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- PDB-4gdj: A subtype N10 neuraminidase-like protein of A/little yellow-shoul... -

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Basic information

Entry
Database: PDB / ID: 4gdj
TitleA subtype N10 neuraminidase-like protein of A/little yellow-shouldered bat/Guatemala/060/2010
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / INFLUENZA VIRUS / NEURAMINIDASE-LIKE / N10 / BETA PROPELLER / ECTODOMAIN
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structures of two subtype N10 neuraminidase-like proteins from bat influenza A viruses reveal a diverged putative active site.
Authors: Zhu, X. / Yang, H. / Guo, Z. / Yu, W. / Carney, P.J. / Li, Y. / Chen, L.M. / Paulson, J.C. / Donis, R.O. / Tong, S. / Stevens, J. / Wilson, I.A.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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_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_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 / _struct_conn.conn_type_id / _struct_conn.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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,29418
Polymers166,9404
Non-polymers4,35414
Water13,295738
1
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9345
Polymers41,7351
Non-polymers1,1994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9345
Polymers41,7351
Non-polymers1,1994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7134
Polymers41,7351
Non-polymers9783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7134
Polymers41,7351
Non-polymers9783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.902, 107.902, 345.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-724-

HOH

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Components

#1: Protein
Neuraminidase


Mass: 41735.004 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus
Strain: A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))
Gene: NA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: H6QM95
#2: Polysaccharide
beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1221m-1a_1-5]/1-2-1-3/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 738 / Source method: isolated from a natural source / Formula: H2O
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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 295 K / pH: 8
Details: 0.2 M Mg nitrate, 20% glycerol, 18% polyethylene glycol 4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2011
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 135663 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 43.1 Å2 / Rsym value: 0.099 / Net I/σ(I): 18.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.67 / % possible all: 86.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.85 Å / SU ML: 0.61 / σ(F): 1.33 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 6797 5.02 %
Rwork0.189 --
obs0.191 135354 97.9 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.73 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.8874 Å20 Å2-0 Å2
2--4.8874 Å2-0 Å2
3----9.7749 Å2
Refinement stepCycle: LAST / Resolution: 2→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9897 0 280 738 10915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310538
X-RAY DIFFRACTIONf_angle_d1.57914266
X-RAY DIFFRACTIONf_dihedral_angle_d22.2683972
X-RAY DIFFRACTIONf_chiral_restr0.0971633
X-RAY DIFFRACTIONf_plane_restr0.0071776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02240.37791960.32133670X-RAY DIFFRACTION85
2.0224-2.04620.35552000.30123881X-RAY DIFFRACTION90
2.0462-2.07120.3062140.28723961X-RAY DIFFRACTION92
2.0712-2.09740.3171770.27094122X-RAY DIFFRACTION95
2.0974-2.1250.31652250.25134170X-RAY DIFFRACTION97
2.125-2.15410.30732380.23754240X-RAY DIFFRACTION98
2.1541-2.18490.26352410.22754255X-RAY DIFFRACTION99
2.1849-2.21750.28942390.23594268X-RAY DIFFRACTION99
2.2175-2.25210.27392090.22994300X-RAY DIFFRACTION99
2.2521-2.28910.28192370.21054296X-RAY DIFFRACTION99
2.2891-2.32850.24322280.19444264X-RAY DIFFRACTION99
2.3285-2.37090.2172360.19434307X-RAY DIFFRACTION100
2.3709-2.41650.27482220.18844343X-RAY DIFFRACTION99
2.4165-2.46580.2482310.19194329X-RAY DIFFRACTION99
2.4658-2.51940.24742180.19044313X-RAY DIFFRACTION100
2.5194-2.5780.23552400.18364345X-RAY DIFFRACTION100
2.578-2.64250.24412260.19054349X-RAY DIFFRACTION100
2.6425-2.71390.25162430.1944329X-RAY DIFFRACTION100
2.7139-2.79380.24622450.17994328X-RAY DIFFRACTION100
2.7938-2.88390.20972090.17734383X-RAY DIFFRACTION100
2.8839-2.9870.21872140.17554395X-RAY DIFFRACTION100
2.987-3.10660.21782190.17194363X-RAY DIFFRACTION100
3.1066-3.24790.20812040.17054426X-RAY DIFFRACTION100
3.2479-3.41910.20812390.17144366X-RAY DIFFRACTION100
3.4191-3.63330.20972310.17384377X-RAY DIFFRACTION99
3.6333-3.91370.19392390.16054374X-RAY DIFFRACTION99
3.9137-4.30740.17392510.14824398X-RAY DIFFRACTION99
4.3074-4.93010.15062510.13644407X-RAY DIFFRACTION98
4.9301-6.20940.19782110.17524473X-RAY DIFFRACTION98
6.2094-48.8630.26522640.24484525X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 25.3619 Å / Origin y: 0.9712 Å / Origin z: 56.9826 Å
111213212223313233
T0.1926 Å2-0.0163 Å20.001 Å2-0.0978 Å20.0048 Å2--0.1546 Å2
L0.2377 °2-0.054 °20.0718 °2-0.0933 °2-0.0837 °2--0.368 °2
S-0.0451 Å °0.0034 Å °-0.0003 Å °0.0078 Å °0.0226 Å °-0.0067 Å °-0.0107 Å °-0.0141 Å °0.0231 Å °
Refinement TLS groupSelection details: ALL

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