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- PDB-5huf: The crystal structure of hemagglutinin from A/gyrfalcon/Washingto... -

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Basic information

Entry
Database: PDB / ID: 5huf
TitleThe crystal structure of hemagglutinin from A/gyrfalcon/Washington/41088-6/2014 influenza virus
Components
  • hemagglutinin HA1
  • hemagglutinin HA2
KeywordsVIRAL PROTEIN / hemagglutinin / influenza virus / H5Nx
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / 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 A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.81 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 / database_PDB_caveat / 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_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 / _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 / _database_PDB_caveat.text / _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_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_mod_residue.auth_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)180,23818
Polymers175,8786
Non-polymers4,36012
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35550 Å2
ΔGint-131 kcal/mol
Surface area63670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.328, 252.385, 70.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14B
24F
15C
25E
16D
26F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUPROPROAA-2 - 3213 - 326
21LEULEUPROPROCC-2 - 3213 - 326
12LEULEUPROPROAA-2 - 3213 - 326
22LEULEUPROPROEE-2 - 3213 - 326
13GLYGLYGLYGLYBB1 - 1761 - 176
23GLYGLYGLYGLYDD1 - 1761 - 176
14GLYGLYGLYGLYBB1 - 1761 - 176
24GLYGLYGLYGLYFF1 - 1761 - 176
15LEULEUPROPROCC-2 - 3213 - 326
25LEULEUPROPROEE-2 - 3213 - 326
16GLYGLYGLYGLYDD1 - 1761 - 176
26GLYGLYGLYGLYFF1 - 1761 - 176

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein hemagglutinin HA1


Mass: 37787.930 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/gyrfalcon/Washington/41088-6/2014(H5N8))
Strain: A/gyrfalcon/Washington/41088-6/2014(H5N8) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0C4X0C0
#2: Protein hemagglutinin HA2


Mass: 20838.119 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/gyrfalcon/Washington/41088-6/2014(H5N8))
Strain: A/gyrfalcon/Washington/41088-6/2014(H5N8) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0C4X0C0
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_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
#4: 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.: 3
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
#5: 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.: 6
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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.1M Sodium Citrate: Citric acid, pH 5.5, 20% PEG (w/v) 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.81→50 Å / Num. obs: 53667 / % possible obs: 96.5 % / Redundancy: 5.2 % / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
RefinementResolution: 2.81→49.66 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.91 / SU B: 39.756 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R: 1.623 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25627 2723 5.1 %RANDOM
Rwork0.22799 ---
obs0.22943 50896 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20 Å2
2--1.93 Å20 Å2
3----0.21 Å2
Refinement stepCycle: 1 / Resolution: 2.81→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11934 0 285 0 12219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01912528
X-RAY DIFFRACTIONr_bond_other_d0.0040.0211544
X-RAY DIFFRACTIONr_angle_refined_deg1.741.96616992
X-RAY DIFFRACTIONr_angle_other_deg0.995326532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.05951494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71225.074609
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.665152103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2521554
X-RAY DIFFRACTIONr_chiral_restr0.0960.21863
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214157
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022895
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_it3.5774.5385994
X-RAY DIFFRACTIONr_mcbond_other3.5624.5385993
X-RAY DIFFRACTIONr_mcangle_it5.8976.7957482
X-RAY DIFFRACTIONr_mcangle_other5.8976.7967483
X-RAY DIFFRACTIONr_scbond_it4.1035.0716534
X-RAY DIFFRACTIONr_scbond_other4.1015.0716534
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6667.4489511
X-RAY DIFFRACTIONr_long_range_B_refined9.79937.01113703
X-RAY DIFFRACTIONr_long_range_B_other9.79937.01113703
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)
11A197510.02
12C197510.02
21A197740.02
22E197740.02
31B91580.05
32D91580.05
41B91010.06
42F91010.06
51C197290.02
52E197290.02
61D91690.05
62F91690.05
LS refinement shellResolution: 2.806→2.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 181 -
Rwork0.376 3492 -
obs--90.6 %
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)
10.0548-0.1506-0.05710.65440.26210.31640.0402-0.0010.0205-0.00720.0397-0.1816-0.06440.0654-0.07990.1760.00670.07360.0571-0.0350.237541.899762.192419.5014
20.4503-0.913-0.41542.24320.9060.40270.04210.0411-0.0419-0.031-0.0755-0.0547-0.0324-0.04990.03340.27730.0607-0.01790.033-0.01680.211543.483511.7978-0.7078
30.0636-0.1102-0.01490.31680.09130.28620.08180.0457-0.0105-0.0968-0.05150.0026-0.073-0.0916-0.03030.24320.07420.00510.08290.00880.139110.463862.44065.8044
40.1988-0.4465-0.20481.9811.1040.670.15370.0493-0.1118-0.0772-0.1470.0798-0.0384-0.0954-0.00670.28290.0492-0.09490.0561-0.07640.216424.979912.7366-10.268
50.0962-0.1605-0.15810.35610.32770.5068-0.0372-0.0397-0.02770.07810.01830.02420.0475-0.05730.01890.20450.03870.00130.08330.02370.147315.410849.277637.1351
60.2031-0.3711-0.2771.38720.53420.4183-0.1198-0.0253-0.04980.02730.03610.13670.14360.01130.08380.33920.0256-0.00360.01680.0060.229426.6314.45239.0204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 321
2X-RAY DIFFRACTION1A501 - 505
3X-RAY DIFFRACTION2B1 - 176
4X-RAY DIFFRACTION2B201 - 202
5X-RAY DIFFRACTION3C-2 - 321
6X-RAY DIFFRACTION3C501 - 505
7X-RAY DIFFRACTION4D1 - 176
8X-RAY DIFFRACTION4D201 - 202
9X-RAY DIFFRACTION5E-2 - 321
10X-RAY DIFFRACTION5E501 - 505
11X-RAY DIFFRACTION6F1 - 176
12X-RAY DIFFRACTION6F201 - 202

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