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- PDB-4bgx: H5 (VN1194) Influenza Virus Haemagglutinin in Complex with Human ... -

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Basic information

Entry
Database: PDB / ID: 4bgx
TitleH5 (VN1194) Influenza Virus Haemagglutinin in Complex with Human Receptor Analogue 6'-SLN
Components(HEMAGGLUTININ) x 2
KeywordsVIRAL PROTEIN / N-GLYCOSYLATION / VIRUS RECEPTOR / BIRD FLU
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 / virion membrane / 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
Biological speciesINFLUENZA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsXiong, X. / Coombs, P. / Martin, S.R. / Liu, J. / Xiao, H. / McCauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. ...Xiong, X. / Coombs, P. / 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. / 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / 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 / _database_PDB_caveat.text / _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_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 2.1Dec 20, 2023Group: 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 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)57,4227
Polymers56,0492
Non-polymers1,3735
Water3,801211
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)172,26621
Polymers168,1466
Non-polymers4,12015
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 area33330 Å2
ΔGint-90.1 kcal/mol
Surface area59180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.338, 101.338, 451.102
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-2023-

HOH

21B-2025-

HOH

31B-2058-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HEMAGGLUTININ / HAEMAGGLUTININ HA1


Mass: 36950.766 Da / Num. of mol.: 1
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-340
Source method: isolated from a natural source
Details: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC)
Source: (natural) INFLUENZA VIRUS / Variant: A/VN/1194/04/NIBRG14 VACCINE STRAIN / Strain: A/VIETNAM/1194/2004(H5N1) / References: UniProt: Q6DQ34
#2: Protein HEMAGGLUTININ / HAEMAGGLUTININ HA2


Mass: 19097.990 Da / Num. of mol.: 1
Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512
Source method: isolated from a natural source
Details: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC)
Source: (natural) INFLUENZA VIRUS / Variant: A/VN/1194/04/NIBRG14 VACCINE STRAIN / Strain: A/VIETNAM/1194/2004(H5N1) / References: UniProt: Q6DQ34

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Sugars , 2 types, 4 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#4: 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.: 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, 212 molecules

#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
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: 3.98 Å3/Da / Density % sol: 69.07 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH 7.0, 0.05 M MGCL2, 28-30% PEG 550

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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: 2.48→37.15 Å / Num. obs: 32249 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 9.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.2
Reflection shellResolution: 2.48→2.61 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IBX

2ibx


Resolution: 2.48→37.18 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 13.959 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21776 1634 5.1 %RANDOM
Rwork0.19361 ---
obs0.1948 30613 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.792 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å22.17 Å20 Å2
2--2.17 Å20 Å2
3----7.05 Å2
Refinement stepCycle: LAST / Resolution: 2.48→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3859 0 89 211 4159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194051
X-RAY DIFFRACTIONr_bond_other_d0.0010.023725
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.9625498
X-RAY DIFFRACTIONr_angle_other_deg0.7113.0038569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26525.174201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7215678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9021517
X-RAY DIFFRACTIONr_chiral_restr0.0650.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02943
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_it1.3883.3751932
X-RAY DIFFRACTIONr_mcbond_other1.3863.3741931
X-RAY DIFFRACTIONr_mcangle_it2.255.062412
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2573.7952119
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: 2.48→2.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 108 -
Rwork0.306 2229 -
obs--99.91 %
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)
10.427-0.0457-0.38190.21670.1274.78550.0415-0.2430.10680.1644-0.07690.1442-0.5871-0.81340.03540.40950.10560.03050.468-0.12420.330234.3807-14.0801-18.8127
22.33530.1802-0.07733.2549-0.95851.8207-0.0307-0.41480.0690.8272-0.15210.1352-0.0569-0.54590.18270.75680.02610.12090.908-0.13210.236332.2627-21.567716.4463
31.2749-0.1683-1.50590.58212.539612.58290.138-0.39110.22660.0479-0.12470.1445-0.2014-0.4945-0.01320.36510.1280.07460.316-0.07530.372235.5691-14.749-26.9442
43.1492-1.68161.80643.595-2.33129.6241-0.03470.0732-0.0840.161-0.09370.2815-0.165-1.06370.12830.05960.0201-0.02740.1732-0.09060.28836.194-21.0566-58.6731
58.26660.73455.12434.41480.697916.9038-0.1-0.14820.2744-0.1467-0.21710.4856-0.5952-0.92550.31710.31780.01630.01060.262-0.03710.223848.1596-22.7221-10.4025
62.163-0.20452.30471.2053-0.912318.21120.0160.2402-0.0161-0.0856-0.1222-0.01990.13230.42470.10610.01180.01490.00270.0416-0.00090.217244.528-23.9884-56.7188
78.2369-5.5888-1.152916.12011.228111.98950.24451.4227-1.4591-0.6736-0.42860.81391.0068-0.90820.18410.35150.0608-0.17840.701-0.24480.551931.5088-26.1711-80.5988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2A106 - 262
3X-RAY DIFFRACTION3A263 - 321
4X-RAY DIFFRACTION4B1 - 60
5X-RAY DIFFRACTION5B61 - 84
6X-RAY DIFFRACTION6B85 - 141
7X-RAY DIFFRACTION7B142 - 163

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