.19130.34641150.28652485X-RAY DIFFRACTION96
3.1913-3.43760.31881470.25232525X-RAY DIFFRACTION100
3.4376-3.78320.31391320.22852570X-RAY DIFFRACTION100
3.7832-4.32980.291190.2192595X-RAY DIFFRACTION100
4.3298-5.45210.22351440.18532610X-RAY DIFFRACTION100
5.4521-36.13280.24571390.20492723X-RAY DIFFRACTION99

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