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- PDB-5e66: The complex structure of Hemagglutinin-esterase-fusion mutant pro... -

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Basic information

Entry
Database: PDB / ID: 5.0E+66
TitleThe complex structure of Hemagglutinin-esterase-fusion mutant protein from the influenza D virus with receptor analog 9-N-Ac-Sia
Components(Hemagglutinin- ...) x 2
KeywordsHYDROLASE / influenza / complex / HEF
Function / homology
Function and homology information


sialate O-acetylesterase activity / sialate O-acetylesterase / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #20 / Haemagglutinin stalk, influenza C / Influenza C hemagglutinin stalk / Haemagglutinin-esterase glycoprotein, haemagglutinin domain / Haemagglutinin-esterase glycoprotein, core / Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein / Hemagglutinin esterase / Ubiquitin Ligase Nedd4; Chain: W; / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B ...Ubiquitin Ligase Nedd4; Chain: W; - #20 / Haemagglutinin stalk, influenza C / Influenza C hemagglutinin stalk / Haemagglutinin-esterase glycoprotein, haemagglutinin domain / Haemagglutinin-esterase glycoprotein, core / Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein / Hemagglutinin esterase / Ubiquitin Ligase Nedd4; Chain: W; / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Single Sheet / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-5KQ / CACODYLATE ION / Hemagglutinin-esterase-fusion glycoprotein
Similarity search - Component
Biological speciesInfluenza D virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSong, H. / Qi, J. / Shi, Y. / Gao, G.F.
CitationJournal: PLoS Pathog. / Year: 2016
Title: An Open Receptor-Binding Cavity of Hemagglutinin-Esterase-Fusion Glycoprotein from Newly-Identified Influenza D Virus: Basis for Its Broad Cell Tropism
Authors: Song, H. / Qi, J. / Khedri, Z. / Diaz, S. / Yu, H. / Chen, X. / Varki, A. / Shi, Y. / Gao, G.F.
History
DepositionOct 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_atom_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 2.1Nov 8, 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 2.2Nov 6, 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-esterase
B: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,50110
Polymers64,0962
Non-polymers3,4058
Water00
1
A: Hemagglutinin-esterase
B: Hemagglutinin-esterase
hetero molecules

A: Hemagglutinin-esterase
B: Hemagglutinin-esterase
hetero molecules

A: Hemagglutinin-esterase
B: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,50230
Polymers192,2876
Non-polymers10,21524
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area43320 Å2
ΔGint67 kcal/mol
Surface area66230 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint22 kcal/mol
Surface area25910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.297, 165.297, 165.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

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Hemagglutinin- ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin-esterase


Mass: 46584.062 Da / Num. of mol.: 1 / Fragment: UNP residues 19-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza D virus (D/swine/Oklahoma/1334/2011)
Strain: D/swine/Oklahoma/1334/2011 / Gene: HEF / Plasmid: PFASTBAC1 / Cell line (production host): HI5 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: K9LG83
#2: Protein Hemagglutinin-esterase


Mass: 17511.521 Da / Num. of mol.: 1 / Fragment: UNP residues 456-621
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza D virus (D/swine/Oklahoma/1334/2011)
Strain: D/swine/Oklahoma/1334/2011 / Gene: HEF / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: K9LG83

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Sugars , 4 types, 7 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-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.: 3 / Source method: obtained synthetically
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
#6: Sugar ChemComp-5KQ / (6R)-5-acetamido-6-[(1S,2S)-3-acetamido-1,2-dihydroxypropyl]-3,5-dideoxy-beta-L-threo-hex-2-ulopyranosonic acid / (6R)-5-(acetylamino)-6-[(1S,2S)-3-(acetylamino)-1,2-dihydroxypropyl]-3,5-dideoxy-beta-L-threo-hex-2-ulopyranosonic acid / (6R)-5-acetamido-6-[(1S,2S)-3-acetamido-1,2-dihydroxypropyl]-3,5-dideoxy-beta-L-threo-hex-2-ulosonic acid / (6R)-5-acetamido-6-[(1S,2S)-3-acetamido-1,2-dihydroxypropyl]-3,5-dideoxy-L-threo-hex-2-ulosonic acid / (6R)-5-acetamido-6-[(1S,2S)-3-acetamido-1,2-dihydroxypropyl]-3,5-dideoxy-threo-hex-2-ulosonic acid


Type: L-saccharide, beta linking / Mass: 350.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H22N2O9
IdentifierTypeProgram
a-D-Neup5Ac9NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#7: 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.: 1 / Source method: obtained synthetically / 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, 1 molecules

#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2

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Details

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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M PCTP (Propionic acid, Cacodylate, Bis-tris propane system) buffer pH 8.5, 22.5 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 13867 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 23.3
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.858 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5.0E+64 / Resolution: 3.1→38.961 Å / SU ML: 0.56 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 31.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 666 4.8 %
Rwork0.2336 --
obs0.2351 13867 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→38.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4353 0 222 0 4575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134675
X-RAY DIFFRACTIONf_angle_d1.546317
X-RAY DIFFRACTIONf_dihedral_angle_d16.0221680
X-RAY DIFFRACTIONf_chiral_restr0.381708
X-RAY DIFFRACTIONf_plane_restr0.013805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0941-3.33290.40431380.33452617X-RAY DIFFRACTION100
3.3329-3.66810.32321110.29682629X-RAY DIFFRACTION100
3.6681-4.19830.30681400.25352601X-RAY DIFFRACTION100
4.1983-5.28740.26771400.21872654X-RAY DIFFRACTION100
5.2874-38.96390.21041370.20162700X-RAY DIFFRACTION99
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)
11.44810.40590.28321.72110.460.7909-0.1418-0.1013-0.15930.28270.0862-0.13110.14360.24720.08880.79160.17440.08290.77490.18830.64412.503-16.475-28.4738
22.0777-0.8678-0.2821.1706-0.62791.38030.24610.2704-0.9663-0.7161-0.30190.40190.3411-0.84350.18941.04590.0406-0.03370.9991-0.09491.1105-36.1964-52.8196-51.1321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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