[English] 日本語
Yorodumi
- PDB-1pp1: Crystal structure of the Borna Disease Virus Nucleoprotein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pp1
TitleCrystal structure of the Borna Disease Virus Nucleoprotein
Componentsp40 nucleoprotein
KeywordsVIRAL PROTEIN / RNA VIRUS NUCLEOPROTEIN TETRAMER
Function / homology
Function and homology information


: / symbiont-mediated arrest of host cell cycle during G2/M transition / : / helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus
Similarity search - Function
borna disease virus nucleoprotein, domain 1 / borna disease virus nucleoprotein, domain 1 / borna disease virus nucleoprotein, domain 2 / borna disease virus nucleoprotein, domain 2 / P40 nucleoprotein, Borna disease virus / P40 nucleoprotein, subdomain 1, Borna disease virus / P40 nucleoprotein superfamily, Borna disease virus / Borna disease virus P40 protein / P40 nucleoprotein, subdomain 2, Borna disease virus / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesBorna disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsRudolph, M.G. / Kraus, I. / Dickmanns, A. / Garten, W. / Ficner, R.
CitationJournal: Structure / Year: 2003
Title: Crystal structure of the Borna Disease Virus nucleoprotein
Authors: Rudolph, M.G. / Kraus, I. / Dickmanns, A. / Eickmann, M. / Garten, W. / Ficner, R.
History
DepositionJun 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The authors state that the crystallographic data strongly support a tetramer. The authors can not confirm this at present, since there are no independent data published as to the oligomeric state of the protein in solution.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: p40 nucleoprotein


Theoretical massNumber of molelcules
Total (without water)42,0721
Polymers42,0721
Non-polymers00
Water6,882382
1
X: p40 nucleoprotein

X: p40 nucleoprotein

X: p40 nucleoprotein

X: p40 nucleoprotein


Theoretical massNumber of molelcules
Total (without water)168,2894
Polymers168,2894
Non-polymers00
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 area19400 Å2
ΔGint-103 kcal/mol
Surface area58530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.261, 100.261, 103.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein p40 nucleoprotein


Mass: 42072.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borna disease virus / Genus: Bornavirus / Plasmid: pMal-c2g / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01552, UniProt: P0C796*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 9 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
215 %PEG550 MME1reservoir
30.1 M1reservoirNaCl
42-5 mMdithiothreitol1reservoir
50.1 MBicine1reservoirpH9.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 0.9793, 0.802, 0.9787
DetectorType: MARRESEARCH / Detector: AREA DETECTOR
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.8021
30.97871
ReflectionResolution: 1.9→30 Å / Num. obs: 38615 / % possible obs: 95.3 % / Redundancy: 3.19 % / Biso Wilson estimate: 20.507 Å2 / Rsym value: 0.06 / Net I/σ(I): 17.07
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 3019 / Rsym value: 0.232 / % possible all: 75.1

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.23 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.377 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.105 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1822 1957 5.1 %RANDOM
Rwork0.15337 ---
obs0.15484 36657 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.554 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 0 382 2973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212662
X-RAY DIFFRACTIONr_bond_other_d0.0020.022450
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9583601
X-RAY DIFFRACTIONr_angle_other_deg1.41135722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7875333
X-RAY DIFFRACTIONr_chiral_restr0.0890.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022917
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02527
X-RAY DIFFRACTIONr_nbd_refined0.2170.2563
X-RAY DIFFRACTIONr_nbd_other0.2380.22661
X-RAY DIFFRACTIONr_nbtor_other0.0860.21400
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.235
X-RAY DIFFRACTIONr_mcbond_it1.0311.51668
X-RAY DIFFRACTIONr_mcangle_it1.91922698
X-RAY DIFFRACTIONr_scbond_it2.6693994
X-RAY DIFFRACTIONr_scangle_it4.3554.5903
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.291 110
Rwork0.246 2179
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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