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- PDB-4uo7: Structure of the A_Canine_Colorado_17864_06 H3 haemagglutinin in ... -

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Basic information

Entry
Database: PDB / ID: 4uo7
TitleStructure of the A_Canine_Colorado_17864_06 H3 haemagglutinin in complex with 6SO4 Sialyl Lewis X
Components(HAEMAGGLUTININ ...) x 2
KeywordsVIRAL PROTEIN / EQUINE / CANINE
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 / membrane
Similarity search - Function
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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVachieri, S.G. / Collins, P.J. / Haire, L.F. / Ogrodowicz, R.W. / Martin, S.R. / Walker, P.A. / Xiong, X. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Recent Evolution of Equine Influenza and the Origin of Canine Influenza.
Authors: Collins, P.J. / Vachieri, S.G. / Haire, L.F. / Ogrodowicz, R.W. / Martin, S.R. / Walker, P.A. / Xiong, X. / Gamblin, S.J. / Skehel, J.J.
History
DepositionMay 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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 / 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 / _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.id / _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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: HAEMAGGLUTININ HA1
B: HAEMAGGLUTININ HA2
C: HAEMAGGLUTININ HA1
D: HAEMAGGLUTININ HA2
E: HAEMAGGLUTININ HA1
F: HAEMAGGLUTININ HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,23428
Polymers169,8586
Non-polymers10,37622
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44770 Å2
ΔGint-96.5 kcal/mol
Surface area61510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.306, 348.485, 95.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2003-

HOH

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Components

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HAEMAGGLUTININ ... , 2 types, 6 molecules ACEBDF

#1: Protein HAEMAGGLUTININ HA1


Mass: 36345.984 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS (A/CANINE/COLORADO/17864/2006(H3N8))
Description: DR. EDWARD J. DUBOVI AND DR. COLIN PARRISH, CORNELL UNIVERSITY, ITHACA, NY, USA
Plasmid: PACGP67 DERIVATIVE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: E0UVR5
#2: Protein HAEMAGGLUTININ HA2


Mass: 20273.373 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS (A/CANINE/COLORADO/17864/2006(H3N8))
Description: DR. EDWARD J. DUBOVI AND DR. COLIN PARRISH, CORNELL UNIVERSITY, ITHACA, NY, USA
Plasmid: PACGP67 DERIVATIVE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: E0UVR5

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Sugars , 5 types, 16 molecules

#3: 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.: 7
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)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 2
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)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose


Type: oligosaccharide / Mass: 900.807 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAc[6S]b1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O_6*OSO/3=O/3=O][a1221m-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a3-b1_a4-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc6SO3]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#8: 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: 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 , 2 types, 144 molecules

#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 4.26 Å3/Da / Density % sol: 71.17 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→47.72 Å / Num. obs: 53827 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.4
Reflection shellResolution: 3→3.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UO4

4uo4


Resolution: 3→174.24 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.859 / SU B: 48.851 / SU ML: 0.386 / Cross valid method: THROUGHOUT / ESU R: 2.353 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27595 2728 5.1 %RANDOM
Rwork0.23297 ---
obs0.23516 50896 94.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.186 Å2
Baniso -1Baniso -2Baniso -3
1-4.63 Å20 Å20 Å2
2---5.1 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 3→174.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11611 0 681 138 12430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01912576
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211395
X-RAY DIFFRACTIONr_angle_refined_deg1.2292.00117106
X-RAY DIFFRACTIONr_angle_other_deg0.827326110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92251474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79324.606584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.932152014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3861575
X-RAY DIFFRACTIONr_chiral_restr0.1380.21980
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022864
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0023.7315920
X-RAY DIFFRACTIONr_mcbond_other1.0013.7325919
X-RAY DIFFRACTIONr_mcangle_it1.7535.5967385
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1993.9886656
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 195 -
Rwork0.325 3801 -
obs--96.71 %
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)
10.978-1.3931-0.04895.0855-0.13340.62410.01360.08250.0826-0.39420.00540.03150.038-0.1262-0.01890.1913-0.0235-0.08480.2136-0.00650.048915.225892.5288-15.5984
20.72820.4573-0.24614.3969-1.35041.0568-0.00120.02780.08870.07520.1023-0.2359-0.08360.0821-0.10110.172-0.01910.02180.21750.00380.077346.244192.5173-5.2206
30.78780.63270.06885.06640.93110.8143-0.0996-0.13220.05910.17550.10840.27-0.0798-0.0081-0.00880.2395-0.0259-0.00020.2143-0.01790.02621.771293.095216.5177
40.64220.87340.15647.55720.72070.154-0.04050.076-0.3213-0.2660.08390.33810.1495-0.0139-0.04340.605-0.0565-0.06960.1805-0.05870.269520.93441.7958-10.3683
50.6169-1.1272-0.2037.44260.11490.2755-0.03280.0177-0.2665-0.2016-0.0486-0.34980.22710.1320.08140.42090.0145-0.01540.2475-0.01690.25939.434441.8353-1.6479
60.47260.20190.07046.0688-0.91390.74260.0686-0.1902-0.27170.3406-0.13670.11910.3133-0.00530.06820.4962-0.08670.06870.17620.05140.26322.692242.00839.9629
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 704
2X-RAY DIFFRACTION2C8 - 704
3X-RAY DIFFRACTION3E8 - 704
4X-RAY DIFFRACTION4B1 - 174
5X-RAY DIFFRACTION5D1 - 175
6X-RAY DIFFRACTION6F1 - 174

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