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- PDB-3zp6: INFLUENZA VIRUS (VN1194) H5 E190D mutant HA with LSTc -

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Basic information

Entry
Database: PDB / ID: 3zp6
TitleINFLUENZA VIRUS (VN1194) H5 E190D mutant HA with LSTc
Components(HAEMAGGLUTININ) x 2
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


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; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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 / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.6 Å
AuthorsLiu, J. / Stevens, D.J. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Virology / Year: 2013
Title: Changes in the Hemagglutinin of H5N1 Viruses During Human Infection - Influence on Receptor Binding.
Authors: Crusat, M. / Liu, J. / Palma, A.S. / Childs, R.A. / Liu, Y. / Wharton, S.A. / Lin, Y.P. / Coombs, P.J. / Martin, S.R. / Matrosovich, M. / Chen, Z. / Stevens, D.J. / Hien, V.M. / Thanh, T.T. ...Authors: Crusat, M. / Liu, J. / Palma, A.S. / Childs, R.A. / Liu, Y. / Wharton, S.A. / Lin, Y.P. / Coombs, P.J. / Martin, S.R. / Matrosovich, M. / Chen, Z. / Stevens, D.J. / Hien, V.M. / Thanh, T.T. / Nhu, L.N.T. / Nguyet, L.A. / Ha, D.Q. / van Doorn, H.R. / Hien, T.T. / Conradt, H.S. / Kiso, M. / Gamblin, S.J. / Chai, W. / Skehel, J.J. / Hay, A.J. / Farrar, J. / De Jong, M.D. / Feizi, T.
History
DepositionFeb 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation_author / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _citation_author.name / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 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

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Assembly

Deposited unit
E: HAEMAGGLUTININ
F: HAEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7855
Polymers56,8712
Non-polymers9143
Water2,414134
1
E: HAEMAGGLUTININ
F: HAEMAGGLUTININ
hetero molecules

E: HAEMAGGLUTININ
F: HAEMAGGLUTININ
hetero molecules

E: HAEMAGGLUTININ
F: HAEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,35515
Polymers170,6136
Non-polymers2,7419
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area31020 Å2
ΔGint-120.9 kcal/mol
Surface area59640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.391, 101.391, 450.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11F-2021-

HOH

21F-2034-

HOH

31F-2043-

HOH

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Components

#1: Protein HAEMAGGLUTININ


Mass: 38480.773 Da / Num. of mol.: 1
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 1-340
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: VIETNAM/1194/2004 (H5N1)
Description: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC)
Variant: VN/1194/04/NIBRG14 VACCINE STRAIN / Organ (production host): EGG / Production host: GALLUS GALLUS (chicken) / References: UniProt: Q6DQ34
#2: Protein HAEMAGGLUTININ


Mass: 18390.303 Da / Num. of mol.: 1
Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-506
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: VIETNAM/1194/2004 (H5N1)
Description: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC)
Variant: VN/1194/04/NIBRG14 VACCINE STRAIN / Organ (production host): EGG / Production host: GALLUS GALLUS (chicken) / References: UniProt: Q6DQ34
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][<C3O1>]{[(1+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69.05 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Type: DIAMOND / Wavelength: 0.9715
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9715 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 27780 / % possible obs: 99.1 % / Observed criterion σ(I): 4.3 / Redundancy: 10.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.8

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Processing

SoftwareName: REFMAC / Version: 5 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 4.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rwork0.223 --
obs-27780 99.1 %
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 53 134 4007

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