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- PDB-7sfz: Crystal structure of Mis18a-yippee domain -

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Basic information

Entry
Database: PDB / ID: 7sfz
TitleCrystal structure of Mis18a-yippee domain
ComponentsProtein Mis18-alpha
KeywordsCELL CYCLE / Mis18a
Function / homology
Function and homology information


: / CENP-A containing chromatin assembly / chromosome, centromeric region / Deposition of new CENPA-containing nucleosomes at the centromere / chromosome segregation / cell division / chromatin / nucleoplasm / identical protein binding / nucleus ...: / CENP-A containing chromatin assembly / chromosome, centromeric region / Deposition of new CENPA-containing nucleosomes at the centromere / chromosome segregation / cell division / chromatin / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Mis18 domain / Mis18 domain profile. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsPark, S.H. / Cho, U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK111465 United States
CitationJournal: To Be Published
Title: Structural Basis for Mis18 Complex Assembly: Implications for Centromere Maintenance
Authors: Park, S.H. / Shimanaka, K. / Cho, U.
History
DepositionOct 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protein Mis18-alpha
A: Protein Mis18-alpha
C: Protein Mis18-alpha
D: Protein Mis18-alpha
E: Protein Mis18-alpha
F: Protein Mis18-alpha
G: Protein Mis18-alpha
H: Protein Mis18-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,65724
Polymers102,3658
Non-polymers1,29216
Water1448
1
B: Protein Mis18-alpha
A: Protein Mis18-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9146
Polymers25,5912
Non-polymers3234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-36 kcal/mol
Surface area10700 Å2
MethodPISA
2
C: Protein Mis18-alpha
D: Protein Mis18-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9146
Polymers25,5912
Non-polymers3234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-17 kcal/mol
Surface area10710 Å2
MethodPISA
3
E: Protein Mis18-alpha
F: Protein Mis18-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8185
Polymers25,5912
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-16 kcal/mol
Surface area10760 Å2
MethodPISA
4
G: Protein Mis18-alpha
H: Protein Mis18-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0107
Polymers25,5912
Non-polymers4195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-37 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.725, 114.864, 116.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Protein Mis18-alpha / FAPP1-associated protein 1


Mass: 12795.674 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIS18A, C21orf45, C21orf46, FASP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NYP9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.61 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, PEG 400, HEPES

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 30063 / % possible obs: 99.3 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Net I/σ(I): 16.5
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 1479 / CC1/2: 0.703

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HJ0

5hj0


Resolution: 3.002→49.985 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1987 6.62 %
Rwork0.2026 --
obs0.2058 30011 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.002→49.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5732 0 48 8 5788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125834
X-RAY DIFFRACTIONf_angle_d1.2947875
X-RAY DIFFRACTIONf_dihedral_angle_d5.4613548
X-RAY DIFFRACTIONf_chiral_restr0.075926
X-RAY DIFFRACTIONf_plane_restr0.007981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0023-3.07740.33891390.26941947X-RAY DIFFRACTION98
3.0774-3.16060.33421340.27971993X-RAY DIFFRACTION100
3.1606-3.25360.31921330.26481974X-RAY DIFFRACTION99
3.2536-3.35860.33411500.25321947X-RAY DIFFRACTION98
3.3586-3.47860.28031220.24552008X-RAY DIFFRACTION99
3.4786-3.61780.28571300.21321966X-RAY DIFFRACTION98
3.6178-3.78240.27071480.21411987X-RAY DIFFRACTION100
3.7824-3.98180.25411490.19312004X-RAY DIFFRACTION100
3.9818-4.23110.22931470.17012001X-RAY DIFFRACTION100
4.2311-4.55760.23231480.15762006X-RAY DIFFRACTION100
4.5576-5.01590.16621390.15352031X-RAY DIFFRACTION99
5.0159-5.74080.26211400.1942029X-RAY DIFFRACTION99
5.7408-7.22930.28311510.23192006X-RAY DIFFRACTION98
7.2293-49.9850.22641570.21212125X-RAY DIFFRACTION98
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)
18.1334-2.4203-3.32987.77532.94519.8599-0.16660.0242-0.6959-0.26770.006-0.66060.72111.03880.15410.43010.10010.02890.4232-0.00540.523932.8497-6.886344.1596
28.2836-1.6634-6.29937.14052.12048.22750.29480.2440.4126-0.0614-0.30290.798-0.9426-1.01880.03460.56560.1459-0.0110.5696-0.05380.469910.37897.554860.315
33.69121.20060.00266.45155.85887.53970.15090.09270.3367-0.905-0.28570.5771-0.8559-0.19850.17630.6830.0072-0.07580.3829-0.02230.599920.108933.906350.3544
46.07742.10592.54156.92885.75729.5927-0.28030.9923-0.3471-1.1720.11850.63950.1153-0.19010.17161.1518-0.0306-0.23430.5723-0.05630.653616.36868.389330.91
58.05022.01487.43522.0842.9558.7768-0.0729-0.78680.48310.1350.2167-0.09110.0705-0.7203-0.11790.44140.0471-0.10720.9393-0.07070.840420.573837.71545.9801
67.96340.7915.18647.67414.32917.0646-0.03780.28810.25350.3515-0.4033-0.1361-0.29260.55480.42610.4904-0.0626-0.07420.8853-0.06550.507145.481142.400327.403
76.3527-0.30952.31178.6894-1.89389.8811-0.2188-0.216-0.4930.41980.3095-0.42280.66440.0938-0.06910.44610.13830.03130.68670.14840.504160.198124.070615.308
83.4263-0.83882.48259.3719-3.12034.521-0.23790.20810.3729-1.5231-0.12440.4811-0.535-0.59720.29340.85390.2279-0.11411.00880.13070.551146.462143.4105-1.9277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 78 through 180)
2X-RAY DIFFRACTION2(chain 'A' and resid 78 through 180)
3X-RAY DIFFRACTION3(chain 'C' and resid 79 through 180)
4X-RAY DIFFRACTION4(chain 'D' and resid 78 through 179)
5X-RAY DIFFRACTION5(chain 'E' and resid 80 through 179)
6X-RAY DIFFRACTION6(chain 'F' and resid 79 through 179)
7X-RAY DIFFRACTION7(chain 'G' and resid 77 through 180)
8X-RAY DIFFRACTION8(chain 'H' and resid 79 through 179)

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