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- PDB-6v46: The crystal structure of hemagglutinin from A/turkey/Ontario/6118... -

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Entry
Database: PDB / ID: 6v46
TitleThe crystal structure of hemagglutinin from A/turkey/Ontario/6118/1968 (H8N4)
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / Influenza / avian / H8
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 / 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: 2.248 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: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / Derived calculations / 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_conn / 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_conn.pdbx_leaving_atom_flag / _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 16, 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)177,84315
Polymers174,1946
Non-polymers3,6489
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35390 Å2
ΔGint-77 kcal/mol
Surface area59510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.047, 98.086, 132.735
Angle α, β, γ (deg.)90.000, 115.200, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain E
12chain B
22chain D
32chain F

NCS domain segments:

Component-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPchain AAA1 - 3235 - 327
21ASPASPchain CCC1 - 3235 - 327
31ASPASPchain EEE1 - 3235 - 327
12ILEILEchain BBB6 - 1716 - 171
22ILEILEchain DDD6 - 1716 - 171
32ILEILEchain FFF6 - 1716 - 171

NCS ensembles :
ID
1
2

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain


Mass: 37294.805 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Turkey/Ontario/6118/1968 H8N4)
Strain: A/Turkey/Ontario/6118/1968 H8N4 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: F2P175, UniProt: P03456*PLUS
#2: Protein Hemagglutinin HA2 chain


Mass: 20770.014 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Turkey/Ontario/6118/1968 H8N4)
Strain: A/Turkey/Ontario/6118/1968 H8N4 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: F2P175, UniProt: P03456*PLUS

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Sugars , 3 types, 9 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}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.: 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

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Non-polymers , 1 types, 557 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.87 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.05M Magnesium Chloride, 0.1M HEPES:NaOH pH7.5, 30% (v/v) PEG 550 MME

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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: Nov 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.248→50 Å / Num. obs: 91049 / % possible obs: 98.2 % / Redundancy: 3.8 % / Rsym value: 0.085 / Net I/σ(I): 3.8
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 4561 / Rsym value: 0.769

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WSR

4wsr


Resolution: 2.248→45.412 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.02
RfactorNum. reflection% reflection
Rfree0.2253 4563 5.01 %
Rwork0.1867 --
obs0.1886 91049 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 210.01 Å2 / Biso mean: 47.6987 Å2 / Biso min: 16.32 Å2
Refinement stepCycle: final / Resolution: 2.248→45.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11688 0 240 557 12485
Biso mean--78.41 45.67 -
Num. residues----1467
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3072X-RAY DIFFRACTION1.112TORSIONAL
12C3072X-RAY DIFFRACTION1.112TORSIONAL
13E3072X-RAY DIFFRACTION1.112TORSIONAL
21B1497X-RAY DIFFRACTION1.112TORSIONAL
22D1497X-RAY DIFFRACTION1.112TORSIONAL
23F1497X-RAY DIFFRACTION1.112TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.248-2.27320.3863810.3491185263
2.2732-2.29990.27371310.2784283994
2.2999-2.32790.30321680.2397290897
2.3279-2.35740.27781620.2347280397
2.3574-2.38840.28651530.2309289697
2.3884-2.42120.2721460.2202285397
2.4212-2.45570.29051560.224293397
2.4557-2.49240.26611610.2174284198
2.4924-2.53130.27161570.2099287398
2.5313-2.57280.27331450.2073294998
2.5728-2.61720.25441480.2117286598
2.6172-2.66480.25721590.214295698
2.6648-2.7160.27121630.218285498
2.716-2.77150.26231380.1997290698
2.7715-2.83170.26731630.1979292898
2.8317-2.89760.24491540.2043291798
2.8976-2.970.24831610.2016289998
2.97-3.05030.24491540.2059294898
3.0503-3.140.24421300.1981289698
3.14-3.24140.21961680.2001295498
3.2414-3.35720.2631490.1994289499
3.3572-3.49160.2411580.1916296699
3.4916-3.65040.21381740.1728291799
3.6504-3.84280.20721710.1755293999
3.8428-4.08340.18841590.1589293299
4.0834-4.39840.18521630.1429294299
4.3984-4.84060.16951500.1442299899
4.8406-5.540.19241450.1545299599
5.54-6.97570.21811410.183301399
6.9757-100.18651550.1827302098
Refinement TLS params.Method: refined / Origin x: 198.4552 Å / Origin y: -40.9481 Å / Origin z: 55.8058 Å
111213212223313233
T0.1945 Å20.0021 Å20.0014 Å2-0.185 Å2-0.0001 Å2--0.2309 Å2
L0.1518 °20 °20.011 °2-0.1417 °20.0065 °2--0.6157 °2
S-0.0011 Å °0.0093 Å °-0.0027 Å °-0.0124 Å °-0.002 Å °-0.0008 Å °-0.0079 Å °0.0031 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 323
2X-RAY DIFFRACTION1allA501 - 702
3X-RAY DIFFRACTION1allB6 - 171
4X-RAY DIFFRACTION1allC1 - 323
5X-RAY DIFFRACTION1allC501 - 702
6X-RAY DIFFRACTION1allD6 - 171
7X-RAY DIFFRACTION1allE1 - 323
8X-RAY DIFFRACTION1allE501 - 702
9X-RAY DIFFRACTION1allF6 - 171
10X-RAY DIFFRACTION1allS1 - 557

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