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- PDB-5t6s: Crystal structure of the A/Shanghai/2/2013 (H7N9) influenza virus... -

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Basic information

Entry
Database: PDB / ID: 5t6s
TitleCrystal structure of the A/Shanghai/2/2013 (H7N9) influenza virus hemagglutinin in complex with the antiviral drug arbidol
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / Ectodomain / N-glycosylation / antiviral
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 / metal ion binding
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
Chem-75U / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsKadam, R.U. / Wilson, I.A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol.
Authors: Kadam, R.U. / Wilson, I.A.
History
DepositionSep 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 4, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
I: Hemagglutinin HA1
J: Hemagglutinin HA2
K: Hemagglutinin HA1
L: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,43641
Polymers336,44912
Non-polymers9,98729
Water17,799988
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,24521
Polymers168,2246
Non-polymers5,02115
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37380 Å2
ΔGint-106 kcal/mol
Surface area56850 Å2
MethodPISA
2
G: Hemagglutinin HA1
H: Hemagglutinin HA2
I: Hemagglutinin HA1
J: Hemagglutinin HA2
K: Hemagglutinin HA1
L: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,19120
Polymers168,2246
Non-polymers4,96714
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37290 Å2
ΔGint-107 kcal/mol
Surface area56910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.419, 231.490, 127.850
Angle α, β, γ (deg.)90.00, 96.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Hemagglutinin ... , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Hemagglutinin HA1


Mass: 34993.559 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/02/2013(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4NN21
#2: Protein
Hemagglutinin HA2


Mass: 21081.207 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/02/2013(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4NN21

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Sugars , 3 types, 22 molecules

#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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.: 2
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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
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 , 3 types, 995 molecules

#6: Chemical
ChemComp-75U / ethyl 6-bromo-4-[(dimethylamino)methyl]-5-hydroxy-1-methyl-2-[(phenylsulfanyl)methyl]-1H-indole-3-carboxylate / Arbidol / Umifenovir / Umifenovir


Mass: 477.415 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C22H25BrN2O3S / Comment: medication, antivirus*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 988 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 17-20% PEG3350, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.36→48.5 Å / Num. obs: 154529 / % possible obs: 97.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 1.4
Reflection shellResolution: 2.36→2.41 Å / Rmerge(I) obs: 0.45

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Processing

Software
NameVersionClassification
PHENIX(1.10refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LN6

4ln6


Resolution: 2.36→48.5 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.25
RfactorNum. reflection% reflection
Rfree0.2496 7624 4.94 %
Rwork0.2039 --
obs0.2062 154344 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.36→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22794 0 636 988 24418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423968
X-RAY DIFFRACTIONf_angle_d0.7832458
X-RAY DIFFRACTIONf_dihedral_angle_d12.85614334
X-RAY DIFFRACTIONf_chiral_restr0.0493546
X-RAY DIFFRACTIONf_plane_restr0.0044244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.38690.30231890.26663818X-RAY DIFFRACTION76
2.3869-2.41490.31352500.2714696X-RAY DIFFRACTION92
2.4149-2.44440.29822180.26994680X-RAY DIFFRACTION94
2.4444-2.47530.3182600.25654693X-RAY DIFFRACTION94
2.4753-2.50790.31622310.24674792X-RAY DIFFRACTION94
2.5079-2.54220.28212470.24134942X-RAY DIFFRACTION98
2.5422-2.57860.27672620.2454950X-RAY DIFFRACTION99
2.5786-2.6170.30742660.25014972X-RAY DIFFRACTION99
2.617-2.65790.29572600.24094973X-RAY DIFFRACTION99
2.6579-2.70150.31332510.24495013X-RAY DIFFRACTION99
2.7015-2.74810.32012650.24384888X-RAY DIFFRACTION99
2.7481-2.79810.34032690.23695021X-RAY DIFFRACTION99
2.7981-2.85190.30922240.22964966X-RAY DIFFRACTION99
2.8519-2.91010.28772580.23625003X-RAY DIFFRACTION99
2.9101-2.97330.30722180.23334973X-RAY DIFFRACTION99
2.9733-3.04250.29282510.23975011X-RAY DIFFRACTION99
3.0425-3.11860.30272450.23524960X-RAY DIFFRACTION98
3.1186-3.20290.27842510.23454872X-RAY DIFFRACTION96
3.2029-3.29710.28342530.23354814X-RAY DIFFRACTION97
3.2971-3.40350.26952810.2245038X-RAY DIFFRACTION100
3.4035-3.52510.25942840.21745010X-RAY DIFFRACTION100
3.5251-3.66620.23912530.20354995X-RAY DIFFRACTION100
3.6662-3.8330.24672710.19624976X-RAY DIFFRACTION99
3.833-4.0350.22432720.18224941X-RAY DIFFRACTION98
4.035-4.28760.19492770.16574916X-RAY DIFFRACTION98
4.2876-4.61850.18322480.14614905X-RAY DIFFRACTION97
4.6185-5.08280.19352640.15614857X-RAY DIFFRACTION96
5.0828-5.81720.20942740.16735028X-RAY DIFFRACTION100
5.8172-7.3250.20962840.18555033X-RAY DIFFRACTION100
7.325-48.51490.21752480.17434984X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 66.5593 Å / Origin y: -22.6311 Å / Origin z: 297.6958 Å
111213212223313233
T0.2226 Å20.0108 Å20.0497 Å2-0.2421 Å2-0.0048 Å2--0.2473 Å2
L0.0945 °2-0.0581 °20.0552 °2-0.2208 °2-0.067 °2--0.1466 °2
S-0.012 Å °-0.0152 Å °-0.0363 Å °0.0476 Å °0.0193 Å °0.0362 Å °0.0059 Å °-0.0166 Å °-0.0063 Å °
Refinement TLS groupSelection details: all

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