[English] 日本語
Yorodumi
- PDB-2vtx: ACTIVATION OF NUCLEOPLASMIN, AN OLIGOMERIC HISTONE CHAPERONE, CHA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vtx
TitleACTIVATION OF NUCLEOPLASMIN, AN OLIGOMERIC HISTONE CHAPERONE, CHALLENGES ITS STABILITY
Components(NPM-A PROTEIN) x 2
KeywordsNUCLEAR PROTEIN / NUCLEOPLASMIN / PHOSPHORYLATION / PROTEIN STABILITY / OLIGOMERIC PROTEIN
Function / homology
Function and homology information


sperm DNA decondensation / importin-alpha family protein binding / histone chaperone activity / single fertilization / nucleosome binding / positive regulation of DNA replication / histone binding / chromatin remodeling / chromatin binding / nucleolus ...sperm DNA decondensation / importin-alpha family protein binding / histone chaperone activity / single fertilization / nucleosome binding / positive regulation of DNA replication / histone binding / chromatin remodeling / chromatin binding / nucleolus / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
Nucleoplasmin core domain / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nucleoplasmin / Npm-A protein
Similarity search - Component
Biological speciesXENOPUS LAEVIS (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTaneva, S.G. / Munoz, I.G. / Franco, G. / Falces, J. / Arregi, I. / Muga, A. / Montoya, G. / Urbaneja, M.A. / Banuelos, S.
CitationJournal: Biochemistry / Year: 2008
Title: Activation of Nucleoplasmin, an Oligomeric Histone Chaperone, Challenges its Stability.
Authors: Taneva, S.G. / Munoz, I.G. / Franco, G. / Falces, J. / Arregi, I. / Muga, A. / Montoya, G. / Urbaneja, M.A. / Banuelos, S.
History
DepositionMay 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NPM-A PROTEIN
B: NPM-A PROTEIN
C: NPM-A PROTEIN
D: NPM-A PROTEIN
E: NPM-A PROTEIN
G: NPM-A PROTEIN
H: NPM-A PROTEIN
I: NPM-A PROTEIN
J: NPM-A PROTEIN
K: NPM-A PROTEIN


Theoretical massNumber of molelcules
Total (without water)133,85410
Polymers133,85410
Non-polymers00
Water3,117173
1
A: NPM-A PROTEIN
B: NPM-A PROTEIN
C: NPM-A PROTEIN
D: NPM-A PROTEIN
E: NPM-A PROTEIN


Theoretical massNumber of molelcules
Total (without water)66,9215
Polymers66,9215
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-88.3 kcal/mol
Surface area18350 Å2
MethodPISA
2
G: NPM-A PROTEIN
H: NPM-A PROTEIN
I: NPM-A PROTEIN
J: NPM-A PROTEIN
K: NPM-A PROTEIN


Theoretical massNumber of molelcules
Total (without water)66,9335
Polymers66,9335
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-89.7 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.034, 94.601, 176.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
NPM-A PROTEIN / CORE NUCLEOPLASMIN WITH 8 MUTATIONS


Mass: 13384.168 Da / Num. of mol.: 9 / Fragment: CORE DOMAIN, RESIDUES 1-120
Source method: isolated from a genetically manipulated source
Details: RESIDUES 2,3,5,7,8,15,66,96 FROM THE WTCORE WERE MUTATED TO ASP
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6GQG6, UniProt: P05221*PLUS
#2: Protein NPM-A PROTEIN / CORE NUCLEOPLASMIN WITH 8 MUTATIONS


Mass: 13396.222 Da / Num. of mol.: 1 / Fragment: CORE DOMAIN, RESIDUES 1-120
Source method: isolated from a genetically manipulated source
Details: RESIDUES 2,3,5,7,8,15,66,96 FROM THE WTCORE WERE MUTATED TO ASP
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6GQG6, UniProt: P05221*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 3 TO ASP ENGINEERED RESIDUE IN CHAIN A, THR 4 TO ASP ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, SER 3 TO ASP ENGINEERED RESIDUE IN CHAIN A, THR 4 TO ASP ENGINEERED RESIDUE IN CHAIN A, SER 6 TO ASP ENGINEERED RESIDUE IN CHAIN A, THR 8 TO ASP ENGINEERED RESIDUE IN CHAIN A, SER 9 TO ASP ENGINEERED RESIDUE IN CHAIN A, SER 16 TO ASP ENGINEERED RESIDUE IN CHAIN A, THR 67 TO ASP ENGINEERED RESIDUE IN CHAIN A, THR 97 TO ASP ENGINEERED RESIDUE IN CHAIN B, SER 3 TO ASP ENGINEERED RESIDUE IN CHAIN B, THR 4 TO ASP ENGINEERED RESIDUE IN CHAIN B, SER 6 TO ASP ENGINEERED RESIDUE IN CHAIN B, THR 8 TO ASP ENGINEERED RESIDUE IN CHAIN B, SER 9 TO ASP ENGINEERED RESIDUE IN CHAIN B, SER 16 TO ASP ENGINEERED RESIDUE IN CHAIN B, THR 67 TO ASP ENGINEERED RESIDUE IN CHAIN B, THR 97 TO ASP ENGINEERED RESIDUE IN CHAIN C, SER 3 TO ASP ENGINEERED RESIDUE IN CHAIN C, THR 4 TO ASP ENGINEERED RESIDUE IN CHAIN C, SER 6 TO ASP ENGINEERED RESIDUE IN CHAIN C, THR 8 TO ASP ENGINEERED RESIDUE IN CHAIN C, SER 9 TO ASP ENGINEERED RESIDUE IN CHAIN C, SER 16 TO ASP ENGINEERED RESIDUE IN CHAIN C, THR 67 TO ASP ENGINEERED RESIDUE IN CHAIN C, THR 97 TO ASP ENGINEERED RESIDUE IN CHAIN D, SER 3 TO ASP ENGINEERED RESIDUE IN CHAIN D, THR 4 TO ASP ENGINEERED RESIDUE IN CHAIN D, SER 6 TO ASP ENGINEERED RESIDUE IN CHAIN D, THR 8 TO ASP ENGINEERED RESIDUE IN CHAIN D, SER 9 TO ASP ENGINEERED RESIDUE IN CHAIN D, SER 16 TO ASP ENGINEERED RESIDUE IN CHAIN D, THR 67 TO ASP ENGINEERED RESIDUE IN CHAIN D, THR 97 TO ASP ENGINEERED RESIDUE IN CHAIN E, SER 3 TO ASP ENGINEERED RESIDUE IN CHAIN E, THR 4 TO ASP ENGINEERED RESIDUE IN CHAIN E, SER 6 TO ASP ENGINEERED RESIDUE IN CHAIN E, THR 8 TO ASP ENGINEERED RESIDUE IN CHAIN E, SER 9 TO ASP ENGINEERED RESIDUE IN CHAIN E, SER 16 TO ASP ENGINEERED RESIDUE IN CHAIN E, THR 67 TO ASP ENGINEERED RESIDUE IN CHAIN E, THR 97 TO ASP ENGINEERED RESIDUE IN CHAIN G, SER 3 TO ASP ENGINEERED RESIDUE IN CHAIN G, THR 4 TO ASP ENGINEERED RESIDUE IN CHAIN G, SER 6 TO ASP ENGINEERED RESIDUE IN CHAIN G, THR 8 TO ASP ENGINEERED RESIDUE IN CHAIN G, SER 9 TO ASP ENGINEERED RESIDUE IN CHAIN G, SER 16 TO ASP ENGINEERED RESIDUE IN CHAIN G, THR 67 TO ASP ENGINEERED RESIDUE IN CHAIN G, THR 97 TO ASP ENGINEERED RESIDUE IN CHAIN H, SER 3 TO ASP ENGINEERED RESIDUE IN CHAIN H, THR 4 TO ASP ENGINEERED RESIDUE IN CHAIN H, SER 6 TO ASP ENGINEERED RESIDUE IN CHAIN H, THR 8 TO ASP ENGINEERED RESIDUE IN CHAIN H, SER 9 TO ASP ENGINEERED RESIDUE IN CHAIN H, SER 16 TO ASP ENGINEERED RESIDUE IN CHAIN H, THR 67 TO ASP ENGINEERED RESIDUE IN CHAIN H, THR 97 TO ASP ENGINEERED RESIDUE IN CHAIN I, SER 3 TO ASP ENGINEERED RESIDUE IN CHAIN I, THR 4 TO ASP ENGINEERED RESIDUE IN CHAIN I, SER 6 TO ASP ENGINEERED RESIDUE IN CHAIN I, THR 8 TO ASP ENGINEERED RESIDUE IN CHAIN I, SER 9 TO ASP ENGINEERED RESIDUE IN CHAIN I, SER 16 TO ASP ENGINEERED RESIDUE IN CHAIN I, THR 67 TO ASP ENGINEERED RESIDUE IN CHAIN I, THR 97 TO ASP ENGINEERED RESIDUE IN CHAIN J, SER 3 TO ASP ENGINEERED RESIDUE IN CHAIN J, THR 4 TO ASP ENGINEERED RESIDUE IN CHAIN J, SER 6 TO ASP ENGINEERED RESIDUE IN CHAIN J, THR 8 TO ASP ENGINEERED RESIDUE IN CHAIN J, SER 9 TO ASP ENGINEERED RESIDUE IN CHAIN J, SER 16 TO ASP ENGINEERED RESIDUE IN CHAIN J, THR 67 TO ASP ENGINEERED RESIDUE IN CHAIN J, THR 97 TO ASP ENGINEERED RESIDUE IN CHAIN K, SER 3 TO ASP ENGINEERED RESIDUE IN CHAIN K, THR 4 TO ASP ENGINEERED RESIDUE IN CHAIN K, SER 6 TO ASP ENGINEERED RESIDUE IN CHAIN K, THR 8 TO ASP ENGINEERED RESIDUE IN CHAIN K, SER 9 TO ASP ENGINEERED RESIDUE IN CHAIN K, SER 16 TO ASP ENGINEERED RESIDUE IN CHAIN K, THR 67 TO ASP ENGINEERED RESIDUE IN CHAIN K, THR 97 TO ASP

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 54.86 % / Description: NONE
Crystal growpH: 4.6
Details: 15 MG/ML PROTEIN, 100MM NAAC, 20MM CACL2, 30% MPD, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9198
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 57758 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 17.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K5J

1k5j


Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.483 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1984 5 %RANDOM
Rwork0.182 ---
obs0.187 37569 100 %-
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: 39.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2--0.66 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7086 0 0 173 7259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0227217
X-RAY DIFFRACTIONr_bond_other_d0.0010.024825
X-RAY DIFFRACTIONr_angle_refined_deg2.4831.9799774
X-RAY DIFFRACTIONr_angle_other_deg1.252311928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9615901
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10925.362276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.298151247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.051520
X-RAY DIFFRACTIONr_chiral_restr0.1490.21159
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021267
X-RAY DIFFRACTIONr_nbd_refined0.2180.21125
X-RAY DIFFRACTIONr_nbd_other0.2110.24693
X-RAY DIFFRACTIONr_nbtor_refined0.1970.23173
X-RAY DIFFRACTIONr_nbtor_other0.1070.23965
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.310.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1660.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8581.55082
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.64427436
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.58232841
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.94.52338
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 136
Rwork0.211 2751

+
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