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- PDB-3wut: Structure basis of inactivating cell abscission -

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Basic information

Entry
Database: PDB / ID: 3wut
TitleStructure basis of inactivating cell abscission
Components
  • Centrosomal protein of 55 kDa
  • Inactive serine/threonine-protein kinase TEX14
KeywordsCELL CYCLE / Coiled-coil
Function / homology
Function and homology information


intercellular bridge organization / negative regulation of cytokinesis / mitotic sister chromatid separation / attachment of spindle microtubules to kinetochore / male meiotic nuclear division / cranial skeletal system development / midbody abscission / Flemming body / intercellular bridge / mitotic spindle assembly checkpoint signaling ...intercellular bridge organization / negative regulation of cytokinesis / mitotic sister chromatid separation / attachment of spindle microtubules to kinetochore / male meiotic nuclear division / cranial skeletal system development / midbody abscission / Flemming body / intercellular bridge / mitotic spindle assembly checkpoint signaling / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cleavage furrow / mitotic cytokinesis / centriole / cellular response to leukemia inhibitory factor / establishment of protein localization / kinetochore / midbody / protein kinase activity / cell division / centrosome / protein kinase binding / extracellular exosome / ATP binding / identical protein binding / membrane / cytoplasm
Similarity search - Function
Inactive serine/threonine-protein kinase TEX14 / Centrosomal protein of 55kDa / TSG101 and ALIX binding domain of CEP55 / TSG101 and ALIX binding domain of CEP55 / Geminin coiled-coil domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats ...Inactive serine/threonine-protein kinase TEX14 / Centrosomal protein of 55kDa / TSG101 and ALIX binding domain of CEP55 / TSG101 and ALIX binding domain of CEP55 / Geminin coiled-coil domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Centrosomal protein of 55 kDa / Inactive serine/threonine-protein kinase TEX14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsKim, H.J. / Matsuura, A. / Lee, H.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural and biochemical insights into the role of testis-expressed gene 14 (TEX14) in forming the stable intercellular bridges of germ cells.
Authors: Kim, H.J. / Yoon, J. / Matsuura, A. / Na, J.H. / Lee, W.K. / Kim, H. / Choi, J.W. / Park, J.E. / Park, S.J. / Kim, K.T. / Chang, R. / Lee, B.I. / Yu, Y.G. / Shin, Y.K. / Jeong, C. / Rhee, K. / Lee, H.H.
History
DepositionMay 5, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centrosomal protein of 55 kDa
B: Centrosomal protein of 55 kDa
C: Inactive serine/threonine-protein kinase TEX14
D: Centrosomal protein of 55 kDa
E: Centrosomal protein of 55 kDa
F: Inactive serine/threonine-protein kinase TEX14
G: Centrosomal protein of 55 kDa
H: Centrosomal protein of 55 kDa
I: Inactive serine/threonine-protein kinase TEX14
J: Centrosomal protein of 55 kDa
K: Centrosomal protein of 55 kDa
L: Inactive serine/threonine-protein kinase TEX14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,94014
Polymers63,75612
Non-polymers1842
Water3,387188
1
A: Centrosomal protein of 55 kDa
B: Centrosomal protein of 55 kDa
C: Inactive serine/threonine-protein kinase TEX14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0314
Polymers15,9393
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-31 kcal/mol
Surface area7840 Å2
MethodPISA
2
D: Centrosomal protein of 55 kDa
E: Centrosomal protein of 55 kDa
F: Inactive serine/threonine-protein kinase TEX14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0314
Polymers15,9393
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-30 kcal/mol
Surface area8850 Å2
MethodPISA
3
G: Centrosomal protein of 55 kDa
H: Centrosomal protein of 55 kDa
I: Inactive serine/threonine-protein kinase TEX14


Theoretical massNumber of molelcules
Total (without water)15,9393
Polymers15,9393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-31 kcal/mol
Surface area8740 Å2
MethodPISA
4
J: Centrosomal protein of 55 kDa
K: Centrosomal protein of 55 kDa
L: Inactive serine/threonine-protein kinase TEX14


Theoretical massNumber of molelcules
Total (without water)15,9393
Polymers15,9393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-31 kcal/mol
Surface area7310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.913, 102.622, 132.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Centrosomal protein of 55 kDa / Cep55 / Up-regulated in colon cancer 6


Mass: 7243.210 Da / Num. of mol.: 8 / Fragment: UNP residues 160-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP55 / Plasmid: pGST2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53EZ4
#2: Protein/peptide
Inactive serine/threonine-protein kinase TEX14 / Protein kinase-like protein SgK307 / Sugen kinase 307 / Testis-expressed sequence 14 / Testis- ...Protein kinase-like protein SgK307 / Sugen kinase 307 / Testis-expressed sequence 14 / Testis-expressed sequence 14 protein


Mass: 1452.650 Da / Num. of mol.: 4 / Fragment: UNP residues 792-804 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8IWB6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1M ammonium phosphate dibasic, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97928 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 3, 2012
RadiationMonochromator: Si 111 DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 34110 / Num. obs: 31519 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 43.14 Å2
Reflection shellHighest resolution: 2.3 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.301→28.884 Å / FOM work R set: 0.801 / SU ML: 0.25 / σ(F): 0.16 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1589 5.04 %RANDOM
Rwork0.2202 ---
all0.2221 34110 --
obs0.2221 31519 94.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.37 Å2 / Biso mean: 61.47 Å2 / Biso min: 31.28 Å2
Refinement stepCycle: LAST / Resolution: 2.301→28.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 0 12 188 3906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073777
X-RAY DIFFRACTIONf_angle_d0.8945074
X-RAY DIFFRACTIONf_chiral_restr0.057556
X-RAY DIFFRACTIONf_plane_restr0.003644
X-RAY DIFFRACTIONf_dihedral_angle_d16.6461461
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3011-2.37540.29691220.25272409253184
2.3754-2.46020.24721350.24532553268889
2.4602-2.55870.31041400.24932545268590
2.5587-2.6750.29241100.25012643275392
2.675-2.81590.31761560.26012632278893
2.8159-2.99220.33621430.25472766290996
2.9922-3.2230.25551470.24282781292897
3.223-3.54680.27351300.22852841297198
3.5468-4.05880.22051450.20342877302299
4.0588-5.1090.22751710.18692901307299
5.109-28.88610.25721900.21122982317298

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