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- PDB-6l30: Crystal structure of the epithelial cell transforming 2 (ECT2) -

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Basic information

Entry
Database: PDB / ID: 6l30
TitleCrystal structure of the epithelial cell transforming 2 (ECT2)
ComponentsProtein ECT2
KeywordsCELL CYCLE / GEF
Function / homology
Function and homology information


regulation of cytokinesis, actomyosin contractile ring assembly / centralspindlin complex / positive regulation of mitotic cytokinetic process / 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 ...regulation of cytokinesis, actomyosin contractile ring assembly / centralspindlin complex / positive regulation of mitotic cytokinetic process / 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 / activation of protein kinase activity / positive regulation of cytokinesis / 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 / positive regulation of GTPase activity / cellular response to ionizing radiation / cell morphogenesis / protein homooligomerization / mitotic spindle / small GTPase binding / cellular response to hydrogen peroxide / 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 / cytoplasm / cytosol
Similarity search - Function
: / : / ECT2, PH domain / ECT2, BRCT0 domain / Guanine nucleotide exchange factor Ect2 / twin BRCT domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily / RhoGEF domain ...: / : / ECT2, PH domain / ECT2, BRCT0 domain / Guanine nucleotide exchange factor Ect2 / twin 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, Z.C. / Chen, M.R. / Pan, H. / Sun, L.F. / Shi, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structure and regulation of human epithelial cell transforming 2 protein.
Authors: Chen, M. / Pan, H. / Sun, L. / Shi, P. / Zhang, Y. / Li, L. / Huang, Y. / Chen, J. / Jiang, P. / Fang, X. / Wu, C. / Chen, Z.
History
DepositionOct 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ECT2


Theoretical massNumber of molelcules
Total (without water)80,7041
Polymers80,7041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.959, 130.579, 131.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 80703.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ECT2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8V3

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.95-1.05 M Potassium/Sodium Tartrate 0.2 M Lithium Sulfate 1 mM TCEP

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→32.851 Å / Num. obs: 23040 / % possible obs: 99.85 % / Redundancy: 6.1 % / CC1/2: 0.72 / Net I/σ(I): 21.42
Reflection shellResolution: 2.8001→2.9275 Å / Num. unique obs: 2692 / CC1/2: 0.717

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N40, 1lb1

4n40

1lb1


Resolution: 2.8→32.851 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 1156 5.02 %
Rwork0.2367 21884 -
obs0.2384 23040 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 235.1 Å2 / Biso mean: 107.9073 Å2 / Biso min: 41 Å2
Refinement stepCycle: final / Resolution: 2.8→32.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4178 0 0 0 4178
Num. residues----518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8001-2.92750.30311440.2812692100
2.9275-3.08170.3691420.28152702100
3.0817-3.27460.34911400.27052697100
3.2746-3.52720.26471440.24552717100
3.5272-3.88170.23791420.23022728100
3.8817-4.44220.27631460.21382751100
4.4422-5.59220.22321440.22932753100
5.5922-32.850.2781540.2376284499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.49941.3985-0.15322.01261.20056.4801-0.28140.23750.0743-0.7618-0.0451-0.1256-0.1624-0.0486-0.0590.5837-0.02990.24270.6038-0.1520.4504-51.4957-39.8103-81.5411
24.3917-1.2902-0.17474.11411.54855.64710.04-0.0359-0.1931-0.04620.02590.1031-0.67240.1210.00510.442-0.00270.08920.44110.04990.3758-48.8879-38.6293-77.2583
33.15840.86351.71034.2692.68352.54190.5537-0.37140.4575-0.1547-0.5364-1.1798-1.01570.6148-0.12030.9362-0.3710.1130.78190.13250.8325-32.9152-25.8154-72.0802
42.5156-0.2216-0.72632.46070.95951.669-0.18490.53080.68190.02080.0121-0.6262-0.84110.76840.00891.2358-0.53020.14841.10750.0551.0765-29.0865-17.6532-74.4705
50.7049-0.04470.3845-0.22490.04440.17761.1045-1.09421.5374-0.62930.79580.16040.3225-0.6265-0.55171.7781-0.17510.13953.46340.65631.7805-35.2198-5.4496-71.5479
63.0373-0.0860.6061.8148-1.2772.0832-0.3446-0.00360.84740.15580.32840.6324-1.0448-0.23590.17821.0675-0.18320.06240.6173-0.03810.8093-39.3625-18.6117-67.4316
72.07681.70561.04631.91411.3625.02390.3911-0.463-0.43130.4251-0.208-0.2950.3391-0.2827-0.1060.5653-0.1163-0.20680.82480.0570.7959-32.5357-26.306-38.9868
81.3775-1.7053-2.14023.2183.58913.478-0.2328-1.8382-0.06410.0050.7604-0.148-0.46541.5748-0.3091.2969-0.0459-0.68581.62360.13721.3798-23.4163-26.0482-20.7528
93.2445-0.05991.61131.6839-1.49583.4886-0.13520.687-0.0233-0.4215-0.255-0.25010.5220.12380.1630.7285-0.0644-0.18090.84150.08820.7253-11.7051-15.9704-28.4481
104.00211.6049-2.89140.7705-0.27935.71980.6355-1.3274-0.37930.3354-0.57330.15950.8713-1.87730.23571.5328-0.1603-0.79871.17790.12631.5663-18.39966.1318-24.1883
113.895-0.00760.94534.2144-0.55073.5345-0.3754-0.09740.72750.4226-0.0259-0.2473-1.1961-0.4740.31211.1620.1384-0.34990.56130.03260.7977-20.5775-0.6024-28.1239
123.93591.0268-1.87215.4882-0.25142.66110.01031.18720.4887-0.906-0.02440.2025-0.7863-0.39110.41691.27020.1539-0.48530.85610.16270.9609-25.3311-2.1685-38.6764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 140:161)A140 - 161
2X-RAY DIFFRACTION2(chain A and resid 162:229)A162 - 229
3X-RAY DIFFRACTION3(chain A and resid 230:254)A230 - 254
4X-RAY DIFFRACTION4(chain A and resid 255:283)A255 - 283
5X-RAY DIFFRACTION5(chain A and resid 284:297)A284 - 297
6X-RAY DIFFRACTION6(chain A and resid 298:323)A298 - 323
7X-RAY DIFFRACTION7(chain A and resid 420:578)A420 - 578
8X-RAY DIFFRACTION8(chain A and resid 579:611)A579 - 611
9X-RAY DIFFRACTION9(chain A and resid 612:645)A612 - 645
10X-RAY DIFFRACTION10(chain A and resid 646:658)A646 - 658
11X-RAY DIFFRACTION11(chain A and resid 659:744)A659 - 744
12X-RAY DIFFRACTION12(chain A and resid 745:782)A745 - 782

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