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- PDB-7sfy: Crystal structure of human Mis18ab_cc -

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Basic information

Entry
Database: PDB / ID: 7sfy
TitleCrystal structure of human Mis18ab_cc
Components
  • Protein Mis18-alpha
  • Protein Mis18-beta
KeywordsCELL CYCLE / Mis18ab complex
Function / homology
Function and homology information


chromocenter / CENP-A containing chromatin assembly / cell communication / : / chromosome, centromeric region / Cajal body / Deposition of new CENPA-containing nucleosomes at the centromere / chromosome segregation / nuclear speck / cell division ...chromocenter / CENP-A containing chromatin assembly / cell communication / : / chromosome, centromeric region / Cajal body / Deposition of new CENPA-containing nucleosomes at the centromere / chromosome segregation / nuclear speck / cell division / intracellular membrane-bounded organelle / chromatin / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Mis18 domain / Mis18 domain profile. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
Similarity search - Domain/homology
Protein Mis18-beta / Protein Mis18-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Mis18-alpha
B: Protein Mis18-alpha
C: Protein Mis18-beta
D: Protein Mis18-alpha
E: Protein Mis18-alpha
F: Protein Mis18-beta


Theoretical massNumber of molelcules
Total (without water)30,7476
Polymers30,7476
Non-polymers00
Water28816
1
A: Protein Mis18-alpha
B: Protein Mis18-alpha
C: Protein Mis18-beta


Theoretical massNumber of molelcules
Total (without water)15,3743
Polymers15,3743
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-44 kcal/mol
Surface area7530 Å2
MethodPISA
2
D: Protein Mis18-alpha
E: Protein Mis18-alpha
F: Protein Mis18-beta


Theoretical massNumber of molelcules
Total (without water)15,3743
Polymers15,3743
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-36 kcal/mol
Surface area6210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.501, 101.815, 88.563
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 5283.056 Da / Num. of mol.: 4
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: Protein/peptide Protein Mis18-beta / Cancer/testis antigen 86 / CT86 / Opa-interacting protein 5 / OIP-5


Mass: 4807.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OIP5, MIS18B / Production host: Escherichia coli (E. coli) / References: UniProt: O43482
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: Magnesium acetate, PEG 3350

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 12467 / % possible obs: 99 % / Redundancy: 5.2 % / Biso Wilson estimate: 49.32 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.2
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 600 / CC1/2: 0.912

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
xia2data reduction
xia2data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→44.28 Å / SU ML: 0.289 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.2322
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2796 655 5.32 %
Rwork0.2477 11650 -
obs0.2494 12305 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.18 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 0 16 1643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791637
X-RAY DIFFRACTIONf_angle_d1.06922183
X-RAY DIFFRACTIONf_chiral_restr0.0469268
X-RAY DIFFRACTIONf_plane_restr0.0072260
X-RAY DIFFRACTIONf_dihedral_angle_d6.65941051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.690.44141430.39932233X-RAY DIFFRACTION97.42
2.69-2.960.40751280.35132293X-RAY DIFFRACTION98.49
2.96-3.390.33621170.29972318X-RAY DIFFRACTION98.86
3.39-4.270.25591170.21362372X-RAY DIFFRACTION99.68
4.27-44.280.23131500.20432434X-RAY DIFFRACTION99.73
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)
11.880665531160.4792279731932.029736944024.41603091565-1.596415127563.284052501331.771381357121.63037300203-0.36588900528-0.192262696111.09023804935-1.337308901511.219762890511.89180707641-0.9090260070120.9517936788760.055071175471-0.03151820432851.47500717734-0.3057522209091.3125625492615.873105475415.8428249268-32.8093965676
210.12353341865.792465927415.123843027535.377754898984.824474463985.169645969850.238386785497-0.01944537082050.172518070570.56618885266-0.129558721160.2130571667661.045340313730.182580456355-0.2951894243160.5047685919230.07227010278320.02450055120720.4180971776660.1429556236110.46142270452219.219321082724.9827765874-14.6890043004
33.378330210830.9479496202621.840568423410.6522730948180.4672494693122.63211680542-0.01340251989550.7683657113590.3336843286210.0106606201865-0.106731058948-0.03260367859820.04169048797221.354850101-0.01321973970320.4418688160620.0162464457990.004663789714940.952611197518-0.000716869565580.51814552341727.71731585127.5128976715-18.1105828009
49.301165847212.651517186373.00663226685.449867252741.653823024626.67180141479-0.5971374585890.5851232236270.853948961287-0.2221184786940.1524827725740.373425719551-0.7345183661370.1279000243360.3497282203780.607756356423-0.023985667450.07737897715080.7231548085950.08687042300810.53237504506917.229669798232.1088186799-21.2743383625
54.68280880064-2.619824657923.200933106945.30596247824-2.048320488613.81999677716-0.173545800793-1.095665290940.195857026270.5654356119320.4140971257740.52979782565-0.377501472042-1.43726893851-0.1811933728710.593999935209-0.04730440789040.01564756061331.44168722711-0.2970654638740.649707258079.1846346567225.33593828735.1297740657
65.99294111228-1.269570709352.262135138585.076159876631.296068839224.918923661660.1865593531710.193324475331-0.509814420337-0.06022624655690.0243264028990.2228152873540.416366408505-0.0564997568515-0.1514524198650.4857330288490.0287140252936-0.06428856872850.772832117705-0.09918136311050.50370899174110.96245344721.8078638496-4.76056677581
78.75846423813-3.205039932252.666404113364.28918422702-5.787922399627.959560776630.06963442220310.07366223136550.4133830326990.351308086529-0.348760822195-0.304074489431-0.1957888110960.1511825895370.2317956128560.631819297994-0.134985578744-0.04317081313430.418742173336-0.1005262481010.53580326843818.136922514224.89103657220.682180753651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 193 through 197 )
2X-RAY DIFFRACTION2chain 'A' and (resid 198 through 230 )
3X-RAY DIFFRACTION3chain 'B' and (resid 188 through 231 )
4X-RAY DIFFRACTION4chain 'C' and (resid 190 through 222 )
5X-RAY DIFFRACTION5chain 'D' and (resid 199 through 227 )
6X-RAY DIFFRACTION6chain 'E' and (resid 197 through 227 )
7X-RAY DIFFRACTION7chain 'F' and (resid 192 through 218 )

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