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- PDB-4m44: Crystal structure of hemagglutinin of influenza virus B/Yamanashi... -

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Basic information

Entry
Database: PDB / ID: 4m44
TitleCrystal structure of hemagglutinin of influenza virus B/Yamanashi/166/1998 in complex with avian-like receptor LSTa
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / receptor binding / fusion / sialic acid
Function / homology
Function and homology information


viral budding from plasma membrane / endocytosis involved in viral entry into 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
Haemagglutinin, influenzavirus 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, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Haemagglutinin, influenzavirus 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, 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 B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNi, F. / Kondrashkina, E. / Wang, Q.
CitationJournal: Virology / Year: 2013
Title: Structural basis for the divergent evolution of influenza B virus hemagglutinin.
Authors: Ni, F. / Kondrashkina, E. / Wang, Q.
History
DepositionAug 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _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 / _struct_ref_seq_dif.details
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 HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,24230
Polymers171,2586
Non-polymers8,98424
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45230 Å2
ΔGint-65 kcal/mol
Surface area61830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.130, 101.520, 137.370
Angle α, β, γ (deg.)90.00, 115.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1


Mass: 37543.043 Da / Num. of mol.: 3 / Fragment: Hemagglutinin HA1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Yamanashi/166/1998 / Gene: HA / Plasmid: pRB21 / Production host: Mammalia (mammals) / Strain (production host): CV-1 / References: UniProt: A3DQM7
#2: Protein Hemagglutinin HA2


Mass: 19542.980 Da / Num. of mol.: 3 / Fragment: Hemagglutinin HA2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Yamanashi/166/1998 / Gene: HA / Plasmid: pRB21 / Production host: Mammalia (mammals) / Strain (production host): CV-1 / References: UniProt: A3DQM7

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Sugars , 3 types, 24 molecules

#3: 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.: 9
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
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-1-3/a3-b1_b3-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+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.: 12
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 , 1 types, 471 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 23% PEG2000MME, 0.1 M Tris, 0.2 M TMNO, pH 8.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.5→39.37 Å / Num. all: 75849 / Num. obs: 75849 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.091
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASESphasing
PHENIX(phenix.refine: dev_1391)refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39.364 Å / SU ML: 0.3 / σ(F): 1.38 / Phase error: 23.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 3787 5 %
Rwork0.1856 --
obs0.1874 75782 99.9 %
all-75849 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→39.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11695 0 588 471 12754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612577
X-RAY DIFFRACTIONf_angle_d1.20417083
X-RAY DIFFRACTIONf_dihedral_angle_d13.4414602
X-RAY DIFFRACTIONf_chiral_restr0.0722053
X-RAY DIFFRACTIONf_plane_restr0.0052153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53170.30761460.26642674X-RAY DIFFRACTION100
2.5317-2.5650.32611370.26632604X-RAY DIFFRACTION100
2.565-2.60010.32221460.24982682X-RAY DIFFRACTION100
2.6001-2.63720.32171370.24032673X-RAY DIFFRACTION100
2.6372-2.67660.26991350.24112662X-RAY DIFFRACTION100
2.6766-2.71840.2831200.22242650X-RAY DIFFRACTION100
2.7184-2.7630.28971640.22132621X-RAY DIFFRACTION100
2.763-2.81060.28161430.222656X-RAY DIFFRACTION100
2.8106-2.86170.2771560.22062634X-RAY DIFFRACTION100
2.8617-2.91670.29651280.21852668X-RAY DIFFRACTION100
2.9167-2.97620.26331600.21152630X-RAY DIFFRACTION100
2.9762-3.04090.27661370.21322663X-RAY DIFFRACTION100
3.0409-3.11160.26751360.20782659X-RAY DIFFRACTION100
3.1116-3.18940.23721460.20212668X-RAY DIFFRACTION100
3.1894-3.27560.24931460.20372690X-RAY DIFFRACTION100
3.2756-3.37190.22941330.18822648X-RAY DIFFRACTION100
3.3719-3.48070.22361470.19192615X-RAY DIFFRACTION100
3.4807-3.6050.22651350.19162698X-RAY DIFFRACTION100
3.605-3.74930.22861510.18652664X-RAY DIFFRACTION100
3.7493-3.91980.18551230.17482663X-RAY DIFFRACTION100
3.9198-4.12620.20681250.1612664X-RAY DIFFRACTION100
4.1262-4.38440.15881390.14732708X-RAY DIFFRACTION100
4.3844-4.72240.19071370.14162687X-RAY DIFFRACTION100
4.7224-5.19670.18211350.15262664X-RAY DIFFRACTION100
5.1967-5.94650.1891500.1662708X-RAY DIFFRACTION100
5.9465-7.48350.18421320.18492691X-RAY DIFFRACTION100
7.4835-39.36890.20831430.18122751X-RAY DIFFRACTION99

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