[English] 日本語
Yorodumi
- PDB-7xvr: Structure of neuraminidase from influenza B-like viruses derived ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xvr
TitleStructure of neuraminidase from influenza B-like viruses derived from spiny eel
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesWuhan spiny eel influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChai, Y. / Gao, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31872745 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structural and inhibitor sensitivity analysis of influenza B-like viral neuraminidases derived from Asiatic toad and spiny eel.
Authors: Li, L. / Chai, Y. / Peng, W. / Li, D. / Sun, L. / Gao, G.F. / Qi, J. / Xiao, H. / Liu, W.J. / von Itzstein, M. / Gao, F.
History
DepositionMay 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2256
Polymers87,7022
Non-polymers5234
Water5,747319
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,44912
Polymers175,4044
Non-polymers1,0458
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 area15160 Å2
ΔGint-55 kcal/mol
Surface area44290 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)176,44912
Polymers175,4044
Non-polymers1,0458
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area15080 Å2
ΔGint-51 kcal/mol
Surface area44990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.513, 126.513, 111.173
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

21B-601-

HOH

31B-743-

HOH

41B-744-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
d_1ens_1
d_2ens_1

NCS oper: (Code: givenMatrix: (-0.505372877498, -0.862900956325, 0.000440752284132), (-0.862900990769, 0.505372548476, -0.000683649468857), (0.000367177675389, -0.000725823481938, -0.99999966918) ...NCS oper: (Code: given
Matrix: (-0.505372877498, -0.862900956325, 0.000440752284132), (-0.862900990769, 0.505372548476, -0.000683649468857), (0.000367177675389, -0.000725823481938, -0.99999966918)
Vector: 63.2097901169, 63.1240080241, -87.7860767264)

-
Components

#1: Protein Neuraminidase


Mass: 43851.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wuhan spiny eel influenza virus / Gene: NA / Plasmid: pFastBac1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A2P1GNP4, exo-alpha-sialidase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4.0 M Potassium formate, 0.1 M BIS-TRIS propane pH 9.0, 2% w/v Polyethylene glycol monomethyl ether 2,000.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35110 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 33.14 Å2 / CC1/2: 0.979 / Rpim(I) all: 0.081 / Net I/σ(I): 10.9
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 4 / CC1/2: 0.811 / Rpim(I) all: 0.384

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K36

3k36


Resolution: 2.4→35.56 Å / SU ML: 0.2503 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.0753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1973 1669 4.93 %
Rwork0.1547 32207 -
obs0.1569 33876 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.77 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5910 0 30 319 6259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836084
X-RAY DIFFRACTIONf_angle_d0.9948275
X-RAY DIFFRACTIONf_chiral_restr0.056937
X-RAY DIFFRACTIONf_plane_restr0.00781075
X-RAY DIFFRACTIONf_dihedral_angle_d13.01542211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.22891350.18162556X-RAY DIFFRACTION94.65
2.47-2.550.24431150.17832664X-RAY DIFFRACTION97.92
2.55-2.640.26121120.182691X-RAY DIFFRACTION98.56
2.64-2.750.24781410.17552679X-RAY DIFFRACTION99.75
2.75-2.870.22461210.1832715X-RAY DIFFRACTION99.79
2.87-3.020.23291340.16162715X-RAY DIFFRACTION99.93
3.02-3.210.1941530.16112695X-RAY DIFFRACTION99.86
3.21-3.460.20461420.14812704X-RAY DIFFRACTION99.86
3.46-3.810.17541610.14622685X-RAY DIFFRACTION99.75
3.81-4.360.17981470.12132689X-RAY DIFFRACTION99.16
4.36-5.490.15551490.12662676X-RAY DIFFRACTION98.36
5.49-35.560.20411590.18082738X-RAY DIFFRACTION99.38
Refinement TLS params.Method: refined / Origin x: 22.8605256714 Å / Origin y: 46.7461024726 Å / Origin z: -43.8890188106 Å
111213212223313233
T0.19819921168 Å20.00966464471915 Å20.00735617118903 Å2-0.213117214592 Å2-0.0088063992652 Å2--0.193130713356 Å2
L0.301921364991 °20.403304434284 °2-0.0835970578079 °2-0.568687737216 °2-0.144009082276 °2--0.0523251869962 °2
S0.00179574442212 Å °-0.00439327276226 Å °0.0309582618339 Å °0.0208549983758 Å °-0.00541910670152 Å °0.0507619980497 Å °-0.00658453839384 Å °0.00236236120029 Å °0.00536307003913 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more