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- PDB-3b0c: Crystal structure of the chicken CENP-T histone fold/CENP-W compl... -

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Basic information

Entry
Database: PDB / ID: 3b0c
TitleCrystal structure of the chicken CENP-T histone fold/CENP-W complex, crystal form I
Components
  • Centromere protein T
  • Centromere protein W
KeywordsDNA BINDING PROTEIN / histone fold / DNA binding
Function / homology
Function and homology information


Mitotic Prometaphase / 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 / kinetochore assembly / chromosome segregation / kinetochore ...Mitotic Prometaphase / 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 / kinetochore assembly / chromosome segregation / kinetochore / mitotic cell cycle / protein heterodimerization activity / cell division / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Centromere protein W / CENP-W protein / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Histone, subunit A / Histone, subunit A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold ...Centromere protein W / CENP-W protein / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Histone, subunit A / Histone, subunit A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / Centromere protein T / Centromere protein W
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.201 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
DepositionJun 8, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: Centromere protein T
W: Centromere protein W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0165
Polymers21,4392
Non-polymers5763
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-44 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.933, 54.933, 122.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Centromere protein T / / CENP-T


Mass: 12746.921 Da / Num. of mol.: 1
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) / References: UniProt: F1NPG5
#2: Protein Centromere protein W / / CENP-W


Mass: 8692.419 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENP-W / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0DJH6*PLUS
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE DATABASE REFERENCE FOR THE CHAIN W DOES NOT CURRENTLY EXIST.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100mM Citrate-NaOH pH 5.0, 30% PEG 600, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL38B111
SYNCHROTRONSPring-8 BL38B120.96423, 0.97946, 0.97899
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDFeb 16, 2010
ADSC QUANTUM 3152CCDJan 24, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITEMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.964231
30.979461
40.978991
ReflectionResolution: 2.2→30.98 Å / Num. obs: 10722 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.3 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.201→30.98 Å / SU ML: 0.82 / σ(F): 0.06 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 2006 18.71 %random
Rwork0.22 ---
obs0.229 10721 94 %-
all-10721 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.062 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.0638 Å20 Å2-0 Å2
2--4.0638 Å20 Å2
3----8.1275 Å2
Refinement stepCycle: LAST / Resolution: 2.201→30.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 39 52 1428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081397
X-RAY DIFFRACTIONf_angle_d1.3581880
X-RAY DIFFRACTIONf_dihedral_angle_d19.355548
X-RAY DIFFRACTIONf_chiral_restr0.085214
X-RAY DIFFRACTIONf_plane_restr0.008234
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2007-2.25570.35121230.272157389
2.2557-2.31670.3781300.261158088
2.3167-2.38480.33331370.268558389
2.3848-2.46170.32991310.250456990
2.4617-2.54970.3691340.259258290
2.5497-2.65170.28241420.245559991
2.6517-2.77230.29711440.227560293
2.7723-2.91840.33731410.242562193
2.9184-3.10110.27951470.259161795
3.1011-3.34030.26591440.233664899
3.3403-3.67590.27091550.226675100
3.6759-4.20670.2321530.2003673100
4.2067-5.29570.20781580.1724681100
5.2957-30.98260.2721670.219171297
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)
10.00010.0002-0.00050.00530.00220.0010.0070.02150.001-0.01680.02460.00770.05520.057100.7290.25650.07070.4230.07840.3733-9.2737-10.612-27.1603
20.0096-0.0350.00140.0534-0.02980.032-0.1010.02640.0919-0.1418-0.056-0.1245-0.00680.0097-0.16130.69820.5427-0.08210.19550.06020.1962-19.3351-3.5388-22.3878
30.0864-0.016-0.07810.00220.01290.0717-0.148-0.0735-0.06540.0425-0.09640.0054-0.0065-0.0221-0.00890.56560.2511-0.11910.4129-0.05490.3827-21.0721-5.784-4.6999
40.0016-0.00140.00110.00550.00070.0009-0.0653-0.0037-0.00840.0082-0.06670.05220.0196-0.031100.50470.15390.01670.35960.010.452-22.0564-19.4831-10.3877
50.03340.0155-0.00940.02740.00880.01360.0136-0.0307-0.02660.0162-0.0257-0.05240.01720.0165-0.00690.31990.1689-0.03490.34430.09430.4924-7.3993-15.9421-8.528
60.02260.0075-0.01550.0175-0.03280.0542-0.0322-0.07340.00090.06160.0156-0.17380.03150.0652-0.00370.70450.1632-0.23150.2907-0.09590.6154-12.18962.567-11.9205
70.0038-0.00730.01870.0052-0.00740.01780.08060.07190.0631-0.2617-0.1346-0.03490.0056-0.0043-0.07080.60860.4615-0.15190.13670.06260.2839-20.2238-12.6052-26.8384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN T AND (RESSEQ 8:19)
2X-RAY DIFFRACTION2CHAIN T AND (RESSEQ 20:52)
3X-RAY DIFFRACTION3CHAIN T AND (RESSEQ 53:69)
4X-RAY DIFFRACTION4CHAIN T AND (RESSEQ 70:78)
5X-RAY DIFFRACTION5CHAIN T AND (RESSEQ 79:98)
6X-RAY DIFFRACTION6CHAIN W AND (RESSEQ 4:26)
7X-RAY DIFFRACTION7CHAIN W AND (RESSEQ 27:76)

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