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- PDB-4bh4: Haemagglutinin from a Transmissible Mutant H5 Influenza Virus in ... -

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Basic information

Entry
Database: PDB / ID: 4bh4
TitleHaemagglutinin from a Transmissible Mutant H5 Influenza Virus 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 / Hemagglutinin
Similarity search - Component
Biological speciesINFLUENZA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 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 / 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 / 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 / _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_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.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8727
Polymers56,4592
Non-polymers2,4125
Water7,152397
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)176,61521
Polymers169,3786
Non-polymers7,23715
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area40100 Å2
ΔGint-84.7 kcal/mol
Surface area61270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.744, 101.744, 329.929
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
11A-2148-

HOH

21A-2159-

HOH

31B-2012-

HOH

41B-2051-

HOH

51B-2120-

HOH

61B-2126-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HEMAGGLUTININ / HAEMAGGLUTININ HA1


Mass: 37204.195 Da / Num. of mol.: 1
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA VIRUS / Strain: A/VIET NAM/1203/2004(H5N1) / Description: DESCRIBED BY M. IMAI ET AL. NATURE (2012) / Variant: TRANSMISSIBLE MUTANT / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q5EP31
#2: Protein HEMAGGLUTININ / HAEMAGGLUTININ HA2


Mass: 19255.184 Da / Num. of mol.: 1
Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 343-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA VIRUS / Strain: A/VIET NAM/1203/2004(H5N1) / Description: DESCRIBED BY M. IMAI ET AL. NATURE (2012) / Variant: TRANSMISSIBLE MUTANT / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q5EP31

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Sugars , 3 types, 4 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-3-4/a4-b1_a6-f1_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)][b-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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, 398 molecules

#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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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: 2.91 Å3/Da / Density % sol: 57.76 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH 7.0, 25-30% JEFFAMINE ED-2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→77.72 Å / Num. obs: 52311 / % possible obs: 100 % / Observed criterion σ(I): 2.6 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→77.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.34 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22331 2669 5.1 %RANDOM
Rwork0.18938 ---
obs0.19117 49642 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.742 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.66 Å20 Å2
2--0.66 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.9→77.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 160 397 4472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194190
X-RAY DIFFRACTIONr_bond_other_d0.0010.023842
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9875694
X-RAY DIFFRACTIONr_angle_other_deg0.7223.0038848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.215491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36325.123203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19215693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7861518
X-RAY DIFFRACTIONr_chiral_restr0.070.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02949
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 186 -
Rwork0.286 3639 -
obs--99.53 %
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)
10.0352-0.0383-0.04470.15210.28723.16180.0109-0.02620.03160.06270.0618-0.1034-0.15710.498-0.07270.1287-0.0289-0.01670.20260.01160.11520.15617.4746-54.7212
22.1005-0.00640.49572.343-0.57971.72910.0307-0.25790.04790.147-0.12-0.1238-0.15230.02930.08930.1202-0.034-0.02240.1554-0.03810.03515.057713.0348-18.1077
30.10880.15130.72310.51190.37366.45480.00660.0816-0.02930.07410.1048-0.1429-0.16790.6117-0.11150.1365-0.0106-0.01370.2569-0.01970.100418.38295.4927-61.9156
41.74140.3788-1.45780.76130.10343.3292-0.03280.02660.0981-0.04630.0261-0.0358-0.23570.1180.00670.0368-0.0264-0.01230.07060.03740.051614.24388.595-93.5823
52.3333.116-1.81625.0439-1.57912.2392-0.0203-0.0992-0.07830.046-0.0578-0.05370.02960.20760.07810.10.0054-0.01220.1474-0.0140.04717.0039-0.5854-45.1155
60.71930.4076-1.05030.7574-1.31069.76-0.04160.13060.0892-0.07670.16690.0760.0839-0.4112-0.12530.0082-0.0165-0.01060.04150.02340.06517.75242.107-92.0122
77.5438-0.2264-0.45254.7203-1.24064.6309-0.27560.87810.5693-0.5950.32890.4342-0.592-0.2733-0.05320.293-0.0487-0.05790.28560.17330.170111.761814.193-117.2256
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 105
2X-RAY DIFFRACTION2A106 - 262
3X-RAY DIFFRACTION3A263 - 322
4X-RAY DIFFRACTION4B1 - 60
5X-RAY DIFFRACTION5B61 - 84
6X-RAY DIFFRACTION6B85 - 141
7X-RAY DIFFRACTION7B142 - 167

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