[English] 日本語
Yorodumi
- PDB-2x8a: Human Nuclear Valosin containing protein Like (NVL), C-terminal A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x8a
TitleHuman Nuclear Valosin containing protein Like (NVL), C-terminal AAA- ATPase domain
ComponentsNUCLEAR VALOSIN-CONTAINING PROTEIN-LIKE
KeywordsNUCLEAR PROTEIN
Function / homology
Function and homology information


regulation of protein localization to nucleolus / preribosome binding / telomerase holoenzyme complex / positive regulation of telomerase activity / ribosomal large subunit biogenesis / rRNA processing / ribosome biogenesis / positive regulation of protein binding / nucleolus / ATP hydrolysis activity ...regulation of protein localization to nucleolus / preribosome binding / telomerase holoenzyme complex / positive regulation of telomerase activity / ribosomal large subunit biogenesis / rRNA processing / ribosome biogenesis / positive regulation of protein binding / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
NVL2, nucleolin binding domain / NVL2, N-terminal domain superfamily / Nucleolin binding domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) ...NVL2, nucleolin binding domain / NVL2, N-terminal domain superfamily / Nucleolin binding domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Nuclear valosin-containing protein-like
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMoche, M. / Schuetz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Moche, M. / Schuetz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Kraulis, P. / Nordlund, P. / Nyman, T. / Persson, C. / Sehic, A. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / VanDenBerg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H.
CitationJournal: To be Published
Title: Human Nuclear Valosin Containing Protein Like (Nvl) , C-Terminal Aaa-ATPase Domain
Authors: Moche, M. / Schuetz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. ...Authors: Moche, M. / Schuetz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Kraulis, P. / Nordlund, P. / Nyman, T. / Persson, C. / Sehic, A. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Vandenberg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H.
History
DepositionMar 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: NUCLEAR VALOSIN-CONTAINING PROTEIN-LIKE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0033
Polymers29,8131
Non-polymers1902
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.989, 77.989, 86.038
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein NUCLEAR VALOSIN-CONTAINING PROTEIN-LIKE


Mass: 29813.424 Da / Num. of mol.: 1 / Fragment: C-TERMINAL AAA-ATPASE DOMAIN, 574-845
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) GOLD PRARE2 / References: UniProt: O15381
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsWE EXPRESSED THE C-TERMINAL DOMAIN OF THIS PROTEIN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.45 %
Description: SEARCH MODEL WAS GENERATED USING THE CASPR SERVER

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→28.9 Å / Num. obs: 8823 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 20.7 % / Biso Wilson estimate: 84.02 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 29.5
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.4 / % possible all: 62.2

-
Processing

Software
NameVersionClassification
BUSTER-TNT2.9.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→17.85 Å / Cor.coef. Fo:Fc: 0.9301 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.354 / SU Rfree Blow DPI: 0.216 / SU Rfree Cruickshank DPI: 0.209
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 832 9.45 %RANDOM
Rwork0.2105 ---
obs0.2141 8806 --
Displacement parametersBiso mean: 81.08 Å2
Baniso -1Baniso -2Baniso -3
1--10.8396 Å20 Å20 Å2
2---10.8396 Å20 Å2
3---21.6791 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.6→17.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1705 0 10 12 1727
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011768HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.162415HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d806SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes264HARMONIC5
X-RAY DIFFRACTIONt_it1768HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion3.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion248SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2146SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.91 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2927 238 10.46 %
Rwork0.2529 2037 -
all0.2573 2275 -

+
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