[English] 日本語
Yorodumi
- PDB-4dyn: Crystal Structure of WSN/A Influenza Nucleoprotein with BMS-88583... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dyn
TitleCrystal Structure of WSN/A Influenza Nucleoprotein with BMS-885838 Ligand Bound
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Chem-0MR / Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLewis, H.A. / Baldwin, E.T. / Steinbacher, S. / Maskos, K. / Mortl, M. / Kiefersauer, R. / Edavettal, S. / McDonnell, P.A. / Pearce, B.C. / Langley, D.R.
CitationJournal: To be Published
Title: To be determined
Authors: Lewis, H.A. / Baldwin, E.T. / Steinbacher, S. / Maskos, K. / Mortl, M. / Kiefersauer, R. / Edavettal, S. / McDonnell, P.A. / Pearce, B.C. / Langley, D.R.
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Nucleocapsid protein
B: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7664
Polymers113,6122
Non-polymers1,1542
Water1,71195
1
A: Nucleocapsid protein
hetero molecules

A: Nucleocapsid protein
hetero molecules

A: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,1496
Polymers170,4183
Non-polymers1,7313
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area14880 Å2
ΔGint-66 kcal/mol
Surface area49720 Å2
MethodPISA
2
B: Nucleocapsid protein
hetero molecules

B: Nucleocapsid protein
hetero molecules

B: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,1496
Polymers170,4183
Non-polymers1,7313
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area10640 Å2
ΔGint-59 kcal/mol
Surface area53610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.610, 145.610, 145.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

-
Components

#1: Protein Nucleocapsid protein / nucleoprotein


Mass: 56806.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/WSN/1933(H1N1) / Gene: NP / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: B4URF1, UniProt: Q1K9H2*PLUS
#2: Chemical ChemComp-0MR / N-[4-chloranyl-5-[4-[[3-(2-methoxyphenyl)-5-methyl-1,2-oxazol-4-yl]carbonyl]piperazin-1-yl]-2-nitro-phenyl]pyridine-2-carboxamide


Mass: 576.988 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H25ClN6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.26 Å3/Da / Density % sol: 45.68 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→43.9 Å / Num. all: 40358 / Num. obs: 40358

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.9 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.2599 / WRfactor Rwork: 0.2204 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7802 / SU B: 8.734 / SU ML: 0.209 / SU R Cruickshank DPI: 0.4217 / SU Rfree: 0.2891 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.422 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2909 981 2.4 %RANDOM
Rwork0.2423 ---
obs0.2435 40344 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.05 Å2 / Biso mean: 42.6526 Å2 / Biso min: 16.99 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6429 0 82 95 6606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216655
X-RAY DIFFRACTIONr_angle_refined_deg0.8181.9669014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.245867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84323.035257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.272151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3041550
X-RAY DIFFRACTIONr_chiral_restr0.050.21006
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025036
X-RAY DIFFRACTIONr_nbd_refined0.1590.22847
X-RAY DIFFRACTIONr_nbtor_refined0.2880.24625
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.2189
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.228
X-RAY DIFFRACTIONr_mcbond_it0.35424451
X-RAY DIFFRACTIONr_mcangle_it0.6232.56871
X-RAY DIFFRACTIONr_scbond_it0.42432673
X-RAY DIFFRACTIONr_scangle_it0.7134.52143
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 72 -
Rwork0.284 2863 -
all-2935 -
obs--99.83 %

+
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