[English] 日本語
Yorodumi
- PDB-3pu0: Crystal Structure of a vesicular stomatitis virus nucleocapsid-po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pu0
TitleCrystal Structure of a vesicular stomatitis virus nucleocapsid-polyC complex
Components
  • Nucleoprotein
  • RNA (45-MER)
KeywordsVIRAL PROTEIN/RNA / RNA / nucleocapsid / VIRAL PROTEIN-RNA complex
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 / Nucleoprotein / Rhabdovirus nucleoprotein-like fold / Rhabdovirus nucleocapsid protein like domain / 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 / RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.09 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 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Apr 11, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / pdbx_entity_src_syn
Item: _diffrn_source.pdbx_synchrotron_beamline / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Feb 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
R: RNA (45-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,75326
Polymers250,3526
Non-polymers5,40120
Water00
1
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
R: RNA (45-MER)
hetero molecules

A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
R: RNA (45-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,50552
Polymers500,70412
Non-polymers10,80140
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area83040 Å2
ΔGint-548 kcal/mol
Surface area174410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.652, 235.554, 75.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:166 or resseq 171: 358 or resseq 365:422 )
211chain B and (resseq 2:166 or resseq 171: 358 or resseq 365:422 )
311chain C and (resseq 2:166 or resseq 171: 358 or resseq 365:422 )
411chain D and (resseq 2:166 or resseq 171: 358 or resseq 365:422 )
511chain E and (resseq 2:166 or resseq 171: 358 or resseq 365:422 )

-
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: RNA chain RNA (45-MER)


Mass: 13688.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Midland Reagent Company / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 20 / 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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 293 K / 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: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MAR 325 CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.09→50 Å / Num. all: 46101 / Num. obs: 46101 / % possible obs: 84.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 73.14 Å2
Reflection shellResolution: 3.09→3.21 Å / % possible all: 68

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOLREPphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→49.75 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.35 / Phase error: 32.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.29 1874 4.34 %
Rwork0.25 --
obs0.252 43132 78.5 %
all-43132 -
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.35 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 104.81 Å2
Baniso -1Baniso -2Baniso -3
1-61.9566 Å2-0 Å2-0 Å2
2---12.4335 Å20 Å2
3----49.5232 Å2
Refinement stepCycle: LAST / Resolution: 3.09→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16517 900 20 0 17437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01117883
X-RAY DIFFRACTIONf_angle_d1.44324402
X-RAY DIFFRACTIONf_dihedral_angle_d21.2776706
X-RAY DIFFRACTIONf_chiral_restr0.0932716
X-RAY DIFFRACTIONf_plane_restr0.0052984
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3256X-RAY DIFFRACTIONPOSITIONAL
12B3256X-RAY DIFFRACTIONPOSITIONAL0.043
13C3241X-RAY DIFFRACTIONPOSITIONAL0.045
14D3256X-RAY DIFFRACTIONPOSITIONAL0.049
15E3256X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0909-3.17450.4198910.34651993X-RAY DIFFRACTION50
3.1745-3.26790.35171050.33992408X-RAY DIFFRACTION60
3.2679-3.37330.37371070.32662490X-RAY DIFFRACTION62
3.3733-3.49390.32331140.30632632X-RAY DIFFRACTION65
3.4939-3.63370.35091270.27882698X-RAY DIFFRACTION68
3.6337-3.7990.34151300.27692798X-RAY DIFFRACTION70
3.799-3.99920.29591380.24673040X-RAY DIFFRACTION75
3.9992-4.24970.26521530.22893274X-RAY DIFFRACTION82
4.2497-4.57760.24561690.21083683X-RAY DIFFRACTION91
4.5776-5.03780.24731780.19953951X-RAY DIFFRACTION97
5.0378-5.76590.27091820.20753967X-RAY DIFFRACTION98
5.7659-7.26080.3011870.23264063X-RAY DIFFRACTION98
7.2608-49.75410.25861930.24524261X-RAY DIFFRACTION99

+
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