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- PDB-5hu8: The crystal structure of hemagglutinin from A/Sichuan/26221/2014 ... -

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Basic information

Entry
Database: PDB / ID: 5hu8
TitleThe crystal structure of hemagglutinin from A/Sichuan/26221/2014 (H5N6) influenza virus
Components(hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / hemagglutinin / influenza virus / H5N6
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 / Hemagglutinin HA2
Similarity search - Component
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å
AuthorsYang, H. / Carney, P.J. / Guo, Z. / Chang, J.C. / Stevens, J.
CitationJournal: J.Virol. / Year: 2016
Title: Molecular Characterizations of Surface Proteins Hemagglutinin and Neuraminidase from Recent H5Nx Avian Influenza Viruses.
Authors: Yang, H. / Carney, P.J. / Mishin, V.P. / Guo, Z. / Chang, J.C. / Wentworth, D.E. / Gubareva, L.V. / Stevens, J.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Jun 8, 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_mod_residue / pdbx_struct_oper_list / pdbx_validate_close_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 / _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_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 HA1
C: hemagglutinin HA1
E: hemagglutinin HA1
B: hemagglutinin HA2
D: hemagglutinin HA2
F: hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,60515
Polymers176,1286
Non-polymers3,4779
Water12,574698
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33750 Å2
ΔGint-95 kcal/mol
Surface area61410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.505, 104.418, 215.692
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13C
23E
14B
24D
15B
25F
16D
26F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A0 - 319
2010C0 - 319
1020A0 - 319
2020E0 - 319
1030C0 - 319
2030E0 - 319
1040B12 - 173
2040D12 - 173
1050B12 - 173
2050F12 - 173
1060D12 - 173
2060F12 - 173

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein hemagglutinin HA1


Mass: 37828.008 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Strain: A/Sichuan/26221/2014 (H5N6) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A182DWE0*PLUS
#2: Protein hemagglutinin HA2


Mass: 20881.170 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A182DWE1*PLUS

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Sugars , 3 types, 9 molecules

#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}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.: 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 , 1 types, 698 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7 / Details: 0.1M Imidazole, pH7, 22.5% PolyPure PEG 0.3-10KDa

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 74754 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 25.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.45→49.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 15.347 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 3763 5 %RANDOM
Rwork0.19118 ---
obs0.19303 70912 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.397 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2---0.53 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.45→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11598 0 228 698 12524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912123
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211181
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.95916452
X-RAY DIFFRACTIONr_angle_other_deg1.166325695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95351440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32825.149606
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.151152064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8211554
X-RAY DIFFRACTIONr_chiral_restr0.0990.21800
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213734
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022826
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_it3.9454.3215778
X-RAY DIFFRACTIONr_mcbond_other3.9424.325777
X-RAY DIFFRACTIONr_mcangle_it6.0186.477212
X-RAY DIFFRACTIONr_mcangle_other6.0196.4717213
X-RAY DIFFRACTIONr_scbond_it4.9954.9816345
X-RAY DIFFRACTIONr_scbond_other4.9954.9826346
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7197.2599241
X-RAY DIFFRACTIONr_long_range_B_refined10.50335.59213772
X-RAY DIFFRACTIONr_long_range_B_other10.54435.41713451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A194050.07
12C194050.07
21A194220.07
22E194220.07
31C193760.07
32E193760.07
41B82920.1
42D82920.1
51B83840.09
52F83840.09
61D83130.1
62F83130.1
LS refinement shellResolution: 2.451→2.515 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 236 -
Rwork0.312 4967 -
obs--95.54 %
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)
10.3884-0.04360.20520.13790.15520.39560.04450.0246-0.00140.02910.00390.01760.06530.0291-0.04830.0739-0.0161-0.01130.09980.01220.1088-19.896831.3088-48.0075
20.4581-0.10360.18760.0524-0.03440.3843-0.0144-0.05980.2071-0.00190.0182-0.0028-0.0559-0.0626-0.00380.06640.0247-0.00060.0279-0.01070.1949-28.729964.3588-44.409
30.3487-0.02640.0680.03530.01450.46650.03150.08670.1814-0.03330.0107-0.0522-0.0530.0939-0.04230.061-0.04480.03730.09810.03290.16360.766756.1254-59.9221
40.5149-0.08390.84540.0854-0.21221.5816-0.0127-0.07720.04720.00240.03960.01990.04740.0034-0.02690.060.0784-0.03650.2548-0.09860.06117.471140.1455-2.8537
50.4670.14260.63130.24080.48821.5290.0031-0.17690.11740.02760.1288-0.05310.07140.0805-0.1320.03130.0538-0.03150.2988-0.17740.18671.19660.0459-0.1327
60.55070.0540.3920.03290.11090.76080.0212-0.1420.1952-0.02160.0617-0.0076-0.02270.208-0.08290.0301-0.02990.00050.3306-0.22240.201818.93156.574-9.5159
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 600
2X-RAY DIFFRACTION2C0 - 600
3X-RAY DIFFRACTION3E0 - 600
4X-RAY DIFFRACTION4B12 - 173
5X-RAY DIFFRACTION5D12 - 173
6X-RAY DIFFRACTION6F12 - 173

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