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- PDB-4bsf: Human H7N9 Influenza Virus Haemagglutinin in Complex with Avian R... -

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Basic information

Entry
Database: PDB / ID: 4bsf
TitleHuman H7N9 Influenza Virus Haemagglutinin in Complex with Avian Receptor Analogue 3'-SLN
Components(HAEMAGGLUTININ ...Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / H7N3 / H7N9 / H5N1 / FOWL PLAGUE VIRUS / GLYCOPROTEIN / GLYCOSYLATION / VIRUS RECEPTOR / BIRD FLU / SIALYLLACTOSAMINE / 3SLN / 6SLN / LSTC / PANDEMIC
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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
Similarity search - Function
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 ...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
3'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesINFLUENZA VIRUS A/ANHUI/1/2013
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsXiong, X. / Haire, L.F. / Martin, S.R. / Wharton, S.A. / Daniels, R.S. / Bennett, M.S. / McCauley, J.W. / Collins, P.J. / Walker, P.A. / Skehel, J.J. / Gamblin, S.J.
CitationJournal: Nature / Year: 2013
Title: Receptor Binding by an H7N9 Influenza Virus from Humans
Authors: Xiong, X. / Martin, S.R. / Haire, L.F. / Wharton, S.A. / Daniels, R.S. / Bennett, M.S. / Mccauley, J.W. / Collins, P.J. / Walker, P.A. / Skehel, J.J. / Gamblin, S.J.
History
DepositionJun 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / 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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _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 2.1Dec 20, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,44720
Polymers55,4362
Non-polymers3,01118
Water1,892105
1
A: HAEMAGGLUTININ HA1
B: HAEMAGGLUTININ HA2
hetero molecules

A: HAEMAGGLUTININ HA1
B: HAEMAGGLUTININ HA2
hetero molecules

A: HAEMAGGLUTININ HA1
B: HAEMAGGLUTININ HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,34260
Polymers166,3086
Non-polymers9,03454
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area45360 Å2
ΔGint-561.3 kcal/mol
Surface area58330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.160, 116.160, 294.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-2016-

HOH

21B-2021-

HOH

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Components

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HAEMAGGLUTININ ... , 2 types, 2 molecules AB

#1: Protein HAEMAGGLUTININ HA1


Mass: 34993.559 Da / Num. of mol.: 1
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 19-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA VIRUS A/ANHUI/1/2013 (H7N9) / Description: WHO CHINESE NATIONAL INFLUENZA CENTER / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: M4YV75
#2: Protein HAEMAGGLUTININ HA2


Mass: 20442.463 Da / Num. of mol.: 1
Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 340-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA VIRUS A/ANHUI/1/2013 (H7N9) / Description: WHO CHINESE NATIONAL INFLUENZA CENTER / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: M4YV75

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Sugars , 3 types, 5 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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, 118 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsGLOBAL INITIATIVE ON SHARING ALL INFLUENZA DATA (GISAID). M4YV75 IS THE CLOSEST AVAILABLE UNIPROT MATCH.

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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: 3.55 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growTemperature: 291 K
Details: 291 K, 0.1 M PIPES PH 7.0, 2.2 M AMMONIUM SULFATE, 1% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.76→41.55 Å / Num. obs: 19900 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.77
Reflection shellResolution: 2.76→2.91 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TI8

1ti8


Resolution: 2.76→38.88 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.87 / SU B: 27.965 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R: 0.764 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2764 1023 5.1 %RANDOM
Rwork0.22323 ---
obs0.2259 19059 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.008 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.21 Å20 Å2
2--0.21 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.76→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 181 105 4078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194043
X-RAY DIFFRACTIONr_bond_other_d0.0010.023676
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.9865481
X-RAY DIFFRACTIONr_angle_other_deg0.733.0038424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2835484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27424.513195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44815663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5191528
X-RAY DIFFRACTIONr_chiral_restr0.0630.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02933
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_it0.3660.8861942
X-RAY DIFFRACTIONr_mcbond_other0.3660.8861941
X-RAY DIFFRACTIONr_mcangle_it0.6641.3292424
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6051.5392101
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: 2.76→2.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 74 -
Rwork0.282 1408 -
obs--99.8 %
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)
11.42060.1888-1.18981.6104-0.46263.30670.27290.14010.1220.0529-0.02720.3956-0.4362-0.042-0.24570.1047-0.03160.00190.1296-0.0490.430537.3485-35.0089-5.6258
20.67720.6839-0.3922.2041-2.28538.39950.3415-0.5148-0.13960.9578-0.2515-0.11680.16270.3798-0.090.6593-0.0912-0.04610.5057-0.01160.428239.2864-50.134526.068
32.70070.06370.29782.79161.1715.23370.3523-0.8115-0.15471.04560.1137-0.108-0.20580.416-0.4660.7663-0.2346-0.03060.5261-0.04410.37940.799-44.256431.7621
43.23821.2868-6.01650.5956-2.658112.16320.00760.1401-0.40460.3334-0.1684-0.0541-1.02450.70580.16081.3613-0.80810.19331.4242-0.64920.7347.8191-36.91632.942
52.19271.1748-0.5653.23221.88083.55680.6142-0.1668-0.25521.1205-0.0207-0.39440.11190.8561-0.59350.511-0.2134-0.05440.3894-0.13580.378542.048-45.101317.7901
61.63930.5153-3.41212.2746-1.97837.90710.08640.32840.1254-0.2230.07170.3728-0.1369-0.438-0.15810.1228-0.0344-0.05730.22980.08340.358241.0292-31.2051-17.3341
72.1106-0.88051.68871.97320.46968.59950.00990.76540.1229-1.1525-0.32810.55910.1129-0.77310.31831.13490.0225-0.31341.10340.17930.427240.6791-29.0632-51.8741
85.0015-1.80944.91054.6352-3.721219.0993-0.06250.2483-0.215-0.4662-0.18650.43931.2687-0.34350.2490.5236-0.0846-0.08570.6066-0.06810.528841.6718-39.7406-37.0107
92.00591.5511-0.3152.58210.18128.02480.0118-0.07160.11510.1222-0.1710.2042-0.174-0.24280.15920.02870.02630.00670.08590.00460.36250.7055-30.8756-5.6966
100.93970.72560.85211.50721.79732.8455-0.22911.07910.0424-0.71210.5058-0.147-0.07290.7126-0.27681.260.0769-0.09961.38270.070.203249.7338-34.4466-53.2611
111.24342.3748-1.23154.7021-2.42051.2705-0.07060.41840.041-0.2780.28220.17680.1-0.221-0.21161.6845-0.066-0.3011.8608-0.11840.557543.5194-38.1432-68.8768
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 102
2X-RAY DIFFRACTION2A103 - 124
3X-RAY DIFFRACTION3A125 - 183
4X-RAY DIFFRACTION4A184 - 217
5X-RAY DIFFRACTION5A218 - 268
6X-RAY DIFFRACTION6A269 - 316
7X-RAY DIFFRACTION7B1 - 31
8X-RAY DIFFRACTION8B32 - 59
9X-RAY DIFFRACTION9B60 - 104
10X-RAY DIFFRACTION10B105 - 136
11X-RAY DIFFRACTION11B137 - 170

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