[English] 日本語
Yorodumi
- PDB-3pto: Crystal Structure of an empty Vesicular Stomatitis Virus Nucleoca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pto
TitleCrystal Structure of an empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / nucleocapsid
Function / homology
Function and homology information


RNA replication / helical viral capsid / viral transcription / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Rhabdovirus nucleoprotein-like fold / Rhabdovirus nucleocapsid protein like domain / Rhabdovirus nucleoprotein-like / Nucleoprotein / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
URANYL (VI) ION / Nucleoprotein
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.008 Å
AuthorsLuo, M. / Green, T.J. / Rowse, M.
CitationJournal: J.Virol. / Year: 2011
Title: Access to RNA Encapsidated in the Nucleocapsid of Vesicular Stomatitis Virus.
Authors: Green, T.J. / Rowse, M. / Tsao, J. / Kang, J. / Ge, P. / Zhou, Z.H. / Luo, M.
History
DepositionDec 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,71420
Polymers236,6645
Non-polymers4,05015
Water00
1
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
hetero molecules

A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)481,42840
Polymers473,32810
Non-polymers8,10130
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area59010 Å2
ΔGint-384 kcal/mol
Surface area178140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.643, 234.062, 75.975
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 3:358 or resseq 365:422 )A3 - 358
121chain A and (resseq 3:358 or resseq 365:422 )A365 - 422
211chain B and (resseq 3:358 or resseq 365:422 )B3 - 358
221chain B and (resseq 3:358 or resseq 365:422 )B365 - 422
311chain C and (resseq 3:358 or resseq 365:422 )C3 - 358
321chain C and (resseq 3:358 or resseq 365:422 )C365 - 422
411chain D and (resseq 3:358 or resseq 365:422 )D3 - 358
421chain D and (resseq 3:358 or resseq 365:422 )D365 - 422
511chain E and (resseq 3:358 or resseq 365:422 )E3 - 358
521chain E and (resseq 3:358 or resseq 365:422 )E365 - 422

-
Components

#1: Protein
Nucleoprotein / NP / Nucleocapsid protein / Protein N


Mass: 47332.750 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Gene: N / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03521
#2: Chemical
ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: O2U
Nonpolymer detailsThe IUM REPRESENT URNAYL (IV) IONS [UO2]2+ EVEN THOUGH THE OXYGEN ATOMS COULD NOT BE ACCURATELY ...The IUM REPRESENT URNAYL (IV) IONS [UO2]2+ EVEN THOUGH THE OXYGEN ATOMS COULD NOT BE ACCURATELY PLACED DUE TO LOW RESOLUTION OF THE STRUCTURE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 5.5 % PEG 3350, 200 mM sodium chloride, 100mM sodium acetate, pH 4.5, vapor diffusion, hanging drop, temperature 293.0K

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MAR 325 CCD / Date: Jun 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 51615 / Num. obs: 51615 / % possible obs: 86.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.071
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.4 / % possible all: 39.4

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.008→38.763 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / σ(F): 0.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2907 1892 3.85 %RANDOM
Rwork0.2579 ---
all0.2592 49082 --
obs0.2592 49082 82.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.204 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso max: 232.58 Å2 / Biso mean: 100.4935 Å2 / Biso min: 57 Å2
Baniso -1Baniso -2Baniso -3
1-29.803 Å2-0 Å2-0 Å2
2---1.5395 Å20 Å2
3----28.2635 Å2
Refinement stepCycle: LAST / Resolution: 3.008→38.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16452 0 15 0 16467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01116827
X-RAY DIFFRACTIONf_angle_d1.37522782
X-RAY DIFFRACTIONf_chiral_restr0.0972479
X-RAY DIFFRACTIONf_plane_restr0.0052926
X-RAY DIFFRACTIONf_dihedral_angle_d17.5116252
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3284X-RAY DIFFRACTIONPOSITIONAL0.05
12B3284X-RAY DIFFRACTIONPOSITIONAL0.05
13C3269X-RAY DIFFRACTIONPOSITIONAL0.044
14D3284X-RAY DIFFRACTIONPOSITIONAL0.061
15E3277X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.008-3.0830.3922490.36511170121929
3.083-3.16630.395680.3351789185744
3.1663-3.25940.3308970.32492283238057
3.2594-3.36460.37461090.33052896300572
3.3646-3.48480.37351330.30413321345482
3.4848-3.62420.31361450.27433641378690
3.6242-3.7890.26011500.26453778392893
3.789-3.98860.2921560.26223862401895
3.9886-4.23820.31151590.25173931409097
4.2382-4.56490.2491610.23064004416598
4.5649-5.02350.26921600.22074057421799
5.0235-5.74830.24161650.22014059422499
5.7483-7.23460.27391680.24634132430099
7.2346-38.76580.27511720.24284267443998

+
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://pdbjlvh1.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