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- PDB-4qn5: Neuraminidase N5 binds LSTa at the second SIA binding site -

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Basic information

Entry
Database: PDB / ID: 4qn5
TitleNeuraminidase N5 binds LSTa at the second SIA binding site
ComponentsNeuraminidase
KeywordsHYDROLASE / 6-BLADED BETA-PROPELLER / CALCIUM BINDING / GLYCOSYLATION
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 / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / 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
N-acetyl-alpha-neuraminic acid / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSun, X. / Li, Q. / Wu, Y. / Liu, Y. / Qi, J. / Vavricka, C.J. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2014
Title: Structure of influenza virus N7: the last piece of the neuraminidase "jigsaw" puzzle.
Authors: Sun, X. / Li, Q. / Wu, Y. / Wang, M. / Liu, Y. / Qi, J. / Vavricka, C.J. / Gao, G.F.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Other
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_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.id / _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_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_label_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_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)89,79312
Polymers87,0642
Non-polymers2,73010
Water13,385743
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,18024
Polymers174,1284
Non-polymers5,05320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area19830 Å2
ΔGint-94 kcal/mol
Surface area47100 Å2
MethodPISA
2
B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,99324
Polymers174,1284
Non-polymers5,86520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area20620 Å2
ΔGint-79 kcal/mol
Surface area47720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.251, 112.251, 66.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-1048-

HOH

21A-1056-

HOH

31A-1062-

HOH

41B-852-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neuraminidase /


Mass: 43531.934 Da / Num. of mol.: 2 / Fragment: UNP residues 79-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/mallard duck/ALB/60/1976(H12N5))
Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q20UH7

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Sugars , 4 types, 8 molecules

#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#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.: 1
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.: 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
#6: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 745 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.5
Details: 0.1M HEPES, 12%(W/V) POLYETHYLENE GLYCOL 3350, pH 7.5, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 125014 / Num. obs: 125014 / % possible obs: 95.7 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Biso Wilson estimate: 9.33 Å2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 100

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Processing

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

3sal


Resolution: 1.7→42.96 Å / FOM work R set: 0.9126 / SU ML: 0.18 / σ(F): 0.08 / Phase error: 15.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1759 4404 4.99 %Random
Rwork0.1172 ---
all0.1201 88296 --
obs0.1201 88296 96.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.695 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 89.02 Å2 / Biso mean: 15.93 Å2 / Biso min: 1.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.0737 Å2-0 Å20 Å2
2---0.0737 Å2-0 Å2
3---0.1474 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 178 743 7005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036442
X-RAY DIFFRACTIONf_angle_d1.0438739
X-RAY DIFFRACTIONf_chiral_restr0.134964
X-RAY DIFFRACTIONf_plane_restr0.0031113
X-RAY DIFFRACTIONf_dihedral_angle_d20.6182316
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 (%)
1.6998-1.71910.21841350.12362557269289
1.7191-1.73930.23121490.11092590273991
1.7393-1.76050.19321450.10572589273490
1.7605-1.78280.23761170.11172594271190
1.7828-1.80630.20451320.10572667279991
1.8063-1.8310.20471520.10912607275992
1.831-1.85720.18981630.1052683284693
1.8572-1.88490.21331330.1072708284194
1.8849-1.91430.19671460.10412744289095
1.9143-1.94570.19061260.09972752287896
1.9457-1.97930.17061460.09652791293795
1.9793-2.01530.17611480.09942811295999
2.0153-2.0540.16451290.10052836296598
2.054-2.09590.18621420.09992873301599
2.0959-2.14150.18311670.09822847301499
2.1415-2.19130.14671490.09432834298399
2.1913-2.24610.16821620.09672870303299
2.2461-2.30690.15091270.09712860298799
2.3069-2.37470.14441420.09992887302999
2.3747-2.45140.17321580.11062834299299
2.4514-2.5390.16971750.11452831300699
2.539-2.64060.20261640.12382858302299
2.6406-2.76080.16921590.12552859301899
2.7608-2.90630.16861690.12642843301298
2.9063-3.08840.19661280.12752885301399
3.0884-3.32670.15991290.128529283057100
3.3267-3.66130.14121540.113429113065100
3.6613-4.19080.16121530.1129373090100
4.1908-5.27840.14741430.108129333076100
5.2784-42.97330.17431620.15322973313599

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