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- PDB-5thb: Crystal structure of H10 hemagglutinin mutant (T193D-Q226L-G228S)... -

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Basic information

Entry
Database: PDB / ID: 5thb
TitleCrystal structure of H10 hemagglutinin mutant (T193D-Q226L-G228S) from Jiangxi-Donghu (2013) H10N8 influenza virus
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / Influenza virus / hemagglutinin / HA / H10N8 (2013) / Receptor specificity
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / 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
Haemagglutinin, influenzavirus 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 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
Hemagglutinin / Hemagglutinin / Hemagglutinin HA2 chain
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsTzarum, N. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI114730 United States
CitationJournal: Cell Rep / Year: 2017
Title: The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus.
Authors: Tzarum, N. / de Vries, R.P. / Peng, W. / Thompson, A.J. / Bouwman, K.M. / McBride, R. / Yu, W. / Zhu, X. / Verheije, M.H. / Paulson, J.C. / Wilson, I.A.
History
DepositionSep 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_validate_close_contact / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,23013
Polymers167,9516
Non-polymers2,2797
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34800 Å2
ΔGint-119 kcal/mol
Surface area57360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.826, 241.286, 70.063
Angle α, β, γ (deg.)90.00, 111.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain


Mass: 35284.852 Da / Num. of mol.: 3 / Mutation: D190T, Q223L, G225S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: Jiangxi-Donghu (2013) H10N8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X252, UniProt: A0A059T4A1*PLUS
#2: Protein Hemagglutinin HA2 chain


Mass: 20698.766 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: Jiangxi-Donghu (2013) H10N8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X253, UniProt: A0A059T4A1*PLUS

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Sugars , 3 types, 7 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 5
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

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Non-polymers , 1 types, 637 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M NaCl, 10% (w/v) PEG 8000, 0.1M CHES pH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.41→50 Å / Num. obs: 74001 / % possible obs: 98.1 % / Redundancy: 3.8 % / Rsym value: 0.08 / Net I/σ(I): 18.7
Reflection shellResolution: 2.41→2.45 Å / % possible obs: 98.5 % / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.7 / CC1/2: 0.942

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TGO

5tgo


Resolution: 2.41→33.055 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.49
RfactorNum. reflection% reflection
Rfree0.2301 3706 5.01 %
Rwork0.1804 --
obs0.1829 73945 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.41→33.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11439 0 148 637 12224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111831
X-RAY DIFFRACTIONf_angle_d2.20716004
X-RAY DIFFRACTIONf_dihedral_angle_d15.4254326
X-RAY DIFFRACTIONf_chiral_restr0.4841774
X-RAY DIFFRACTIONf_plane_restr0.0112091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4026-2.43420.27921010.21799X-RAY DIFFRACTION64
2.4342-2.46750.28591500.21052705X-RAY DIFFRACTION99
2.4675-2.50280.31051380.21072779X-RAY DIFFRACTION99
2.5028-2.54010.27581470.21412723X-RAY DIFFRACTION99
2.5401-2.57980.2991410.20832760X-RAY DIFFRACTION98
2.5798-2.62210.24361670.20242708X-RAY DIFFRACTION98
2.6221-2.66730.29391660.20992712X-RAY DIFFRACTION98
2.6673-2.71570.26141420.20212720X-RAY DIFFRACTION98
2.7157-2.7680.24311360.19352737X-RAY DIFFRACTION98
2.768-2.82440.2651180.19882702X-RAY DIFFRACTION96
2.8244-2.88580.24831550.20432761X-RAY DIFFRACTION99
2.8858-2.95290.27281450.20942734X-RAY DIFFRACTION99
2.9529-3.02670.3051560.20282787X-RAY DIFFRACTION99
3.0267-3.10850.25761510.20832702X-RAY DIFFRACTION98
3.1085-3.19990.24221210.20062792X-RAY DIFFRACTION98
3.1999-3.30310.26141500.20412705X-RAY DIFFRACTION98
3.3031-3.4210.25811280.19472725X-RAY DIFFRACTION97
3.421-3.55780.21831580.18552696X-RAY DIFFRACTION97
3.5578-3.71950.21871470.17282759X-RAY DIFFRACTION99
3.7195-3.91530.21291470.16362745X-RAY DIFFRACTION99
3.9153-4.16020.20861410.1562765X-RAY DIFFRACTION98
4.1602-4.48070.19391430.14052718X-RAY DIFFRACTION97
4.4807-4.93030.15011270.13992724X-RAY DIFFRACTION97
4.9303-5.64060.17161590.14732749X-RAY DIFFRACTION99
5.6406-7.0950.20481310.16642750X-RAY DIFFRACTION97
7.095-33.05810.17351410.15822782X-RAY DIFFRACTION98

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