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- PDB-3vh5: Crystal structure of the chicken CENP-T histone fold/CENP-W/CENP-... -

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Basic information

Entry
Database: PDB / ID: 3vh5
TitleCrystal structure of the chicken CENP-T histone fold/CENP-W/CENP-S/CENP-X heterotetrameric complex, crystal form I
Components
  • CENP-S
  • CENP-T
  • CENP-W
  • CENP-X
KeywordsDNA BINDING PROTEIN / histone fold / chromosome segregation / DNA binding / nucleus
Function / homology
Function and homology information


PKR-mediated signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / Deposition of new CENPA-containing nucleosomes at the centromere / Fanconi Anemia Pathway / FANCM-MHF complex / Fanconi anaemia nuclear complex ...PKR-mediated signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / Deposition of new CENPA-containing nucleosomes at the centromere / Fanconi Anemia Pathway / FANCM-MHF complex / Fanconi anaemia nuclear complex / resolution of meiotic recombination intermediates / kinetochore assembly / replication fork processing / chromosome segregation / kinetochore / mitotic cell cycle / protein heterodimerization activity / cell division / DNA repair / chromatin binding / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4980 / Centromere protein W / : / CENP-W protein / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4980 / Centromere protein W / : / CENP-W protein / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / Histone, subunit A / Histone, subunit A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Histone-fold / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Centromere protein S / Centromere protein T / Centromere protein W / Centromere protein X
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsNishino, T. / Takeuchi, K. / Gascoigne, K.E. / Suzuki, A. / Hori, T. / Oyama, T. / Morikawa, K. / Cheeseman, I.M. / Fukagawa, T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: CENP-T-W-S-X Forms a Unique Centromeric Chromatin Structure with a Histone-like Fold
Authors: Nishino, T. / Takeuchi, K. / Gascoigne, K.E. / Suzuki, A. / Hori, T. / Oyama, T. / Morikawa, K. / Cheeseman, I.M. / Fukagawa, T.
History
DepositionAug 23, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CENP-S
D: CENP-X
T: CENP-T
W: CENP-W


Theoretical massNumber of molelcules
Total (without water)46,4624
Polymers46,4624
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-89 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.100, 137.100, 46.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CENP-S


Mass: 15561.421 Da / Num. of mol.: 1 / Mutation: C26A, C28A, C55A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: E1BSW7*PLUS
#2: Protein CENP-X


Mass: 9361.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P0DJH7*PLUS
#3: Protein CENP-T


Mass: 12682.790 Da / Num. of mol.: 1 / Fragment: C-terminal histone fold / Mutation: C87A, C161A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENPT / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: F1NPG5
#4: Protein CENP-W


Mass: 8855.593 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P0DJH6*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DATABASE REFERENCES FOR CHAIN A, D, W DO NOT CURRENTLY EXIST. CHAIN A IS C26A, C28A, C55A MUTANT.

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.16M MgCl2, 0.25M NaCl, 24% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2011
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→38.025 Å / Num. all: 17916 / Num. obs: 17899 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.9 % / Biso Wilson estimate: 46.67 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.053 / Net I/σ(I): 30.17
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1752 / Rsym value: 0.505 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B0B, 3B0C

3b0b

3b0c


Resolution: 2.402→38.025 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8153 / SU ML: 0.84 / σ(F): 1.34 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 2000 11.2 %random
Rwork0.1879 ---
all0.1942 17899 --
obs0.1942 17856 99.84 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.061 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 133.89 Å2 / Biso mean: 56.517 Å2 / Biso min: 20.39 Å2
Baniso -1Baniso -2Baniso -3
1-2.5434 Å20 Å2-0 Å2
2--2.5434 Å20 Å2
3----4.8807 Å2
Refinement stepCycle: LAST / Resolution: 2.402→38.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 0 132 2901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082806
X-RAY DIFFRACTIONf_angle_d1.0063767
X-RAY DIFFRACTIONf_chiral_restr0.065438
X-RAY DIFFRACTIONf_plane_restr0.004479
X-RAY DIFFRACTIONf_dihedral_angle_d14.471088
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 (%)
2.4024-2.46250.36561400.25421114125499
2.4625-2.52910.31121370.239810851222100
2.5291-2.60350.34821420.237111211263100
2.6035-2.68750.31361400.221111121252100
2.6875-2.78350.28161400.22811131253100
2.7835-2.89490.32221420.221211241266100
2.8949-3.02660.30961390.204111011240100
3.0266-3.18610.29491430.203911321275100
3.1861-3.38560.27371410.195411231264100
3.3856-3.64680.23641430.177511311274100
3.6468-4.01340.21891440.181711361280100
4.0134-4.59330.21361460.146211621308100
4.5933-5.78390.19231490.166111751324100
5.7839-38.02940.2081540.18791227138199

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