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- PDB-4bsd: Human H7N9 Influenza Virus Haemagglutinin (with Asn-133 Glycosyla... -

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Basic information

Entry
Database: PDB / ID: 4bsd
TitleHuman H7N9 Influenza Virus Haemagglutinin (with Asn-133 Glycosylation) in Complex with Avian Receptor Analogue 3'-SLN
Components(HEMAGGLUTININ) x 2
KeywordsVIRAL PROTEIN / FOWL PLAGUE VIRUS / SIALYLLACTOSAMINE
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: 2.4 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 / pdbx_struct_special_symmetry / 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: HEMAGGLUTININ
B: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,80922
Polymers55,4802
Non-polymers3,32920
Water2,522140
1
A: HEMAGGLUTININ
B: HEMAGGLUTININ
hetero molecules

A: HEMAGGLUTININ
B: HEMAGGLUTININ
hetero molecules

A: HEMAGGLUTININ
B: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,42666
Polymers166,4406
Non-polymers9,98660
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 area46900 Å2
ΔGint-590.1 kcal/mol
Surface area59090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.950, 115.950, 295.380
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-1176-

SO4

21A-2019-

HOH

31B-2021-

HOH

41B-2028-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HEMAGGLUTININ / / HAEMAGGLUTININ HA1


Mass: 35037.613 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 HEMAGGLUTININ / / 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, 6 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.: 4
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, 154 molecules

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


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsGLOBAL INITIATIVE ON SHARING ALL INFLUENZA DATA (GISAID) V10L, A125T SUBSTITUTIONS ON GISAID- ...GLOBAL INITIATIVE ON SHARING ALL INFLUENZA DATA (GISAID) V10L, A125T SUBSTITUTIONS ON GISAID-EPI439507 AMINO ACID SEQUENCE WERE OBSERVED

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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 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→59.56 Å / Num. obs: 30146 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.37
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1 / % possible all: 98.9

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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: 2.4→59.56 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.901 / SU B: 20.172 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27691 1467 5.1 %RANDOM
Rwork0.23682 ---
obs0.23887 27439 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.762 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.24 Å20 Å2
2--0.24 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.4→59.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 200 140 4135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194065
X-RAY DIFFRACTIONr_bond_other_d0.0010.023689
X-RAY DIFFRACTIONr_angle_refined_deg1.0321.9925512
X-RAY DIFFRACTIONr_angle_other_deg0.7053.0038451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80924.513195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24115665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1831528
X-RAY DIFFRACTIONr_chiral_restr0.0580.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024563
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_it0.5061.81942
X-RAY DIFFRACTIONr_mcbond_other0.5061.81941
X-RAY DIFFRACTIONr_mcangle_it0.9072.72424
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.342.4252121
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 88 -
Rwork0.388 1869 -
obs--87.92 %
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)
10.99260.2128-0.85431.1916-0.40372.52610.23010.01750.08210.1359-0.01030.3047-0.19010.0247-0.21970.088-0.05110.02840.1261-0.04410.295937.479-36.324-3.6213
23.3470.20520.33151.22040.95434.80890.2692-0.7183-0.06170.83440.0698-0.00230.14250.0331-0.3390.8343-0.2001-0.00610.4374-0.02640.326640.3274-44.97632.7885
34.32690.7521-3.36180.24430.10567.5567-0.38810.5014-0.7446-0.04080.2065-0.1877-0.29390.57220.18150.9718-0.57150.0670.7516-0.21230.547647.7001-36.854732.9369
41.40891.2303-0.10463.04221.62951.97530.3229-0.0891-0.23960.90870.0759-0.45540.24890.5198-0.39870.4258-0.1839-0.03510.3312-0.09760.347941.8951-45.037617.8515
51.0858-0.4054-2.31941.6178-0.2865.89880.03290.2409-0.0618-0.10280.05960.4067-0.0155-0.5872-0.09250.0555-0.078-0.03680.18690.05340.276940.9452-31.1201-17.2821
61.1954-1.88980.06163.1569-0.09596.86820.25250.3769-0.0277-0.4757-0.28090.2472-0.0537-0.59950.02840.5734-0.0882-0.23250.80660.24490.386540.5835-28.9116-51.8048
75.2477-1.61196.53184.2932-3.503322.5919-0.0102-0.1616-0.2670.02930.24980.20930.6305-0.8176-0.23960.265-0.0981-0.05040.3429-0.02680.450441.5732-39.5857-36.798
81.58710.6332-0.14222.1506-0.64876.37880.115-0.09560.09290.2061-0.12860.1714-0.0813-0.44080.01360.0223-0.01060.01560.07230.01090.268850.5997-30.9149-5.562
90.6841-0.4359-1.45352.4321.60865.38060.03170.39670.0934-0.76060.203-0.18750.07110.3296-0.23470.62570.0041-0.1080.84410.02440.254449.5582-34.3361-53.114
108.37893.0833-2.74635.1153-4.0575.1525-0.21710.9264-0.0167-1.04450.28180.75990.1444-0.4863-0.06461.1234-0.0777-0.31381.1344-0.08870.415543.3597-37.8661-68.7231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 114
2X-RAY DIFFRACTION2A115 - 183
3X-RAY DIFFRACTION3A184 - 217
4X-RAY DIFFRACTION4A218 - 268
5X-RAY DIFFRACTION5A269 - 317
6X-RAY DIFFRACTION6B1 - 31
7X-RAY DIFFRACTION7B32 - 59
8X-RAY DIFFRACTION8B60 - 104
9X-RAY DIFFRACTION9B105 - 136
10X-RAY DIFFRACTION10B137 - 170

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