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- PDB-6n4f: The crystal structure of hemagglutinin from A/canine/IL/11613/201... -

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Basic information

Entry
Database: PDB / ID: 6n4f
TitleThe crystal structure of hemagglutinin from A/canine/IL/11613/2015 (H3N2) influenza virus.
Components
  • Hemagglutinin HA1
  • Hemagglutinin HA2
KeywordsVIRAL PROTEIN / Hemagglutinin / canine influenza virus
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 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsYang, H. / Stevesn, J.
CitationJournal: J. Infect. Dis. / Year: 2017
Title: Assessment of Molecular, Antigenic, and Pathological Features of Canine Influenza A(H3N2) Viruses That Emerged in the United States.
Authors: Pulit-Penaloza, J.A. / Simpson, N. / Yang, H. / Creager, H.M. / Jones, J. / Carney, P. / Belser, J.A. / Yang, G. / Chang, J. / Zeng, H. / Thor, S. / Jang, Y. / Killian, M.L. / Jenkins-Moore, ...Authors: Pulit-Penaloza, J.A. / Simpson, N. / Yang, H. / Creager, H.M. / Jones, J. / Carney, P. / Belser, J.A. / Yang, G. / Chang, J. / Zeng, H. / Thor, S. / Jang, Y. / Killian, M.L. / Jenkins-Moore, M. / Janas-Martindale, A. / Dubovi, E. / Wentworth, D.E. / Stevens, J. / Tumpey, T.M. / Davis, C.T. / Maines, T.R.
History
DepositionNov 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
G: Hemagglutinin HA1
H: Hemagglutinin HA2


Theoretical massNumber of molelcules
Total (without water)230,5458
Polymers230,5458
Non-polymers00
Water00
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
G: Hemagglutinin HA1
H: Hemagglutinin HA2


Theoretical massNumber of molelcules
Total (without water)172,9096
Polymers172,9096
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30940 Å2
ΔGint-154 kcal/mol
Surface area56080 Å2
MethodPISA
2
E: Hemagglutinin HA1
F: Hemagglutinin HA2

E: Hemagglutinin HA1
F: Hemagglutinin HA2

E: Hemagglutinin HA1
F: Hemagglutinin HA2


Theoretical massNumber of molelcules
Total (without water)172,9096
Polymers172,9096
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area30930 Å2
ΔGint-154 kcal/mol
Surface area56080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)241.148, 241.148, 147.958
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

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
11ASNASNPROPROAA8 - 32413 - 329
21ASNASNPROPROCC8 - 32413 - 329
12ASNASNPROPROAA8 - 32413 - 329
22ASNASNPROPROEE8 - 32413 - 329
13ASNASNPROPROAA8 - 32413 - 329
23ASNASNPROPROGG8 - 32413 - 329
14GLYGLYGLNGLNBB1 - 1721 - 172
24GLYGLYGLNGLNDD1 - 1721 - 172
15GLYGLYGLNGLNBB1 - 1721 - 172
25GLYGLYGLNGLNFF1 - 1721 - 172
16GLYGLYGLNGLNBB1 - 1721 - 172
26GLYGLYGLNGLNHH1 - 1721 - 172
17ASNASNPROPROCC8 - 32413 - 329
27ASNASNPROPROEE8 - 32413 - 329
18ASNASNPROPROCC8 - 32413 - 329
28ASNASNPROPROGG8 - 32413 - 329
19GLYGLYGLNGLNDD1 - 1721 - 172
29GLYGLYGLNGLNFF1 - 1721 - 172
110GLYGLYGLNGLNDD1 - 1721 - 172
210GLYGLYGLNGLNHH1 - 1721 - 172
111ASNASNPROPROEE8 - 32413 - 329
211ASNASNPROPROGG8 - 32413 - 329
112GLYGLYGLNGLNFF1 - 1721 - 172
212GLYGLYGLNGLNHH1 - 1721 - 172

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Hemagglutinin HA1


Mass: 36695.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A218KIQ1
#2: Protein
Hemagglutinin HA2


Mass: 20941.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A2U5FPI7
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: 3.59 Å3/Da / Density % sol: 65.75 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.2M Calcium acetate, 0.1M Tris pH 7.0, 20% (w/v) PEG 3000

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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 300 mm CCD / Detector: CCD / Date: Jul 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 62940 / % possible obs: 98.9 % / Redundancy: 3.7 % / Net I/σ(I): 17.3
Reflection shellResolution: 3→3.12 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.923 / SU B: 18.857 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R Free: 0.376 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24153 3188 5.1 %RANDOM
Rwork0.21328 ---
obs0.21474 59748 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 103.378 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0.49 Å20 Å2
2---0.99 Å20 Å2
3---3.21 Å2
Refinement stepCycle: 1 / Resolution: 3.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15352 0 0 0 15352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01915688
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214536
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.93221288
X-RAY DIFFRACTIONr_angle_other_deg0.848333388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9351948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55124.899792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.318152624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3421596
X-RAY DIFFRACTIONr_chiral_restr0.0780.22320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218264
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023776
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_it8.06310.337816
X-RAY DIFFRACTIONr_mcbond_other8.05910.3297815
X-RAY DIFFRACTIONr_mcangle_it12.20715.479756
X-RAY DIFFRACTIONr_mcangle_other12.20715.4729757
X-RAY DIFFRACTIONr_scbond_it7.39710.5097872
X-RAY DIFFRACTIONr_scbond_other7.39710.517873
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.2315.61411533
X-RAY DIFFRACTIONr_long_range_B_refined15.55381.03417541
X-RAY DIFFRACTIONr_long_range_B_other15.55281.0417542
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 / Rms dev position: 0 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A18871
12C18871
21A18878
22E18878
31A18878
32G18878
41B9326
42D9326
51B9326
52F9326
61B9328
62H9328
71C18871
72E18871
81C18879
82G18879
91D9326
92F9326
101D9327
102H9327
111E18885
112G18885
121F9325
122H9325
LS refinement shellResolution: 3.009→3.087 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 206 -
Rwork0.316 4350 -
obs--98.25 %

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