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- PDB-1flc: X-RAY STRUCTURE OF THE HAEMAGGLUTININ-ESTERASE-FUSION GLYCOPROTEI... -

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Basic information

Entry
Database: PDB / ID: 1flc
TitleX-RAY STRUCTURE OF THE HAEMAGGLUTININ-ESTERASE-FUSION GLYCOPROTEIN OF INFLUENZA C VIRUS
Components(HAEMAGGLUTININ-ESTERASE-FUSION GLYCOPROTEIN) x 2
KeywordsHYDROLASE / ESTERASE / RECEPTOR BINDING / MEMBRANE FUSION / VIRUS / INFLUENZA
Function / homology
Function and homology information


sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase / viral budding from plasma membrane / endocytosis involved in viral entry into 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 ...sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase / viral budding from plasma membrane / endocytosis involved in viral entry into 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
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, influenzavirus A/B / Viral capsid/haemagglutinin protein / Single Sheet / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Hemagglutinin-esterase-fusion glycoprotein
Similarity search - Component
Biological speciesInfluenza C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 3.2 Å
AuthorsRosenthal, P.B. / Zhang, X. / Formanowski, F. / Fitz, W. / Wong, C.H. / Meier-Ewert, H. / Skehel, J.J. / Wiley, D.C.
CitationJournal: Nature / Year: 1998
Title: Structure of the haemagglutinin-esterase-fusion glycoprotein of influenza C virus.
Authors: Rosenthal, P.B. / Zhang, X.
History
DepositionFeb 22, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
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 / database_PDB_caveat / 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_chiral / 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 / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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
A: HAEMAGGLUTININ-ESTERASE-FUSION GLYCOPROTEIN
B: HAEMAGGLUTININ-ESTERASE-FUSION GLYCOPROTEIN
C: HAEMAGGLUTININ-ESTERASE-FUSION GLYCOPROTEIN
D: HAEMAGGLUTININ-ESTERASE-FUSION GLYCOPROTEIN
E: HAEMAGGLUTININ-ESTERASE-FUSION GLYCOPROTEIN
F: HAEMAGGLUTININ-ESTERASE-FUSION GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,42321
Polymers201,6256
Non-polymers8,79815
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41110 Å2
ΔGint-38 kcal/mol
Surface area72290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.400, 155.400, 414.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.546421, -0.051165, 0.834464), (0.764319, -0.373731, -0.525426), (0.338723, 0.926131, -0.165943)11.46942, 15.63929, -29.80567
2given(0.546417, 0.76482, 0.341354), (-0.048534, -0.377932, 0.924611), (0.836076, -0.521792, -0.169364)-7.99589, 34.09477, -6.44017

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Components

#1: Protein HAEMAGGLUTININ-ESTERASE-FUSION GLYCOPROTEIN


Mass: 48230.699 Da / Num. of mol.: 3 / Fragment: HEF1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza C virus (C/Johannesburg/1/66)
Genus: Influenzavirus C / Species: Influenza C virus / Strain: C/JOHANNESBURG/1/66 / References: UniProt: P07975
#2: Protein HAEMAGGLUTININ-ESTERASE-FUSION GLYCOPROTEIN


Mass: 18977.541 Da / Num. of mol.: 3 / Fragment: HEF2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza C virus (C/Johannesburg/1/66)
Genus: Influenzavirus C / Species: Influenza C virus / Strain: C/JOHANNESBURG/1/66 / References: GenBank: 325318, UniProt: P07975*PLUS
#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.2 Å3/Da / Density % sol: 76 %
Crystal growpH: 7.1 / Details: pH 7.10
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlprotein1drop
210 mMTris-HCl1drop
3140 mM1dropNaCl
410 mM1dropCaCl2
50.1 %1dropNaN3
656-60 %satammonium sulfate1reservoir
710 mMTris-HCl1reservoir
8140 mM1reservoirNaCl
910 mM1reservoirCaCl2
100.1 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 3.2→15 Å / Num. obs: 80900 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 40 Å2 / Rsym value: 0.1 / Net I/σ(I): 12
Reflection shellResolution: 3.2→10 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 12 / Rsym value: 0.3 / % possible all: 91
Reflection
*PLUS
Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 91 %

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
X-PLOR3.54refinement
RefinementMethod to determine structure: SIR / Resolution: 3.2→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.267 -5 %RANDOM
Rwork0.223 ---
obs0.223 80000 99 %-
Displacement parametersBiso mean: 40 Å2
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13700 0 585 0 14285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS

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