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- PDB-3b0b: Crystal structure of the chicken CENP-S/CENP-X complex -

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Basic information

Entry
Database: PDB / ID: 3b0b
TitleCrystal structure of the chicken CENP-S/CENP-X complex
Components
  • Centromere protein S
  • Centromere protein X
KeywordsDNA BINDING PROTEIN / histone fold / DNA binding / DNA / 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 / kinetochore / protein heterodimerization activity / cell division / DNA repair / chromatin binding / DNA binding
Similarity search - Function
GTP Cyclohydrolase I; Chain A, domain 1 - #30 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4980 / GTP Cyclohydrolase I; Chain A, domain 1 / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / Histone, subunit A / Histone, subunit A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...GTP Cyclohydrolase I; Chain A, domain 1 - #30 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4980 / GTP Cyclohydrolase I; Chain A, domain 1 / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / Histone, subunit A / Histone, subunit A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Histone-fold / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Centromere protein S / Centromere protein X
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Centromere protein S
C: Centromere protein X
A: Centromere protein S
D: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)42,9484
Polymers42,9484
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Centromere protein S
C: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)21,4742
Polymers21,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-40 kcal/mol
Surface area9380 Å2
MethodPISA
3
A: Centromere protein S
D: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)21,4742
Polymers21,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-43 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.741, 48.741, 345.633
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Centromere protein S / CENP-S


Mass: 12065.315 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENP-S / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E1BSW7*PLUS
#2: Protein Centromere protein X / CENP-X


Mass: 9408.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENP-X / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0DJH7*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE DATABASE REFERENCES FOR THESE PROTEINS DO 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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5
Details: 100mM Citrate-BisPropane pH 9.5, 500mM NaCl, 100mM MgSO4, and 30% PEG 600, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL38B110.9642, 0.97944, 0.97889, 0.9951
SYNCHROTRONSPring-8 BL44XU20.9
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 21, 2010
ADSC QUANTUM 2102CCDNov 14, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITEMADMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.96421
20.979441
30.978891
40.99511
50.91
ReflectionResolution: 2.15→42.211 Å / Num. all: 25152 / Num. obs: 25152 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.15→2.23 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: 2.15→42.211 Å / SU ML: 0.55 / σ(F): 0 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 1963 7.96 %RANDOM
Rwork0.1863 ---
obs0.1901 24657 98.19 %-
all-25111 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.788 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.3091 Å2-0 Å2-0 Å2
2--5.3091 Å20 Å2
3----20.0662 Å2
Refinement stepCycle: LAST / Resolution: 2.15→42.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 0 119 2874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072781
X-RAY DIFFRACTIONf_angle_d0.9593729
X-RAY DIFFRACTIONf_dihedral_angle_d14.8391067
X-RAY DIFFRACTIONf_chiral_restr0.068435
X-RAY DIFFRACTIONf_plane_restr0.003483
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.22680.27581870.218218493
2.2268-2.3160.27081950.2087222397
2.316-2.42140.27721910.1998225698
2.4214-2.5490.26171980.2045226099
2.549-2.70870.28421950.2067230799
2.7087-2.91780.25851950.2204227499
2.9178-3.21130.29122010.2096228899
3.2113-3.67580.22631970.19352317100
3.6758-4.63020.20092020.15322291100
4.6302-42.21910.21072020.1756229499
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)
12.44120.58151.69332.69051.61994.9176-0.2799-0.5695-0.37730.23340.15070.24850.4735-0.03780.15270.669-0.03290.08850.26180.03370.3467-3.56240.135532.0144
22.35140.7623-0.74123.1932-0.61622.2495-0.2808-0.0979-0.2477-0.05430.1418-0.36310.30740.40120.0460.5081-0.16980.04330.3184-0.07280.34392.37864.296921.019
32.6857-2.15330.94331.8897-0.77521.8171-0.83930.6741-0.0017-0.40681.06620.20540.07440.1479-0.2650.639-0.28590.04920.46740.02250.4878-0.892912.461512.2426
49.0786-1.6101-0.347.92765.68167.7223-0.0838-0.53370.6547-0.5689-0.43431.0866-1.2794-1.2842-0.0560.824-0.0707-0.0820.58050.14850.8608-9.579317.830816.5707
58.44140.9242-1.81723.5628-1.39834.5713-0.1418-0.94510.48210.7610.2288-0.2744-0.27670.5128-0.14370.6593-0.119-0.05260.4438-0.09350.44056.599911.533227.2914
65.52872.7751.87073.42613.12933.5774-0.39740.33320.3872-0.15560.59280.8768-0.0480.1421-0.14740.4787-0.15380.00530.3880.07620.5016-8.76353.496320.727
71.80522.07530.30672.73910.8240.71880.2203-0.4438-0.67980.0549-0.33190.72570.2865-0.2501-0.26430.8885-0.25890.08530.3859-0.06130.8068-17.3068-14.478321.942
87.18420.98350.16144.22840.65733.09970.19790.9170.1328-0.23010.5604-0.44910.41980.3578-0.37410.7846-0.23240.07150.3349-0.06320.4552-5.3675-6.656915.2433
98.093-2.80732.87194.4806-3.00065.45080.7435-0.0526-1.08340.023-0.49080.60660.42120.1719-0.14350.5564-0.2319-0.04520.703-0.03640.38674.7214-5.8965-12.6704
101.654-0.49660.38749.10843.18343.39370.44840.05270.04590.7903-0.68550.51370.1915-0.3940.17710.5833-0.25060.01140.5270.01920.32892.15382.7111-1.9415
113.7042-1.16330.22457.73050.024.3775-0.00460.4787-0.2650.43180.3655-1.5713-0.30271.2063-0.3450.6079-0.2553-0.01750.732-0.12220.700415.90618.49882.9884
127.9342-5.9947-3.17449.31892.38879.73670.12291.3470.5674-1.0932-0.2115-0.0496-0.7294-0.1022-0.06350.7075-0.29780.03740.7325-0.01430.42967.79356.3529-12.1383
133.9243-3.21881.75559.50724.01615.54590.06420.70910.5243-0.27460.0097-0.2983-1.1411-0.19050.03650.8528-0.28160.08090.69850.02410.35731.81115.5297-5.2253
144.86771.1948-1.07222.0298-1.48754.05930.1554-0.4507-0.43451.33840.27-0.8761-0.0640.4978-0.3790.647-0.0652-0.11290.86-0.01450.445211.4751-5.9158-1.7297
156.6296-2.4853-0.8459.41031.77356.6682-0.2951-0.7401-1.12110.96850.72810.42451.05140.4545-0.28091.0145-0.2411-0.05070.78440.1510.59383.8472-14.16751.7979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESSEQ 8:35)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 36:75)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 76:86)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 87:104)
5X-RAY DIFFRACTION5CHAIN C AND (RESSEQ 6:29)
6X-RAY DIFFRACTION6CHAIN C AND (RESSEQ 30:57)
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 58:64)
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 65:80)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 5:40)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 41:69)
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 70:102)
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 6:18)
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 19:29)
14X-RAY DIFFRACTION14CHAIN D AND (RESSEQ 30:58)
15X-RAY DIFFRACTION15CHAIN D AND (RESSEQ 59:80)

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