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- PDB-4wsw: The crystal structure of hemagglutinin from A/green-winged teal/T... -

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Basic information

Entry
Database: PDB / ID: 4wsw
TitleThe crystal structure of hemagglutinin from A/green-winged teal/Texas/Y171/2006 influenza virus
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Hemagglutinin / influenza virus / H10
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 chain
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.
CitationJournal: J.Virol. / Year: 2015
Title: Structure and receptor binding preferences of recombinant hemagglutinins from avian and human h6 and h10 influenza a virus subtypes.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / citation ...chem_comp / citation / database_PDB_caveat / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,95918
Polymers169,3056
Non-polymers2,65412
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35640 Å2
ΔGint-122 kcal/mol
Surface area57020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.917, 144.629, 209.662
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
13B
23D
14B
24F
15C
25E
16D
26F

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA0 - 3184 - 322
21GLUGLUCC0 - 3184 - 322
12GLUGLUAA0 - 3184 - 322
22GLUGLUEE0 - 3184 - 322
13ASNASNBB1 - 1721 - 172
23ASNASNDD1 - 1721 - 172
14ASNASNBB1 - 1721 - 172
24ASNASNFF1 - 1721 - 172
15GLUGLUCC0 - 3184 - 322
25GLUGLUEE0 - 3184 - 322
16ASNASNDD1 - 1721 - 172
26ASNASNFF1 - 1721 - 172

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 35494.855 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/green-winged teal/Texas/Y171/2006 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X250*PLUS
#2: Protein Hemagglutinin HA2 chain


Mass: 20940.072 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/green-winged teal/Texas/Y171/2006 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X251*PLUS
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5 / Details: 0.1M MES pH 6.5 and 30% (v/v) PEG 300

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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: Nov 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 54072 / % possible obs: 98.8 % / Redundancy: 4.6 % / Net I/σ(I): 12.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M5G

3m5g


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.901 / SU B: 31.527 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 0.94 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1975 3.7 %RANDOM
Rwork0.224 ---
obs0.225 52097 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.48 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å20 Å20 Å2
2--4.1 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11466 0 168 0 11634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911928
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210950
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.95316143
X-RAY DIFFRACTIONr_angle_other_deg1.201325176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03851467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41525.185567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.733152028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3681557
X-RAY DIFFRACTIONr_chiral_restr0.0910.21773
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213677
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022748
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_it4.4615.5595886
X-RAY DIFFRACTIONr_mcbond_other4.4615.5585885
X-RAY DIFFRACTIONr_mcangle_it6.6878.3417347
X-RAY DIFFRACTIONr_mcangle_other6.6868.3437348
X-RAY DIFFRACTIONr_scbond_it6.1476.3116042
X-RAY DIFFRACTIONr_scbond_other6.1466.316042
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.3129.2168797
X-RAY DIFFRACTIONr_long_range_B_refined13.47445.48413080
X-RAY DIFFRACTIONr_long_range_B_other13.47245.48513080
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)
11A178560.1
12C178560.1
21A176650.11
22E176650.11
31B87300.11
32D87300.11
41B82840.15
42F82840.15
51C175650.12
52E175650.12
61D81820.16
62F81820.16
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 146 -
Rwork0.296 3808 -
obs--98.48 %
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)
10.09940.041-0.18070.0985-0.06630.33980.0094-0.01790.01830.00190.01620.0681-0.05920.0294-0.02560.17980.0132-0.0290.0359-0.00280.1221-38.755121.5139-0.3374
20.26870.2302-0.54920.247-0.41651.2615-0.02760.0257-0.0243-0.09730.03-0.0674-0.0451-0.1126-0.00250.23870.00330.03040.0622-0.00760.0598-17.24540.1813-43.5286
30.21680.0823-0.15270.132-0.22680.533-0.0162-0.00090.01010.0246-0.0139-0.06550.10540.06640.030.17530.0486-0.07480.0191-0.00130.1378-9.309510.08883.5868
40.04940.115-0.1220.5229-0.78241.90520.05990.0026-0.01590.0295-0.01170.0128-0.05860.3772-0.04820.154-0.06920.02410.1905-0.03380.08610.138328.6187-43.5087
50.1695-0.048-0.17470.5443-0.54120.9584-0.08880.02-0.0154-0.08010.1218-0.03670.1965-0.1806-0.0330.2043-0.0585-0.05840.04020.01370.1221-31.825-7.5222-11.931
60.5745-0.0779-0.68270.4433-0.41421.40570.1042-0.02990.0877-0.0427-0.0031-0.0148-0.080.0387-0.10110.229-0.06010.07860.0208-0.03350.0656-17.032521.4127-52.4037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 318
2X-RAY DIFFRACTION2B1 - 172
3X-RAY DIFFRACTION3C0 - 318
4X-RAY DIFFRACTION4D1 - 172
5X-RAY DIFFRACTION5E0 - 318
6X-RAY DIFFRACTION6F1 - 172

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