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- PDB-5e64: Hemagglutinin-esterase-fusion protein structure of influenza D virus -

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Basic information

Entry
Database: PDB / ID: 5.0E+64
TitleHemagglutinin-esterase-fusion protein structure of influenza D virus
Components(Hemagglutinin- ...) x 2
KeywordsHYDROLASE / influenza virus / HEF / surface
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
CACODYLATE ION / Hemagglutinin-esterase-fusion glycoprotein
Similarity search - Component
Biological speciesInfluenza D virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / 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_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 13, 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
C: Hemagglutinin-esterase
D: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,24816
Polymers128,1914
Non-polymers6,05712
Water10,196566
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)202,34624
Polymers192,2876
Non-polymers10,05918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area46300 Å2
ΔGint94 kcal/mol
Surface area66750 Å2
MethodPISA
2
C: Hemagglutinin-esterase
D: Hemagglutinin-esterase
hetero molecules

C: Hemagglutinin-esterase
D: Hemagglutinin-esterase
hetero molecules

C: Hemagglutinin-esterase
D: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,40024
Polymers192,2876
Non-polymers8,11318
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area42290 Å2
ΔGint58 kcal/mol
Surface area67310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.221, 165.221, 165.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Hemagglutinin- ... , 2 types, 4 molecules ACBD

#1: Protein Hemagglutinin-esterase


Mass: 46584.062 Da / Num. of mol.: 2 / 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.: 2 / 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 , 3 types, 10 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.: 3
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.: 5 / 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-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: 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 , 2 types, 568 molecules

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


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
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: Oct 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 58686 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 19.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.524 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLC

1flc


Resolution: 2.4→47.7 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 2965 5.05 %
Rwork0.201 --
obs0.203 58686 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8695 0 392 566 9653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069323
X-RAY DIFFRACTIONf_angle_d1.29912641
X-RAY DIFFRACTIONf_dihedral_angle_d14.6783422
X-RAY DIFFRACTIONf_chiral_restr0.051440
X-RAY DIFFRACTIONf_plane_restr0.0061606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4016-2.4410.30651500.22752621X-RAY DIFFRACTION100
2.441-2.4830.27731390.22232655X-RAY DIFFRACTION100
2.483-2.52820.30571430.21752598X-RAY DIFFRACTION100
2.5282-2.57680.27371560.21952629X-RAY DIFFRACTION100
2.5768-2.62940.31541270.22192641X-RAY DIFFRACTION100
2.6294-2.68660.27781420.21672611X-RAY DIFFRACTION100
2.6866-2.74910.25981390.21742657X-RAY DIFFRACTION100
2.7491-2.81780.27171250.22462626X-RAY DIFFRACTION100
2.8178-2.8940.28491430.21252643X-RAY DIFFRACTION100
2.894-2.97910.27271750.21062620X-RAY DIFFRACTION100
2.9791-3.07530.26131540.20962629X-RAY DIFFRACTION100
3.0753-3.18520.26031310.20962664X-RAY DIFFRACTION100
3.1852-3.31270.27051560.212600X-RAY DIFFRACTION100
3.3127-3.46340.25781460.20222646X-RAY DIFFRACTION100
3.4634-3.64590.26131490.1912660X-RAY DIFFRACTION100
3.6459-3.87420.21361180.18242659X-RAY DIFFRACTION100
3.8742-4.17320.16971310.17542689X-RAY DIFFRACTION100
4.1732-4.59290.17991260.15872681X-RAY DIFFRACTION100
4.5929-5.25680.19471480.16492674X-RAY DIFFRACTION100
5.2568-6.62010.25811290.20642730X-RAY DIFFRACTION100
6.6201-47.70460.24561380.23722788X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -6.9429 Å / Origin y: 2.2969 Å / Origin z: -39.7052 Å
111213212223313233
T0.0776 Å20.0019 Å20.0047 Å2-0.0962 Å20.0128 Å2--0.0955 Å2
L0.0514 °20.0069 °20.0049 °2-0.1226 °2-0.0895 °2--0.0472 °2
S-0.003 Å °0.024 Å °0.0036 Å °-0.0216 Å °-0.0027 Å °-0.0049 Å °0.0088 Å °0.0216 Å °-0.0003 Å °
Refinement TLS groupSelection details: ALL

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