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- PDB-6v49: The crystal structure of hemagglutinin from A/wedge-tailed shearw... -

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Basic information

Entry
Database: PDB / ID: 6v49
TitleThe crystal structure of hemagglutinin from A/wedge-tailed shearwater/Western Australia/2576/1979 (H15N9)
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Influenza / avian / H15
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYang, H. / Stevens, J.
CitationJournal: Heliyon / Year: 2020
Title: Molecular characterization and three-dimensional structures of avian H8, H11, H14, H15 and swine H4 influenza virus hemagglutinins
Authors: Yang, H. / Carney, P.J. / Chang, J. / Stevens, J.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Oct 11, 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 / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)171,55712
Polymers169,6206
Non-polymers1,9376
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33360 Å2
ΔGint-98 kcal/mol
Surface area61500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.667, 101.380, 163.270
Angle α, β, γ (deg.)90.000, 90.740, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14B
24F
15C
25E
16D
26F

NCS domain segments:

Component-ID: _ / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA0 - 3281 - 329
21GLYGLYCC0 - 3281 - 329
12GLYGLYAA0 - 3281 - 329
22GLYGLYEE0 - 3281 - 329
13ALAALABB5 - 1715 - 171
23ALAALADD5 - 1715 - 171
14ALAALABB5 - 1715 - 171
24ALAALAFF5 - 1715 - 171
15GLYGLYCC0 - 3281 - 329
25GLYGLYEE0 - 3281 - 329
16ALAALADD5 - 1715 - 171
26ALAALAFF5 - 1715 - 171

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 36316.891 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9))
Strain: A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9)
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q20ND8
#2: Protein Hemagglutinin HA2 chain


Mass: 20223.229 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9))
Strain: A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9)
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q20ND8
#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.: 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
#4: 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.: 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
Has ligand of interestN
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.1M Sodium acetate trihydrate, pH5.0, 20% (v/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 57980 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rsym value: 0.069 / Net I/σ(I): 21.8
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 3096 / Rsym value: 0.608

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4m5g

4m5g


Resolution: 2.5→44.09 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / SU B: 29.578 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.611 / ESU R Free: 0.304
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 3096 5.1 %RANDOM
Rwork0.2301 ---
obs0.2319 57980 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 230.53 Å2 / Biso mean: 70.255 Å2 / Biso min: 25.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å22.57 Å2
2---1.17 Å20 Å2
3---1.04 Å2
Refinement stepCycle: final / Resolution: 2.5→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11655 0 126 0 11781
Biso mean--110.26 --
Num. residues----1488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01212024
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.65416263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.94651482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35822.882687
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.814152058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5291584
X-RAY DIFFRACTIONr_chiral_restr0.1330.21599
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029303
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A100610.03
12C100610.03
21A100480.02
22E100480.02
31B54520.03
32D54520.03
41B54350.03
42F54350.03
51C100460.03
52E100460.03
61D54510.03
62F54510.03
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 237 -
Rwork0.401 4020 -
all-4257 -
obs--94.14 %
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)
11.69670.2521-2.21710.11-0.35733.1377-0.30750.3605-0.30490.07050.09620.02070.2963-0.34410.21130.2615-0.01750.22240.32780.00110.3495-23.6376-31.419151.8757
21.5168-0.5787-1.01640.38570.31240.7485-0.1361-0.1264-0.03730.05760.0352-0.01620.10680.00610.10090.0293-0.01370.06210.2858-0.0770.220215.8489-24.55420.951
30.58220.4385-0.20540.4104-0.31830.7620.1492-0.04610.24460.11280.06550.1359-0.1291-0.359-0.21460.0560.00620.09710.36480.07290.2945-31.8134-1.676940.3639
41.2938-0.1456-1.12140.02830.0741.2636-0.06710.04050.02260.01440.0087-0.00240.0822-0.05390.05850.0781-0.01930.08350.15940.01580.245313.2566-2.745517.3381
51.8804-0.6004-0.83870.46180.35260.57070.0629-0.48590.02280.0003-0.0201-0.0158-0.12570.2734-0.04270.2129-0.05750.17550.3478-0.01110.2245-12.769-4.255167.3223
62.79840.544-2.36680.1826-0.42742.02440.3752-0.51450.32970.1058-0.04830.0345-0.30630.4188-0.32690.0727-0.04560.07050.32150.03280.2925.4284-9.788834.5657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 502
2X-RAY DIFFRACTION2B5 - 301
3X-RAY DIFFRACTION3C0 - 502
4X-RAY DIFFRACTION4D5 - 301
5X-RAY DIFFRACTION5E0 - 502
6X-RAY DIFFRACTION6F5 - 301

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