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- PDB-4bh1: H5 (tyTy) Influenza Virus Haemagglutinin in Complex with Avian Re... -

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Basic information

Entry
Database: PDB / ID: 4bh1
TitleH5 (tyTy) Influenza Virus Haemagglutinin in Complex with Avian Receptor Analogue 3'-SLN
Components(HEMAGGLUTININ) x 2
KeywordsVIRAL PROTEIN / N-GLYCOSYLATION / VIRUS RECEPTOR / BIRD FLU
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 / PHOSPHATE ION / Hemagglutinin
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsXiong, X. / Coombs, P.J. / Martin, S.R. / Liu, J. / Xiao, H. / McCauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. ...Xiong, X. / Coombs, P.J. / Martin, S.R. / Liu, J. / Xiao, H. / McCauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. / Skehel, J.J. / Gamblin, S.J.
CitationJournal: Nature / Year: 2013
Title: Receptor Binding by a Ferret-Transmissible H5 Avian Influenza Virus
Authors: Xiong, X. / Coombs, P.J. / R Martin, S. / Liu, J. / Xiao, H. / Mccauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. / Skehel, J.J. / Gamblin, S.J.
History
DepositionMar 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2May 15, 2013Group: Database references
Revision 1.3May 22, 2013Group: Database references
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 / 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_database_status.status_code_sf / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMAGGLUTININ
B: HEMAGGLUTININ
C: HEMAGGLUTININ
D: HEMAGGLUTININ
E: HEMAGGLUTININ
F: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,09016
Polymers168,0236
Non-polymers3,06710
Water14,916828
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27860 Å2
ΔGint-117.1 kcal/mol
Surface area61280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.859, 228.288, 71.920
Angle α, β, γ (deg.)90.00, 113.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein HEMAGGLUTININ / / HAEMAGGLUTININ HA1


Mass: 36881.602 Da / Num. of mol.: 3
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/TURKEY/TURKEY/1/2005(H5N1) / Variant: A/VN/1194/04/NIBRG14 VACCINE STRAIN / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q207Z6
#2: Protein HEMAGGLUTININ / / HAEMAGGLUTININ HA2


Mass: 19126.004 Da / Num. of mol.: 3
Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/TURKEY/TURKEY/1/2005(H5N1) / Variant: A/VN/1194/04/NIBRG14 VACCINE STRAIN / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q207Z6

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Sugars , 2 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.: 3
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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, 832 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 828 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMULTIBASIC SITE REMOVED

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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: 3.18 Å3/Da / Density % sol: 61.26 % / Description: NONE
Crystal growDetails: BIS-TRIS PROPANE PH 7.5, 0.05 - 0.15 M K/NAPO4 (PH 7.0), 15-18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.15→2.27 Å / Num. obs: 110762 / % possible obs: 98.1 % / Observed criterion σ(I): 2.1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→62.48 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.74 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22411 5544 5 %RANDOM
Rwork0.20518 ---
obs0.20611 105217 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.15→62.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10952 0 200 828 11980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01911415
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210417
X-RAY DIFFRACTIONr_angle_refined_deg1.0721.95315517
X-RAY DIFFRACTIONr_angle_other_deg0.7433.00323905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.22651387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70225.187561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61151866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.571551
X-RAY DIFFRACTIONr_chiral_restr0.0550.21702
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213078
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022671
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 398 -
Rwork0.309 7720 -
obs--97.18 %
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)
17.4949-4.83542.43189.8843-3.151.19540.4357-0.916-2.44251.82110.41791.5295-0.1492-0.1784-0.85351.93840.25980.14750.63890.45681.5418-21.8602-27.911754.9828
21.476-0.14980.35661.0117-0.29442.3445-0.05860.00270.0330.07250.10850.1229-0.095-0.1962-0.04990.0170.02490.02880.22250.03170.0711-39.146529.654939.7871
31.6982-2.9125-0.92817.75981.8610.7894-0.306-0.3785-0.44380.27710.2723-0.03830.39580.01060.03370.3283-0.05490.01920.35990.22980.4269-33.10712.165851.3416
43.5782-8.36243.879825.2262-9.18984.30360.0853-0.3222-1.03740.61980.89151.13640.3457-0.3542-0.97680.87560.03670.16070.27460.28780.9939-20.6352-20.764851.7826
52.41081.4957-3.84980.9287-2.3896.5787-0.3594-0.9571-0.1862-0.2463-0.6129-0.14670.50881.15870.97232.65830.0384-0.02591.39630.59342.8442-20.2019-42.874768.3868
60.44741.0555-1.04948.249-7.74427.3121-0.4232-0.6595-0.4023-0.3270.266-0.27740.2848-0.03760.15722.43280.170.04471.9750.45251.5174-16.822-18.449865.7635
73.645-0.7884-2.198513.6571-9.016110.52970.019-0.4506-0.40740.30560.2730.45470.182-0.2966-0.2920.1485-0.05-0.01950.22720.04530.1404-20.65699.623439.5971
82.7311-2.01111.764317.3043-9.92937.3601-0.0052-0.8254-1.43650.85620.1295-0.42380.91850.0093-0.12431.43410.24140.00540.76190.47241.1159-10.6439-31.199263.3388
90.8301-0.96550.74734.4357-2.34621.82290.02180.1073-0.2269-0.2105-0.2755-0.69550.68050.36020.25380.68760.26160.08750.2980.04230.3436-2.1695-1.043223.9994
102.05430.2894-0.26721.016-0.25552.0555-0.04350.19420.0237-0.14860.00820.0440.1527-0.12720.03530.06670.0209-0.00510.20670.02890.0134-19.629828.518610.8748
114.2687-1.93662.51673.3019-1.00943.5212-0.02340.0559-0.4479-0.2774-0.05420.17390.71240.03420.07760.59250.16360.13250.25250.02840.3137-4.7295-2.436922.4441
120.9286-3.0031.571312.054-6.3074.72430.02980.0556-0.35330.1902-0.0533-0.10730.47580.16610.02350.8410.33210.01180.18760.02030.87441.9781-14.22437.802
134.5002-0.9601-3.775215.13816.89255.65080.08650.6913-0.86842.069-0.2437-1.3180.7842-0.59080.15721.83420.3967-0.13210.65840.07171.451112.1314-43.802843.8175
142.9752-7.35183.005418.2213-7.52923.2353-0.1386-0.3162-0.1683-0.30210.79060.5360.4294-0.6563-0.6521.8537-0.145-0.22951.19960.09882.0323-3.4138-28.987940.3046
152.3252-5.47551.704217.2626-3.87221.82080.1314-0.0402-0.4062-0.0826-0.017-0.15210.61170.0861-0.11430.50030.13540.10320.34140.09470.4468-3.2478-8.781443.4779
169.66164.3823-8.33972.6163-4.09647.37990.3393-1.1027-0.12111.4555-0.37660.2118-1.0180.72570.03732.88030.3144-0.05921.0943-0.2271.49747.6866-54.022653.8585
171.9932-0.75740.88965.8915-2.01273.23310.2671-0.4669-0.5580.5246-0.06750.16620.53530.1701-0.19960.2884-0.0115-0.09840.56750.13440.18582.321112.442862.5159
181.9409-0.52720.1281.8039-0.55222.0654-0.035-0.22060.1681-0.0352-0.0372-0.143-0.17130.15110.07220.0387-0.0369-0.02130.31940.00140.0941-1.833136.896942.5469
192.3117-0.3279-0.29661.1655-0.67242.66750.0009-0.03470.36540.1173-0.0139-0.0407-0.47390.03130.0130.1127-0.0467-0.03090.1588-0.01120.1175-7.094544.686138.0439
204.38383.98661.20748.18821.18082.01570.4283-0.3608-0.80110.3195-0.296-0.65840.77430.2855-0.13240.35320.0466-0.10910.51490.17580.252.13098.006261.876
211.9614-2.4018-1.03143.52861.48720.63170.3684-0.21380.15580.29290.0324-1.32220.16170.0081-0.40081.9185-0.0758-0.6751.68520.70962.440813.1163-20.980772.2519
2211.8777-5.96666.479610.9036-5.64775.6558-0.09540.0656-0.34930.4792-0.1418-0.81750.24770.47050.23720.17850.0531-0.0090.30610.03990.1472-11.065913.53647.0853
237.301-12.40266.602326.3847-13.42237.8587-0.10360.0792-0.25280.5033-0.4293-1.77070.68760.39240.53290.90680.1974-0.26150.73610.31691.02092.1671-20.321263.359
241.4419-5.3253-1.426919.79415.31831.4328-0.5625-0.0706-0.38081.27080.29551.51270.29050.12630.26691.9851-0.1539-0.31681.87310.34551.958520.0184-39.331578.3265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 39
2X-RAY DIFFRACTION2A40 - 255
3X-RAY DIFFRACTION3A256 - 305
4X-RAY DIFFRACTION4A306 - 321
5X-RAY DIFFRACTION5B1 - 37
6X-RAY DIFFRACTION6B38 - 59
7X-RAY DIFFRACTION7B60 - 82
8X-RAY DIFFRACTION8B83 - 162
9X-RAY DIFFRACTION9C-1 - 104
10X-RAY DIFFRACTION10C105 - 257
11X-RAY DIFFRACTION11C258 - 300
12X-RAY DIFFRACTION12C301 - 321
13X-RAY DIFFRACTION13D1 - 31
14X-RAY DIFFRACTION14D32 - 61
15X-RAY DIFFRACTION15D62 - 124
16X-RAY DIFFRACTION16D125 - 157
17X-RAY DIFFRACTION17E-1 - 85
18X-RAY DIFFRACTION18E86 - 123
19X-RAY DIFFRACTION19E124 - 267
20X-RAY DIFFRACTION20E268 - 321
21X-RAY DIFFRACTION21F1 - 57
22X-RAY DIFFRACTION22F58 - 83
23X-RAY DIFFRACTION23F84 - 136
24X-RAY DIFFRACTION24F137 - 157

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