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- PDB-3wuu: Structure basis of inactivating cell abscission with chimera peptide 1 -

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Basic information

Entry
Database: PDB / ID: 3wuu
TitleStructure basis of inactivating cell abscission with chimera peptide 1
Components
  • Centrosomal protein of 55 kDa
  • TEX-14
KeywordsCELL CYCLE / Coiled-coil
Function / homology
Function and homology information


intercellular bridge organization / negative regulation of cytokinesis / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mitotic sister chromatid separation / attachment of spindle microtubules to kinetochore / male meiotic nuclear division / cranial skeletal system development / midbody abscission / Flemming body / mitotic spindle assembly checkpoint signaling ...intercellular bridge organization / negative regulation of cytokinesis / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mitotic sister chromatid separation / attachment of spindle microtubules to kinetochore / male meiotic nuclear division / cranial skeletal system development / midbody abscission / Flemming body / mitotic spindle assembly checkpoint signaling / cleavage furrow / mitotic cytokinesis / intercellular bridge / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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: 2.904 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 / Category: citation / database_2 / struct_ref_seq_dif
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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centrosomal protein of 55 kDa
B: Centrosomal protein of 55 kDa
C: TEX-14
D: Centrosomal protein of 55 kDa
E: Centrosomal protein of 55 kDa
F: TEX-14
G: Centrosomal protein of 55 kDa
H: Centrosomal protein of 55 kDa
I: TEX-14
J: Centrosomal protein of 55 kDa
K: Centrosomal protein of 55 kDa
L: TEX-14


Theoretical massNumber of molelcules
Total (without water)63,79612
Polymers63,79612
Non-polymers00
Water1,33374
1
A: Centrosomal protein of 55 kDa
B: Centrosomal protein of 55 kDa
C: TEX-14


Theoretical massNumber of molelcules
Total (without water)15,9493
Polymers15,9493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-25 kcal/mol
Surface area8910 Å2
MethodPISA
2
D: Centrosomal protein of 55 kDa
E: Centrosomal protein of 55 kDa
F: TEX-14


Theoretical massNumber of molelcules
Total (without water)15,9493
Polymers15,9493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-29 kcal/mol
Surface area7520 Å2
MethodPISA
3
G: Centrosomal protein of 55 kDa
H: Centrosomal protein of 55 kDa
L: TEX-14


Theoretical massNumber of molelcules
Total (without water)15,9493
Polymers15,9493
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-28 kcal/mol
Surface area8220 Å2
MethodPISA
4
I: TEX-14
J: Centrosomal protein of 55 kDa
K: Centrosomal protein of 55 kDa


Theoretical massNumber of molelcules
Total (without water)15,9493
Polymers15,9493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-28 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.252, 104.795, 131.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11I-904-

HOH

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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
TEX-14


Mass: 1462.603 Da / Num. of mol.: 4 / Mutation: P791D/I802P/P803G/P804Y / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8IWB6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 57.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20%(w/v) polyacrylic acid 5100, 0.2M magnesium chloride, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9781 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2014
RadiationMonochromator: si 111 DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 17398 / Num. obs: 17000 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 62.34 Å2
Reflection shellHighest resolution: 2.9 Å / % possible all: 99.8

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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: 2.904→49.374 Å / FOM work R set: 0.7863 / SU ML: 0.35 / σ(F): 1.34 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2596 1686 10 %RANDOM
Rwork0.2244 ---
obs0.228 16857 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.08 Å2 / Biso mean: 48.88 Å2 / Biso min: 12.01 Å2
Refinement stepCycle: LAST / Resolution: 2.904→49.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3713 0 0 74 3787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053773
X-RAY DIFFRACTIONf_angle_d0.8935068
X-RAY DIFFRACTIONf_chiral_restr0.062549
X-RAY DIFFRACTIONf_plane_restr0.004646
X-RAY DIFFRACTIONf_dihedral_angle_d16.9241452
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9041-2.98960.35671370.27121227136498
2.9896-3.08610.27061370.259912441381100
3.0861-3.19630.33721380.263412361374100
3.1963-3.32430.38161410.256512601401100
3.3243-3.47550.29631370.241412361373100
3.4755-3.65870.24831390.226512521391100
3.6587-3.88790.25881400.217612601400100
3.8879-4.18790.22961400.216812611401100
4.1879-4.60910.25911410.19712661407100
4.6091-5.27540.24581430.198812941437100
5.2754-6.64390.2771450.26512921437100
6.6439-49.38150.20531480.20691343149197

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