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- PDB-4yya: The structure of hemagglutinin from a H6N1 influenza virus (A/Tai... -

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Basic information

Entry
Database: PDB / ID: 4yya
TitleThe structure of hemagglutinin from a H6N1 influenza virus (A/Taiwan/2/2013) in complex with avian receptor analog 3'SLNLN
Components
  • HA1
  • HA2
KeywordsIMMUNE SYSTEM / Hemagglutinin
Function / homology
Function and homology information


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
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, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin ...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, 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
Hemagglutinin HA2 chain / Hemagglutinin
Similarity search - Component
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.595 Å
AuthorsWang, F. / Qi, J. / Bi, Y. / Zhang, W. / Wang, M. / Wang, M. / Liu, J. / Yan, J. / Shi, Y. / Gao, G.F.
Funding support China, 5items
OrganizationGrant numberCountry
China Ministry of Science and Technology National 973 Project2011CB504703 China
Intramural Special Grant for Influenza Virus Research from the Chinese Academy of SciencesKJZD-EW-L09 China
Intramural Special Grant for Strategic Priority Research Program of the Chinese Academy of SciencesXDB08020100 China
National Natural Science Foundation of China31402196 China
China National Grand S&T Special Project2014ZX10004002 China
CitationJournal: To Be Published
Title: Structure of hemagglutinin from a H6N1 influenza virus (A/chicken/Taiwan/A2837/2013)
Authors: Wang, F. / Qi, J. / Bi, Y. / Zhang, W. / Wang, M. / Wang, M. / Liu, J. / Yan, J. / Shi, Y. / Gao, G.F.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / 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_struct_oper_list / pdbx_unobs_or_zero_occ_residues / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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: HA1
B: HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0666
Polymers56,2002
Non-polymers1,8664
Water2,450136
1
A: HA1
B: HA2
hetero molecules

A: HA1
B: HA2
hetero molecules

A: HA1
B: HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,19718
Polymers168,6006
Non-polymers5,59712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area35510 Å2
ΔGint-102 kcal/mol
Surface area61810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.194, 114.194, 164.962
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HA1


Mass: 36548.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: A0A0J9X268*PLUS
#2: Protein HA2


Mass: 19651.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: A0A0J9X267*PLUS

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Sugars , 3 types, 4 molecules

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


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-3DGalpb1-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_b4-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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: obtained synthetically / 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, 136 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.52 Å3/Da / Density % sol: 77.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium acetate, 0.1M sodium acetate pH4.0, 15%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.07138 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07138 Å / Relative weight: 1
ReflectionResolution: 2.595→50 Å / Num. obs: 37568 / % possible obs: 99.9 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 22
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 6.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data processing
PHASERphasing
Cootmodel building
PHENIX1.8.3_1479refinement
SCALAdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.595→46.946 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 1879 5 %
Rwork0.1821 --
obs0.1834 37568 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.595→46.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4073 0 0 136 4209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064175
X-RAY DIFFRACTIONf_angle_d1.0375664
X-RAY DIFFRACTIONf_dihedral_angle_d14.5921527
X-RAY DIFFRACTIONf_chiral_restr0.29632
X-RAY DIFFRACTIONf_plane_restr0.018723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5946-2.66480.26331280.2232674X-RAY DIFFRACTION97
2.6648-2.74320.22091530.21042721X-RAY DIFFRACTION100
2.7432-2.83170.221230.20862770X-RAY DIFFRACTION100
2.8317-2.93290.25941440.22112748X-RAY DIFFRACTION100
2.9329-3.05030.24231350.2122753X-RAY DIFFRACTION100
3.0503-3.18910.22971520.19792754X-RAY DIFFRACTION100
3.1891-3.35720.19761410.19812755X-RAY DIFFRACTION100
3.3572-3.56750.2371380.19812743X-RAY DIFFRACTION100
3.5675-3.84280.18461650.16892726X-RAY DIFFRACTION100
3.8428-4.22930.18991430.15272765X-RAY DIFFRACTION100
4.2293-4.84080.18181440.13892748X-RAY DIFFRACTION100
4.8408-6.09680.1821540.16152763X-RAY DIFFRACTION100
6.0968-46.95380.21971590.20042769X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -40.9282 Å / Origin y: 39.6371 Å / Origin z: -10.1962 Å
111213212223313233
T0.1573 Å2-0.0207 Å2-0.0221 Å2-0.2237 Å20.0092 Å2--0.2427 Å2
L0.1321 °20.0041 °2-0.0509 °2-0.1797 °20.0444 °2--0.749 °2
S0.0019 Å °-0.0087 Å °0.0167 Å °0.0395 Å °0.0092 Å °-0.0555 Å °0.0124 Å °0.1233 Å °0 Å °
Refinement TLS groupSelection details: all

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