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- PDB-4bh2: Crystal Structure of the Haemagglutinin from a Transmissible Muta... -

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Basic information

Entry
Database: PDB / ID: 4bh2
TitleCrystal Structure of the Haemagglutinin from a Transmissible Mutant H5 Influenza Virus
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
Biological speciesINFLUENZA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / pdbx_validate_symm_contact / 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_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)58,0516
Polymers56,4592
Non-polymers1,5924
Water4,234235
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)174,15318
Polymers169,3786
Non-polymers4,77512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area35820 Å2
ΔGint-119.8 kcal/mol
Surface area62360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.620, 101.620, 331.126
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-2027-

HOH

21B-2070-

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) / 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) / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q5EP31

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Sugars , 2 types, 3 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-3/a4-b1_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]{}}}}}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.: 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, 236 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.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsPROTEINS ARE FROM A TRANSMISSIBLE MUTANT OF A/VIET NAM/1203/2004 (H5N1) PUBLISHED IN 10.1038/NATURE10831

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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: 57.79 % / 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: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.12→30.99 Å / Num. obs: 36665 / % possible obs: 97.3 % / Observed criterion σ(I): 2.3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 2.12→2.23 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.3 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→30.88 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.246 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23517 1825 5 %RANDOM
Rwork0.21326 ---
obs0.21442 34840 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å21.03 Å20 Å2
2--1.03 Å20 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.12→30.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 104 235 4254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194131
X-RAY DIFFRACTIONr_bond_other_d0.0010.023805
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.9715606
X-RAY DIFFRACTIONr_angle_other_deg0.6863.0038750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76625.123203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78215693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.551518
X-RAY DIFFRACTIONr_chiral_restr0.0620.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214659
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_it0.6972.2781964
X-RAY DIFFRACTIONr_mcbond_other0.6972.2771963
X-RAY DIFFRACTIONr_mcangle_it1.2033.4122452
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1032.5792167
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: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 129 -
Rwork0.296 2574 -
obs--98.11 %
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)
10.2335-0.07640.55820.16180.01783.93270.0352-0.1202-0.14090.05110.07650.03390.7446-0.1081-0.11170.2505-0.03370.02560.17450.02490.2034-3.64837.4940.2102
22.6767-0.3637-0.4992.5174-0.09622.5293-0.0357-0.2503-0.16270.5246-0.0540.01690.27440.05240.08980.34230.0126-0.03030.20390.06870.13453.922939.107436.829
30.4928-0.19160.31990.421-1.82239.20420.077-0.1293-0.2382-0.09110.06260.08620.754-0.0726-0.13960.2749-0.0328-0.01720.17770.01810.1668-4.442139.9709-7.0642
41.18350.77770.60911.95011.20613.03120.01080.1101-0.089-0.043-0.0009-0.08040.4280.2172-0.00990.09230.04330.01910.0388-0.01190.10840.173142.0519-38.7802
50.7134-1.05760.24152.78891.49242.8907-0.0094-0.0624-0.03240.12750.07270.0180.2172-0.0064-0.06340.1904-0.01430.00410.17890.02630.1022-4.017752.89239.8023
60.6579-0.0676-0.47391.37951.981310.40240.01170.0594-0.0242-0.22530.0336-0.095-0.24880.1201-0.04520.0447-0.00430.01070.0084-0.0090.0879-2.077250.9086-37.1605
79.43062.2043-1.596710.3510.39455.50560.08780.6170.2786-1.01060.0853-0.6582-0.06950.9669-0.17310.410.00840.20450.3153-0.06090.24626.282941.3205-62.4544
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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