[English] 日本語
Yorodumi
- PDB-7bwu: Restructuring hemagglutinin-neuraminidase (HN) of Newcastle disea... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bwu
TitleRestructuring hemagglutinin-neuraminidase (HN) of Newcastle disease virus produced from Oryza sativa
ComponentsHemagglutinin-neuraminidase
KeywordsVIRAL PROTEIN / hemagglutinin-neuraminidase / Plant-produced / Restructuring tetramer
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane ...: / : / : / exo-alpha-sialidase / host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / plasma membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesAvian avulavirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsMa, F.S. / Zhang, G.P.
CitationJournal: To Be Published
Title: Restructuring a dimer antigen in transgenic rice system for high efficient B cell activation: Development of a super effective vaccine against Newcastle Disease Virus
Authors: Ma, F.S. / Zhang, E.Q. / Xu, Q.R. / Guo, J.Q. / Zhang, G.P.
History
DepositionApr 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 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
B: Hemagglutinin-neuraminidase
D: Hemagglutinin-neuraminidase
A: Hemagglutinin-neuraminidase
C: Hemagglutinin-neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,93416
Polymers232,5214
Non-polymers1,41412
Water20,3751131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Comparing crystal structure with the structure envelop obtained by SAXS, the results show that the structure obtained by SAXS can be well matched with the crystal structure of HN tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-33 kcal/mol
Surface area59960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.880, 142.070, 191.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Hemagglutinin-neuraminidase


Mass: 58130.156 Da / Num. of mol.: 4 / Mutation: M443T
Source method: isolated from a genetically manipulated source
Details: Authos linked two HN domains in the expression but the link is missing in the coordinate and they don't know which two molecules should be linked together.
Source: (gene. exp.) Avian avulavirus 1 / Gene: HN / Production host: Oryza sativa (Asian cultivated rice) / References: UniProt: I7EFR1
#2: 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.: 4
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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 1131 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60% Tacsimate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.87→41.53 Å / Num. obs: 188493 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.032 / Rrim(I) all: 0.118 / Net I/σ(I): 15
Reflection shellResolution: 1.87→1.93 Å / Num. unique obs: 18656 / CC1/2: 0.999

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data processing
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T1E

3t1e


Resolution: 1.87→39.863 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.62
RfactorNum. reflection% reflection
Rfree0.1951 9289 4.93 %
Rwork0.1668 --
obs0.1682 188462 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.96 Å2 / Biso mean: 38.5067 Å2 / Biso min: 18.42 Å2
Refinement stepCycle: final / Resolution: 1.87→39.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13727 0 84 1131 14942
Biso mean--57.55 44.39 -
Num. residues----1779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714176
X-RAY DIFFRACTIONf_angle_d0.91919305
X-RAY DIFFRACTIONf_chiral_restr0.0562181
X-RAY DIFFRACTIONf_plane_restr0.0062478
X-RAY DIFFRACTIONf_dihedral_angle_d4.1658417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.87-1.89130.32063000.27445914
1.8913-1.91350.30883070.25965958
1.9135-1.93680.30023010.24965872
1.9368-1.96140.28753330.24195863
1.9614-1.98720.27243250.23165947
1.9872-2.01440.26993050.21365891
2.0144-2.04320.24082890.20845930
2.0432-2.07370.25422810.2025951
2.0737-2.10610.22312920.19395951
2.1061-2.14060.22463190.19045930
2.1406-2.17750.22463110.18275923
2.1775-2.21710.23543100.18755937
2.2171-2.25970.21953170.17955933
2.2597-2.30580.21562960.17885901
2.3058-2.3560.21073160.17295956
2.356-2.41080.2143430.17725925
2.4108-2.47110.20722950.1765979
2.4711-2.53790.22353050.17455944
2.5379-2.61250.21583470.17595921
2.6125-2.69680.20983230.17075947
2.6968-2.79320.19373020.16566005
2.7932-2.9050.20173280.16615945
2.905-3.03720.20992900.16325964
3.0372-3.19720.21563020.15985993
3.1972-3.39740.17042910.15256047
3.3974-3.65960.15752970.14446055
3.6596-4.02760.152830.14246057
4.0276-4.60960.15073110.13246077
4.6096-5.80480.16623430.14246106
5.8048-100.18813270.18356351
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9968-0.0874-0.02232.10230.3951.50440.05770.2928-0.0191-0.49790.0335-0.099-0.25320.0538-0.02050.3515-0.00890.06010.37120.00510.2752-63.2754-28.2995-67.2989
20.96570.26180.09591.82780.3661.4022-0.02410.4072-0.182-0.55550.0776-0.2191-0.11130.139-0.04170.38450.01870.07480.4596-0.11980.3056-63.2626-44.9725-75.9106
30.75790.0897-0.0191.08140.35091.03530.01770.1243-0.3498-0.06260.0724-0.12980.12390.1161-0.05870.21230.0164-0.01080.2771-0.080.3987-66.8212-52.1562-56.8872
40.7640.4248-0.02821.1352-0.04220.70810.0501-0.0533-0.08440.2249-0.03130.06880.07-0.02-0.03050.2414-0.00040.020.2056-0.01950.2356-11.6088-67.0075-34.7416
51.4886-0.1289-0.33921.691-0.01740.98690.0537-0.14090.17790.21360.03720.1505-0.109-0.0838-0.07070.21490.00480.04860.2247-0.03050.2764-19.8925-58.6764-37.474
60.87450.0920.04980.70140.1581.24190.0263-0.3059-0.01260.3751-0.03530.09750.0288-0.03060.0110.4953-0.03210.06250.3632-0.00770.283-13.8428-60.2566-14.2682
71.05710.32180.09051.0304-0.43341.13050.0509-0.0525-0.09780.318-0.0646-0.26520.00870.16720.02830.26110.0047-0.02140.22-0.01440.2268-1.9073-64.9615-32.287
81.2178-0.3318-0.3141.03510.00450.88570.02480.13320.0593-0.02290.07290.2866-0.0308-0.2283-0.10640.19090.014-0.00760.28290.04730.3353-24.8893-48.1501-51.8378
91.2887-0.15630.47032.36820.51810.9774-0.01550.0171-0.0411-0.07940.02410.16550.0143-0.0451-0.09050.2117-0.0007-0.01430.23720.01630.2868-19.7676-58.2735-49.284
100.87210.0933-0.22371.7787-0.20460.98120.01670.40790.0853-0.55510.07190.25340.0979-0.178-0.08140.3678-0.0053-0.09070.43910.05820.2759-18.6391-51.6326-72.45
110.9663-0.02210.00120.7859-0.21481.03350.03780.10730.42360.01340.03550.1083-0.1581-0.1023-0.05630.22090.01670.01620.28220.0460.4135-18.7624-39.3353-54.2492
120.72860.31880.03661.1513-0.26660.79610.0403-0.01540.03570.2371-0.0037-0.0201-0.13910.0166-0.03530.2563-0.0023-0.02230.19810.01530.2443-73.1968-23.6382-34.6893
131.5113-0.43840.38091.56360.07250.93380.0517-0.1012-0.20890.24650.0352-0.06050.08070.0466-0.08750.233-0.0051-0.05250.21690.0140.2628-64.716-32.1016-36.6886
140.8084-0.01930.11060.7578-0.20830.86620.0745-0.1076-0.24630.2899-0.1155-0.26210.03980.13040.04320.4315-0.018-0.14610.30760.02150.374-59.6728-35.9268-20.711
150.84940.01510.10331.1532-0.11671.26040.1585-0.2990.07010.5691-0.1005-0.0553-0.0341-0.0414-0.03070.5823-0.0755-0.02750.3310.00020.2429-73.9798-27.2737-10.4533
161.14450.3935-0.05230.76010.10691.14580.0881-0.1110.05260.3882-0.0350.2147-0.0477-0.1796-0.03810.28580.00390.0430.20580.00230.2171-83.864-27.062-29.0687
171.1090.00590.19130.92180.11820.7910.03990.104-0.179-0.01290.0412-0.28430.07470.2034-0.06630.20480.0245-0.00960.2896-0.03640.3833-59.6367-43.6764-50.7669
181.136-0.0215-0.3971.8776-0.17951.3150.03980.145-0.04280.0133-0.0064-0.1407-0.05620.049-0.09250.18520.00830.00310.2249-0.01810.2934-63.9768-32.7515-48.218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 230 through 320 )C230 - 320
2X-RAY DIFFRACTION2chain 'C' and (resid 321 through 444 )C321 - 444
3X-RAY DIFFRACTION3chain 'C' and (resid 445 through 569 )C445 - 569
4X-RAY DIFFRACTION4chain 'B' and (resid 126 through 192 )B126 - 192
5X-RAY DIFFRACTION5chain 'B' and (resid 193 through 229 )B193 - 229
6X-RAY DIFFRACTION6chain 'B' and (resid 230 through 477 )B230 - 477
7X-RAY DIFFRACTION7chain 'B' and (resid 478 through 569 )B478 - 569
8X-RAY DIFFRACTION8chain 'D' and (resid 122 through 192 )D122 - 192
9X-RAY DIFFRACTION9chain 'D' and (resid 193 through 229 )D193 - 229
10X-RAY DIFFRACTION10chain 'D' and (resid 230 through 477 )D230 - 477
11X-RAY DIFFRACTION11chain 'D' and (resid 478 through 568 )D478 - 568
12X-RAY DIFFRACTION12chain 'A' and (resid 126 through 192 )A126 - 192
13X-RAY DIFFRACTION13chain 'A' and (resid 193 through 229 )A193 - 229
14X-RAY DIFFRACTION14chain 'A' and (resid 230 through 285 )A230 - 285
15X-RAY DIFFRACTION15chain 'A' and (resid 286 through 444 )A286 - 444
16X-RAY DIFFRACTION16chain 'A' and (resid 445 through 568 )A445 - 568
17X-RAY DIFFRACTION17chain 'C' and (resid 125 through 192 )C125 - 192
18X-RAY DIFFRACTION18chain 'C' and (resid 193 through 229 )C193 - 229

+
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