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- PDB-6v47: The crystal structure of hemagglutinin from A/duck/Memphis/546/19... -

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Basic information

Entry
Database: PDB / ID: 6v47
TitleThe crystal structure of hemagglutinin from A/duck/Memphis/546/1974 (H11N9)
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Influenza / avian / H11
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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

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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)172,5999
Polymers171,3266
Non-polymers1,2733
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27120 Å2
ΔGint-114 kcal/mol
Surface area60610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.120, 121.149, 217.733
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: _ / 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
11ASPASPPROPROAA1 - 3211 - 321
21ASPASPPROPROCC1 - 3211 - 321
12ASPASPPROPROAA1 - 3211 - 321
22ASPASPPROPROEE1 - 3211 - 321
13ALAALAILEILEBB7 - 1737 - 173
23ALAALAILEILEDD7 - 1737 - 173
14ALAALAILEILEBB7 - 1737 - 173
24ALAALAILEILEFF7 - 1737 - 173
15ASPASPPROPROCC1 - 3211 - 321
25ASPASPPROPROEE1 - 3211 - 321
16ALAALAILEILEDD7 - 1737 - 173
26ALAALAILEILEFF7 - 1737 - 173

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 36223.723 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/duck/Memphis/546/1974(H11N9))
Strain: A/duck/Memphis/546/1974(H11N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q0A426
#2: Protein Hemagglutinin HA2 chain


Mass: 20885.021 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/duck/Memphis/546/1974(H11N9))
Strain: A/duck/Memphis/546/1974(H11N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A2V851
#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
Has ligand of interestN

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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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.1M MOPS, pH7.0, 18% (w/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: Jun 30, 2014
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: 45007 / % possible obs: 93.1 % / Redundancy: 8.1 % / Rsym value: 0.122 / Net I/σ(I): 25.8
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 2370 / Rsym value: 0.55

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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: 4F23

4f23


Resolution: 2.8→49.21 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.895 / SU B: 38.858 / SU ML: 0.329 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.419
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 2370 5 %RANDOM
Rwork0.234 ---
obs0.2362 45007 89.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 169.98 Å2 / Biso mean: 62.558 Å2 / Biso min: 34.95 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å20 Å2
2--1.16 Å20 Å2
3---1.12 Å2
Refinement stepCycle: final / Resolution: 2.8→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11628 0 84 0 11712
Biso mean--111.41 --
Num. residues----1464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01311988
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710572
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.64916239
X-RAY DIFFRACTIONr_angle_other_deg1.3241.58624633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.21251458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68723.186678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.358152022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2741569
X-RAY DIFFRACTIONr_chiral_restr0.0760.21563
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213533
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022571
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A101670.04
12C101670.04
21A100830.05
22E100830.05
31B52400.03
32D52400.03
41B52460.03
42F52460.03
51C100790.04
52E100790.04
61D52440.03
62F52440.03
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 159 -
Rwork0.332 2823 -
all-2982 -
obs--77.11 %
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)
10.030.103-0.06420.4111-0.26450.1763-0.0096-0.0165-0.04160.0121-0.0097-0.042-0.05190.00940.01930.32720.010.00930.26570.01040.3073-22.500622.8543-46.489
20.235-0.46950.70731.2371-1.77072.64150.0487-0.0247-0.04060.0180.00590.065-0.05810.0727-0.05460.35570.0556-0.03210.20610.05830.2542-27.5593-3.1694-0.2176
30.34440.1077-0.08930.8778-0.49340.32320.00230.10820.03630.11390.015-0.0763-0.02740.0425-0.01730.3499-0.0058-0.01020.1695-0.01050.1855-46.029643.8527-32.545
40.49950.03790.33460.9023-0.45872.42230.0843-0.1413-0.09760.3141-0.0694-0.11580.34190.3228-0.01490.50950.0769-0.06040.1760.01690.2212-41.005811.49349.5398
50.6585-0.71770.25731.09830.20840.9870.16720.0580.3324-0.4009-0.2011-0.3675-0.3234-0.10490.03390.23660.06410.12990.15480.01040.2455-56.425115.3687-48.8716
60.6820.6682-1.36542.3709-3.00644.92490.037-0.2320.05880.36810.0223-0.0072-0.30550.2257-0.05930.16120.009-0.00610.1402-0.02990.0078-49.3759-6.4502-0.7223
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 502
2X-RAY DIFFRACTION2B7 - 173
3X-RAY DIFFRACTION3C1 - 502
4X-RAY DIFFRACTION4D7 - 173
5X-RAY DIFFRACTION5E1 - 502
6X-RAY DIFFRACTION6F7 - 173

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