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- PDB-3ti4: Crystal structure of 2009 pandemic H1N1 neuraminidase complexed w... -

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Basic information

Entry
Database: PDB / ID: 3ti4
TitleCrystal structure of 2009 pandemic H1N1 neuraminidase complexed with laninamivir octanoate
ComponentsNeuraminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 6-BLADED BETA-PROPELLER / Calcium Binding / Glycosylation / antiviral / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / identical protein binding / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Chem-LVO / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 Å
AuthorsVavricka, C.J. / Li, Q. / Wu, Y. / Qi, J. / Wang, M. / Liu, Y. / Gao, F. / Liu, J. / Feng, E. / He, J. ...Vavricka, C.J. / Li, Q. / Wu, Y. / Qi, J. / Wang, M. / Liu, Y. / Gao, F. / Liu, J. / Feng, E. / He, J. / Wang, J. / Liu, H. / Jiang, H. / Gao, G.F.
CitationJournal: Plos Pathog. / Year: 2011
Title: Structural and functional analysis of laninamivir and its octanoate prodrug reveals group specific mechanisms for influenza NA inhibition
Authors: Vavricka, C.J. / Li, Q. / Wu, Y. / Qi, J. / Wang, M. / Liu, Y. / Gao, F. / Liu, J. / Feng, E. / He, J. / Wang, J. / Liu, H. / Jiang, H. / Gao, G.F.
History
DepositionAug 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2011Provider: 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_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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: Neuraminidase
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,49220
Polymers85,4552
Non-polymers3,03718
Water22,0321223
1
A: Neuraminidase
B: Neuraminidase
hetero molecules

A: Neuraminidase
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,98540
Polymers170,9114
Non-polymers6,07436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area18410 Å2
ΔGint-143 kcal/mol
Surface area45090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.664, 137.102, 118.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-603-

CA

21A-651-

HOH

31B-750-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neuraminidase /


Mass: 42727.629 Da / Num. of mol.: 2 / Fragment: UNP residues 82-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/California/04/2009(H1N1) / Gene: NA / Plasmid: pAcGP67-B / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C3W5S3

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Sugars , 3 types, 6 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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.: 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
#5: Sugar ChemComp-LVO / 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-9-O-octanoyl-D-glycero-D-galacto-non-2-enonic acid / 5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-9-O-octanoyl-D-glycero-D-galacto-non-2-enonic acid / Laninamivir octanoate


Type: D-saccharide / Mass: 472.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N4O8

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Non-polymers , 4 types, 1235 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1223 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16M calcium acetate hydrate, 0.08M sodium cacodylate trihydrate, 14.4% polyethylene glycol 8000, 20% glycerol , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 125553 / Num. obs: 125553 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 7.63 Å2
Reflection shellResolution: 1.6→1.66 Å / % possible all: 99

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NSS

3nss


Resolution: 1.602→25.895 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.9133 / SU ML: 0.16 / σ(F): 0.11 / Phase error: 15.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 6161 5.02 %RANDOM
Rwork0.14 ---
obs0.1419 122842 97.27 %-
all-122842 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.497 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 55.6 Å2 / Biso mean: 12.2263 Å2 / Biso min: 1.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.0229 Å20 Å2-0 Å2
2--2.1119 Å20 Å2
3----2.1348 Å2
Refinement stepCycle: LAST / Resolution: 1.602→25.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5982 0 181 1223 7386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046393
X-RAY DIFFRACTIONf_angle_d1.0698682
X-RAY DIFFRACTIONf_dihedral_angle_d21.8812329
X-RAY DIFFRACTIONf_chiral_restr0.073928
X-RAY DIFFRACTIONf_plane_restr0.0081123
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6022-1.62040.20361790.13213365354485
1.6204-1.63950.18552050.12173655386093
1.6395-1.65950.17982150.12163714392994
1.6595-1.68050.16732030.11983731393494
1.6805-1.70260.19541980.12023713391194
1.7026-1.72590.18661770.1193782395995
1.7259-1.75050.16632060.11973800400696
1.7505-1.77670.18972020.11873846404896
1.7767-1.80440.18131900.1243791398196
1.8044-1.8340.16242060.11943829403597
1.834-1.86560.17672090.11733908411797
1.8656-1.89950.16562050.11763851405698
1.8995-1.9360.1531940.11553932412698
1.936-1.97560.14571950.11853922411798
1.9756-2.01850.1522230.11563941416499
2.0185-2.06540.15031980.11323889408799
2.0654-2.11710.161990.11823967416699
2.1171-2.17430.16412050.12433937414299
2.1743-2.23820.18491940.13073966416099
2.2382-2.31040.17732420.13243906414899
2.3104-2.39290.17952090.13573975418499
2.3929-2.48870.17162190.13863968418799
2.4887-2.60180.1982030.14823990419399
2.6018-2.73890.18441970.15173994419199
2.7389-2.91030.19042140.15373995420999
2.9103-3.13460.15762060.149540294235100
3.1346-3.44940.14972250.142940054230100
3.4494-3.9470.15752120.141840864298100
3.947-4.96710.1612140.142440624276100
4.9671-25.8980.2262170.19774132434998

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