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- PDB-5hj0: Crystal Structure of Mis18 'Yippee-like' Domain -

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Basic information

Entry
Database: PDB / ID: 5hj0
TitleCrystal Structure of Mis18 'Yippee-like' Domain
ComponentsKinetochore protein mis18
KeywordsLIGASE / Centromere / Mis18
Function / homology
Function and homology information


CENP-A recruiting complex / CENP-A containing chromatin assembly / chromosome, centromeric region / chromosome segregation / kinetochore / cell division / chromatin / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Mis18 domain / Mis18 domain profile. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
Similarity search - Domain/homology
Kinetochore protein mis18
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 Å
AuthorsMedina-Pritchard, B. / Subramanian, L. / Allshire, R. / Arockia Jeyaprakash, A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust095822 United Kingdom
Wellcome Trust092076 United Kingdom
Wellcome Trust091020 United Kingdom
European Commission334291 United Kingdom
CitationJournal: Embo Rep. / Year: 2016
Title: Centromere localization and function of Mis18 requires Yippee-like domain-mediated oligomerization.
Authors: Subramanian, L. / Medina-Pritchard, B. / Barton, R. / Spiller, F. / Kulasegaran-Shylini, R. / Radaviciute, G. / Allshire, R.C. / Arockia Jeyaprakash, A.
History
DepositionJan 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinetochore protein mis18
B: Kinetochore protein mis18
C: Kinetochore protein mis18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5946
Polymers41,3983
Non-polymers1963
Water18010
1
A: Kinetochore protein mis18
B: Kinetochore protein mis18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7304
Polymers27,5992
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-7 kcal/mol
Surface area10750 Å2
MethodPISA
2
C: Kinetochore protein mis18
hetero molecules

C: Kinetochore protein mis18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7304
Polymers27,5992
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+y+1,y,-z+1/31
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.069, 121.069, 73.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 19 - 118 / Label seq-ID: 19 - 118

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Kinetochore protein mis18


Mass: 13799.396 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: mis18, SPCC970.12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P802
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Diffraction quality crystals were obtained using well buffer containing 0.2 M Ammonium chloride/formate/acetate/phosphate and 20% PEG 3350 (with the measured pH of the solution in the range ...Details: Diffraction quality crystals were obtained using well buffer containing 0.2 M Ammonium chloride/formate/acetate/phosphate and 20% PEG 3350 (with the measured pH of the solution in the range of 6.2 to 8). 15-20 mg/ml protein sample was mixed with the well buffer in a 1:1 ratio.
PH range: 6.2 - 8

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0311.2825
SYNCHROTRONDiamond I0320.9763
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELJan 21, 2014
DECTRIS PILATUS3 6M2PIXELMay 29, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.28251
20.97631
ReflectionResolution: 3.9→47 Å / Num. obs: 5669 / % possible obs: 97.2 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.3
Reflection shellResolution: 3.9→4 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 3.7 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.64→39.63 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 29.772 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.261 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 970 5.4 %RANDOM
Rwork0.21955 ---
obs0.22176 17128 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 96.108 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å21.18 Å20 Å2
2--2.36 Å20 Å2
3----7.66 Å2
Refinement stepCycle: 1 / Resolution: 2.64→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 3 10 2374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022416
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9463266
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0145297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34524.786117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.33615405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.591512
X-RAY DIFFRACTIONr_chiral_restr0.1270.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021825
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0526.3211197
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5169.4831491
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0956.421217
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.52552.6953470
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A2580.03
12B2580.03
21A2740.1
22C2740.1
31B2740.06
32C2740.06
LS refinement shellResolution: 2.64→2.708 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 69 -
Rwork0.343 1250 -
obs--99.55 %
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)
10.6968-0.66250.12893.5315-1.76354.6613-0.1882-0.0477-0.2309-0.066-0.05410.16260.4764-0.08750.24240.2892-0.03840.0980.2570.0550.104721.7257-4.370781.5389
23.1499-0.767-1.60470.72440.16565.74360.00710.02410.1669-0.2426-0.2495-0.2820.04810.32590.24240.3170.06080.13250.33640.10960.131336.01187.844456.0777
32.41190.4331-2.83533.37140.71114.89390.06350.19160.1854-0.00790.06630.092-0.518-0.4235-0.12980.7190.1140.30990.60780.05040.222550.91313.384524.7615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 1001
2X-RAY DIFFRACTION2B19 - 1001
3X-RAY DIFFRACTION3C19 - 1001

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