- PDB-6eqt: CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE PROTEIN CENP-N -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6eqt
Title
CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE PROTEIN CENP-N
Components
Centromere protein N
Keywords
DNA BINDING PROTEIN / DNA-binding / pyrin domain / Cenp-NL homology domain / related to Iml3
Function / homology
Function and homology information
CENP-A containing chromatin assembly / inner kinetochore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / chromosome segregation / RHO GTPases Activate Formins / Separation of Sister Chromatids ...CENP-A containing chromatin assembly / inner kinetochore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / chromosome segregation / RHO GTPases Activate Formins / Separation of Sister Chromatids / nucleoplasm / nucleus / cytosol Similarity search - Function
Journal: Elife / Year: 2017 Title: Decoding the centromeric nucleosome through CENP-N. Authors: Satyakrishna Pentakota / Keda Zhou / Charlotte Smith / Stefano Maffini / Arsen Petrovic / Garry P Morgan / John R Weir / Ingrid R Vetter / Andrea Musacchio / Karolin Luger / Abstract: Centromere protein (CENP) A, a histone H3 variant, is a key epigenetic determinant of chromosome domains known as centromeres. Centromeres nucleate kinetochores, multi-subunit complexes that capture ...Centromere protein (CENP) A, a histone H3 variant, is a key epigenetic determinant of chromosome domains known as centromeres. Centromeres nucleate kinetochores, multi-subunit complexes that capture spindle microtubules to promote chromosome segregation during mitosis. Two kinetochore proteins, CENP-C and CENP-N, recognize CENP-A in the context of a rare CENP-A nucleosome. Here, we reveal the structural basis for the exquisite selectivity of CENP-N for centromeres. CENP-N uses charge and space complementarity to decode the L1 loop that is unique to CENP-A. It also engages in extensive interactions with a 15-base pair segment of the distorted nucleosomal DNA double helix, in a position predicted to exclude chromatin remodelling enzymes. Besides CENP-A, stable centromere recruitment of CENP-N requires a coincident interaction with a newly identified binding motif on nucleosome-bound CENP-C. Collectively, our studies clarify how CENP-N and CENP-C decode and stabilize the non-canonical CENP-A nucleosome to enforce epigenetic centromere specification and kinetochore assembly.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97793 Å / Relative weight: 1
Reflection
Resolution: 2.735→87.3 Å / Num. obs: 16182 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 79.69 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.082 / Net I/σ(I): 17.28 / Num. measured all: 152272
Reflection shell
Resolution (Å)
Rmerge F obs
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. possible
Num. unique obs
Rrim(I) all
% possible all
2.735-2.81
0.711
1.461
1.37
10344
1190
1172
1.551
98.5
2.81-2.88
0.812
1.125
1.88
10476
1166
1164
1.195
99.8
2.88-2.97
0.888
0.753
2.86
10870
1125
1123
0.795
99.8
2.97-3.06
0.935
0.569
3.8
10935
1104
1102
0.6
99.8
3.06-3.16
0.969
0.419
5.12
10553
1072
1072
0.442
100
3.16-3.27
0.982
0.297
6.93
9800
1012
1010
0.314
99.8
3.27-3.39
0.991
0.205
9.76
9435
992
992
0.217
100
3.39-3.53
0.996
0.153
12.33
8684
974
972
0.163
99.8
3.53-3.69
0.996
0.122
15.87
8829
926
925
0.129
99.9
3.69-3.87
0.997
0.099
19.63
8593
869
869
0.105
100
3.87-4.08
0.998
0.076
25.4
8146
836
836
0.08
100
4.08-4.32
0.999
0.06
29.24
7447
790
788
0.064
99.7
4.32-4.62
0.999
0.054
32.35
6708
753
752
0.057
99.9
4.62-4.99
0.999
0.049
36.1
6612
700
699
0.052
99.9
4.99-5.47
0.999
0.048
36.98
6151
632
632
0.051
100
5.47-6.12
0.999
0.05
36.18
5566
584
584
0.053
100
6.12-7.06
0.998
0.05
35.16
4499
522
522
0.053
100
7.06-8.65
0.999
0.037
44.97
4082
432
432
0.039
100
8.65-12.23
0.999
0.034
50.98
3088
346
345
0.037
99.7
12.23-87.3
0.999
0.044
46.41
1454
195
191
0.047
97.9
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0135
refinement
XSCALE
datareduction
PDB_EXTRACT
3.11
dataextraction
XSCALE
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.735→87.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2545 / WRfactor Rwork: 0.1993 / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.7416 / SU B: 16.243 / SU ML: 0.31 / SU R Cruickshank DPI: 0.8841 / SU Rfree: 0.3358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.884 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2538
812
5 %
RANDOM
Rwork
0.2056
15370
-
-
obs
0.208
16182
99.75 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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