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- PDB-3wuv: Structure basis of inactivating cell abscission with chimera peptide 2 -

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Basic information

Entry
Database: PDB / ID: 3wuv
TitleStructure basis of inactivating cell abscission with chimera peptide 2
Components
  • Centrosomal protein of 55 kDa
  • peptide from Programmed cell death 6-interacting protein
KeywordsCELL CYCLE / Coiled-coil
Function / homology
Function and homology information


proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / extracellular exosome biogenesis / viral budding / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of membrane permeability ...proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / extracellular exosome biogenesis / viral budding / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of membrane permeability / regulation of centrosome duplication / bicellular tight junction assembly / cranial skeletal system development / positive regulation of exosomal secretion / midbody abscission / actomyosin / multivesicular body assembly / Flemming body / RIPK1-mediated regulated necrosis / viral budding via host ESCRT complex / endoplasmic reticulum exit site / cleavage furrow / Uptake and function of anthrax toxins / mitotic cytokinesis / immunological synapse / bicellular tight junction / intercellular bridge / centriole / macroautophagy / establishment of protein localization / Budding and maturation of HIV virion / protein homooligomerization / Regulation of necroptotic cell death / calcium-dependent protein binding / melanosome / protein transport / extracellular vesicle / midbody / endosome / focal adhesion / apoptotic process / centrosome / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Centrosomal protein of 55kDa / TSG101 and ALIX binding domain of CEP55 / TSG101 and ALIX binding domain of CEP55 / Geminin coiled-coil domain / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. ...Centrosomal protein of 55kDa / TSG101 and ALIX binding domain of CEP55 / TSG101 and ALIX binding domain of CEP55 / Geminin coiled-coil domain / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Centrosomal protein of 55 kDa / Programmed cell death 6-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: peptide from Programmed cell death 6-interacting protein
D: Centrosomal protein of 55 kDa
E: Centrosomal protein of 55 kDa
F: peptide from Programmed cell death 6-interacting protein
G: Centrosomal protein of 55 kDa
H: Centrosomal protein of 55 kDa
I: peptide from Programmed cell death 6-interacting protein
J: Centrosomal protein of 55 kDa
K: Centrosomal protein of 55 kDa
L: peptide from Programmed cell death 6-interacting protein
M: Centrosomal protein of 55 kDa
N: Centrosomal protein of 55 kDa
O: peptide from Programmed cell death 6-interacting protein
P: Centrosomal protein of 55 kDa
Q: Centrosomal protein of 55 kDa
R: peptide from Programmed cell death 6-interacting protein


Theoretical massNumber of molelcules
Total (without water)96,18118
Polymers96,18118
Non-polymers00
Water3,063170
1
A: Centrosomal protein of 55 kDa
B: Centrosomal protein of 55 kDa
C: peptide from Programmed cell death 6-interacting protein


Theoretical massNumber of molelcules
Total (without water)16,0303
Polymers16,0303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-30 kcal/mol
Surface area9650 Å2
MethodPISA
2
D: Centrosomal protein of 55 kDa
E: Centrosomal protein of 55 kDa
F: peptide from Programmed cell death 6-interacting protein


Theoretical massNumber of molelcules
Total (without water)16,0303
Polymers16,0303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-29 kcal/mol
Surface area8800 Å2
MethodPISA
3
G: Centrosomal protein of 55 kDa
H: Centrosomal protein of 55 kDa
I: peptide from Programmed cell death 6-interacting protein


Theoretical massNumber of molelcules
Total (without water)16,0303
Polymers16,0303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-28 kcal/mol
Surface area8730 Å2
MethodPISA
4
J: Centrosomal protein of 55 kDa
K: Centrosomal protein of 55 kDa
L: peptide from Programmed cell death 6-interacting protein


Theoretical massNumber of molelcules
Total (without water)16,0303
Polymers16,0303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-31 kcal/mol
Surface area9660 Å2
MethodPISA
5
M: Centrosomal protein of 55 kDa
N: Centrosomal protein of 55 kDa
O: peptide from Programmed cell death 6-interacting protein


Theoretical massNumber of molelcules
Total (without water)16,0303
Polymers16,0303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-29 kcal/mol
Surface area9030 Å2
MethodPISA
6
P: Centrosomal protein of 55 kDa
Q: Centrosomal protein of 55 kDa
R: peptide from Programmed cell death 6-interacting protein


Theoretical massNumber of molelcules
Total (without water)16,0303
Polymers16,0303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-30 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.066, 134.671, 88.325
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121

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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.: 12 / 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 BL21(DE3) (bacteria) / References: UniProt: Q53EZ4
#2: Protein/peptide
peptide from Programmed cell death 6-interacting protein / ALG-2-interacting protein X / ALIX


Mass: 1543.673 Da / Num. of mol.: 6 / Mutation: P796D/P807I/G808P/Y809P / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WUM4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 7.21 Å3/Da / Density % sol: 82.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.8M ammonium sulfate, pH 5.0, 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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2014
RadiationMonochromator: si 111 DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. all: 67538 / Num. obs: 67471 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 46.75 Å2
Reflection shellHighest resolution: 2.8 Å / % possible all: 99.9

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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
Starting model: 3EIR

3eir


Resolution: 2.79→48.644 Å / FOM work R set: 0.8209 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 2008 2.98 %RANDOM
Rwork0.2009 ---
obs0.2017 67339 99.11 %-
all-67538 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.22 Å2 / Biso mean: 62.97 Å2 / Biso min: 14.16 Å2
Refinement stepCycle: LAST / Resolution: 2.79→48.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6129 0 0 170 6299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066240
X-RAY DIFFRACTIONf_angle_d0.8638394
X-RAY DIFFRACTIONf_chiral_restr0.059900
X-RAY DIFFRACTIONf_plane_restr0.0031083
X-RAY DIFFRACTIONf_dihedral_angle_d19.0732390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7898-2.85960.26221320.26494336446891
2.8596-2.93690.31591530.255946654818100
2.9369-3.02330.28091450.246746274772100
3.0233-3.12090.27151340.247946884822100
3.1209-3.23240.26181330.231447094842100
3.2324-3.36180.2841530.215347134866100
3.3618-3.51480.2221410.207946314772100
3.5148-3.70.21951390.195847024841100
3.7-3.93170.19561560.193247004856100
3.9317-4.23510.18991470.178947304877100
4.2351-4.6610.21791480.18446734821100
4.661-5.33480.19011420.170646984840100
5.3348-6.71840.26561470.235547704917100
6.7184-48.65160.19871380.16934689482798

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