[English] 日本語
Yorodumi
- PDB-3l46: Crystal structure of the second BRCT domain of epithelial cell tr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l46
TitleCrystal structure of the second BRCT domain of epithelial cell transforming 2 (ECT2)
ComponentsProtein ECT2
KeywordsSIGNALING PROTEIN / Guanine-nucleotide releasing factor / Phosphoprotein / Proto-oncogene / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of cytokinesis, actomyosin contractile ring assembly / centralspindlin complex / regulation of attachment of spindle microtubules to kinetochore / bicellular tight junction assembly / activation of GTPase activity / regulation of protein kinase activity / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / positive regulation of cytokinesis ...regulation of cytokinesis, actomyosin contractile ring assembly / centralspindlin complex / regulation of attachment of spindle microtubules to kinetochore / bicellular tight junction assembly / activation of GTPase activity / regulation of protein kinase activity / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / positive regulation of cytokinesis / activation of protein kinase activity / cleavage furrow / CDC42 GTPase cycle / mitotic cytokinesis / RHOA GTPase cycle / bicellular tight junction / RAC1 GTPase cycle / cellular response to calcium ion / positive regulation of neuron differentiation / GTPase activator activity / guanyl-nucleotide exchange factor activity / cellular response to ionizing radiation / protein homooligomerization / cell morphogenesis / mitotic spindle / cellular response to hydrogen peroxide / small GTPase binding / positive regulation of GTPase activity / positive regulation of protein import into nucleus / G alpha (12/13) signalling events / cell-cell junction / protein transport / nervous system development / cell cortex / midbody / positive regulation of canonical NF-kappaB signal transduction / cell differentiation / nuclear body / intracellular signal transduction / positive regulation of apoptotic process / centrosome / protein homodimerization activity / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / ECT2, PH domain / ECT2, BRCT0 domain / Guanine nucleotide exchange factor Ect2 / twin BRCT domain / BRCT domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily ...: / : / ECT2, PH domain / ECT2, BRCT0 domain / Guanine nucleotide exchange factor Ect2 / twin BRCT domain / BRCT domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / PH-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.482 Å
AuthorsNedyalkova, L. / Tempel, W. / Tong, Y. / Crombet, L. / Wang, H. / Guan, X. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Nedyalkova, L. / Tempel, W. / Tong, Y. / Crombet, L. / Wang, H. / Guan, X. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the second BRCT domain of epithelial cell transforming 2 (ECT2)
Authors: Nedyalkova, L. / Tempel, W. / Tong, Y. / Crombet, L. / Wang, H. / Guan, X. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionDec 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 17, 2014Group: Data collection / Version format compliance
Revision 1.3Oct 26, 2016Group: Other
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Protein ECT2
B: Protein ECT2


Theoretical massNumber of molelcules
Total (without water)26,2785
Polymers26,2782
Non-polymers03
Water2,144119
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-8 kcal/mol
Surface area9680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.158, 60.630, 74.004
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAuthors state that the biological unit of this fragment is not known.

-
Components

#1: Protein Protein ECT2 / Epithelial cell-transforming sequence 2 oncogene


Mass: 13138.763 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ECT2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9H8V3
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.8 Å3/Da / Density % sol: 31.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M sodium citrate, 0.1M TRIS, 1:100 (w/w) subtilisin, pH 7.5, vapor diffusion, hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. obs: 32244 / % possible obs: 100 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.088 / Χ2: 1.504 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.48-1.518.40.92816001.6321100
1.51-1.538.50.77815501.527199.9
1.53-1.568.50.67415811.471100
1.56-1.598.60.58115971.4741100
1.59-1.638.60.4916001.3831100
1.63-1.678.60.43715791.3341100
1.67-1.718.60.3715861.3521100
1.71-1.758.60.31416011.3281100
1.75-1.818.60.25915911.281100
1.81-1.868.60.215901.2871100
1.86-1.938.60.16216051.3621100
1.93-2.018.60.12616021.3991100
2.01-2.18.60.1116011.5241100
2.1-2.218.60.09716101.7051100
2.21-2.358.50.08716121.7921100
2.35-2.538.50.07416271.6741100
2.53-2.788.40.06116331.5791100
2.78-3.198.30.04716481.7231100
3.19-4.018.50.03516621.7141100
4.01-308.10.03217691.547199.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2COU

2cou


Resolution: 1.482→25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.173 / SU B: 1.098 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. ARP/WARP, COOT and the MOLPROBITY server were also used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1570 4.879 %thin shells (sftools)
Rwork0.181 ---
obs0.182 32180 99.929 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.175 Å2
Baniso -1Baniso -2Baniso -3
1--0.296 Å20 Å20 Å2
2---0.163 Å20 Å2
3---0.459 Å2
Refinement stepCycle: LAST / Resolution: 1.482→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 3 119 1585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221538
X-RAY DIFFRACTIONr_bond_other_d0.0010.021032
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9672096
X-RAY DIFFRACTIONr_angle_other_deg0.88532537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0285197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90525.61673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01815261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.13154
X-RAY DIFFRACTIONr_chiral_restr0.0870.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02301
X-RAY DIFFRACTIONr_mcbond_it0.9411.5941
X-RAY DIFFRACTIONr_mcbond_other0.261.5378
X-RAY DIFFRACTIONr_mcangle_it1.66521526
X-RAY DIFFRACTIONr_scbond_it2.6043597
X-RAY DIFFRACTIONr_scangle_it4.1484.5563
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.482-1.520.2931360.2342169232499.182
1.52-1.5620.2081160.2122159227699.956
1.562-1.6070.2451010.21321252226100
1.607-1.6560.2231060.1882022212999.953
1.656-1.710.1781070.17420002107100
1.71-1.770.2021150.1791921203799.951
1.77-1.8360.2281040.17518651969100
1.836-1.9110.1881120.17317541866100
1.911-1.9950.1891150.17117131828100
1.995-2.0920.242360.17417121748100
2.092-2.2040.205920.17115581650100
2.204-2.3370.222560.17115331589100
2.337-2.4960.203540.17814251479100
2.496-2.6940.233750.18413081383100
2.694-2.9480.237550.2112331288100
2.948-3.290.239520.18511311183100
3.29-3.7880.16520.1669871039100
3.788-4.6130.131290.144877906100
4.613-6.4160.156310.189688719100
6.416-250.247260.19943045799.781

+
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