[English] 日本語
Yorodumi
- PDB-2o4x: Crystal structure of human P100 tudor domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o4x
TitleCrystal structure of human P100 tudor domain
Components(Staphylococcal nuclease domain-containing protein 1) x 2
KeywordsHYDROLASE / OB fold / beta barrel / aromatic cage
Function / homology
Function and homology information


regulation of cell cycle process / miRNA catabolic process / RISC complex binding / dense body / nuclease activity / regulatory ncRNA-mediated gene silencing / RISC complex / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / mRNA catabolic process ...regulation of cell cycle process / miRNA catabolic process / RISC complex binding / dense body / nuclease activity / regulatory ncRNA-mediated gene silencing / RISC complex / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / mRNA catabolic process / RNA endonuclease activity / transcription coregulator activity / osteoblast differentiation / melanosome / Signaling by BRAF and RAF1 fusions / endonuclease activity / cadherin binding / RNA binding / extracellular exosome / membrane / nucleus / cytosol
Similarity search - Function
: / RNA-induced silencing complex, nuclease component Tudor-SN / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / Thermonuclease active site / Thermonuclease family signature 2. ...: / RNA-induced silencing complex, nuclease component Tudor-SN / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Staphylococcal nuclease domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Pt-SAS / Resolution: 2 Å
AuthorsShaw, N. / Zhao, M. / Cheng, C. / Xu, H. / Yang, J. / Silvennoinen, O. / Rao, Z. / Wang, B.C. / Liu, Z.J.
CitationJournal: To be Published
Title: Crystal structure of human P100 tudor domain
Authors: Shaw, N. / Zhao, M. / Cheng, C. / Xu, H. / Yang, J. / Silvennoinen, O. / Rao, Z. / Wang, B.C. / Liu, Z.J.
History
DepositionDec 5, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Staphylococcal nuclease domain-containing protein 1
B: Staphylococcal nuclease domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)34,9582
Polymers34,9582
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.931, 93.413, 95.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Staphylococcal nuclease domain-containing protein 1 / p100 co-activator / 100 kDa coactivator / EBNA2 coactivator p100


Mass: 24569.662 Da / Num. of mol.: 1 / Fragment: residues 654-870
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7KZF4
#2: Protein Staphylococcal nuclease domain-containing protein 1 / p100 co-activator / 100 kDa coactivator / EBNA2 coactivator p100


Mass: 10388.744 Da / Num. of mol.: 1 / Fragment: residues 680-795
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7KZF4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.18 Å3/Da / Density % sol: 61.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 2.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10.0mg/ml), RESERVOIR SOLUTION CONTAING 20% PEG 8000, 100.0mM PHOSPHATE, 0.1M HEPES pH 4.2 , VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 16, 2006
RadiationMonochromator: SI Channel 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→44.24 Å / Num. obs: 29102 / Rsym value: 0.078
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
XFITdata reduction
RefinementMethod to determine structure: Pt-SAS / Resolution: 2→44 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.794 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24919 1701 5.5 %RANDOM
Rwork0.23338 ---
obs0.23427 29102 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.325 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--0.84 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 0 156 2592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222493
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9523381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3865301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12323.52125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1115414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8981521
X-RAY DIFFRACTIONr_chiral_restr0.0730.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021933
X-RAY DIFFRACTIONr_nbd_refined0.2190.31062
X-RAY DIFFRACTIONr_nbtor_refined0.3190.51708
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.5243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.512
X-RAY DIFFRACTIONr_mcbond_it1.15921572
X-RAY DIFFRACTIONr_mcangle_it1.83732465
X-RAY DIFFRACTIONr_scbond_it1.12821049
X-RAY DIFFRACTIONr_scangle_it1.7283916
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 126 -
Rwork0.295 2060 -
obs--100 %

+
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