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- EMDB-50219: Negative staining EM map for Mis18 core complex -

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Basic information

Entry
Database: EMDB / ID: EMD-50219
TitleNegative staining EM map for Mis18 core complex
Map data
Sample
  • Complex: Mis18 alpha, Mis18 beta, Mis18BP1 20-130
    • Protein or peptide: Mis18 alpha
    • Protein or peptide: Mis18 beta
    • Protein or peptide: Mis18BP1
KeywordsCentromere / CENP-A / Mis18 complex / Centromere Inheritance / Integrative structural analysis / CELL CYCLE
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 cycle ...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 cycle / cell division / intracellular membrane-bounded organelle / chromatin / DNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
SANT associated / Mis18 domain / KNL2-like / SANTA (SANT Associated) / Mis18 domain profile. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / SANT domain profile. / SANT domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...SANT associated / Mis18 domain / KNL2-like / SANTA (SANT Associated) / Mis18 domain profile. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / SANT domain profile. / SANT domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Protein Mis18-beta / Mis18-binding protein 1 / Protein Mis18-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 24.8 Å
AuthorsJeyaprakash AA / Medina-Pritchard B
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
Wellcome Trust202811 United Kingdom
European Research Council (ERC)101054950European Union
Medical Research Council (MRC, United Kingdom)MR/X0012451/1 United Kingdom
CitationJournal: To be published
Title: Structural Basis for Mis18 Complex Assembly: Implications for Centromere Maintenance
Authors: Jeyaprakash AA / Medina-Pritchard B
History
DepositionApr 30, 2024-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50219.png

Downloads & links

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Map

FileDownload / File: emd_50219.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.48 Å
Density
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-0.44062433 - 3.4794223
Average (Standard dev.)0.00020436132 (±0.17593786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 426.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50219_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50219_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50219_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mis18 alpha, Mis18 beta, Mis18BP1 20-130

EntireName: Mis18 alpha, Mis18 beta, Mis18BP1 20-130
Components
  • Complex: Mis18 alpha, Mis18 beta, Mis18BP1 20-130
    • Protein or peptide: Mis18 alpha
    • Protein or peptide: Mis18 beta
    • Protein or peptide: Mis18BP1

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Supramolecule #1: Mis18 alpha, Mis18 beta, Mis18BP1 20-130

SupramoleculeName: Mis18 alpha, Mis18 beta, Mis18BP1 20-130 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mis18 alpha

MacromoleculeName: Mis18 alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAAGVRSLR CSRGCAGGCE CGDKGKCSDS SLLGKRLSED SSRHQLLQKW ASMWSSMSED ASVADMERAQ LEEEAAAAEE RPLVFLCSGC RRPLGDSLSW VASQEDTNCI LLRCVSCNVS VDKEQKLSKR EKENGCVLET LCCAGCSLNL GYVYRCTPKN LDYKRDLFCL ...String:
SNAAGVRSLR CSRGCAGGCE CGDKGKCSDS SLLGKRLSED SSRHQLLQKW ASMWSSMSED ASVADMERAQ LEEEAAAAEE RPLVFLCSGC RRPLGDSLSW VASQEDTNCI LLRCVSCNVS VDKEQKLSKR EKENGCVLET LCCAGCSLNL GYVYRCTPKN LDYKRDLFCL SVEAIESYVL GSSEKQIVSE DKELFNLESR VEIEKSLTQM EDVLKALQMK LWEAESKLSF ATCKS

UniProtKB: Protein Mis18-alpha

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Macromolecule #2: Mis18 beta

MacromoleculeName: Mis18 beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAAAQPLRH RSRCATPPRG DFCGGTERAI DQASFTTSME WDTQVVKGSS PLGPAGLGAE EPAAGPQLPS WLQPERCAVF QCAQCHAVLA DSVHLAWDLS RSLGAVVFSR VTNNVVLEAP FLVGIEGSLK GSTYNLLFCG SCGIPVGFHL YSTHAALAAL RGHFCLSSDK ...String:
SNAAAQPLRH RSRCATPPRG DFCGGTERAI DQASFTTSME WDTQVVKGSS PLGPAGLGAE EPAAGPQLPS WLQPERCAVF QCAQCHAVLA DSVHLAWDLS RSLGAVVFSR VTNNVVLEAP FLVGIEGSLK GSTYNLLFCG SCGIPVGFHL YSTHAALAAL RGHFCLSSDK MVCYLLKTKA IVNASEMDIQ NVPLSEKIAE LKEKIVLTHN RLKSLMKILS EVTPDQSKPE N

UniProtKB: Protein Mis18-beta

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Macromolecule #3: Mis18BP1

MacromoleculeName: Mis18BP1 / type: protein_or_peptide / ID: 3 / Details: 20-130 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPDSMQRRNL PMDAIFFDSI PSGTLTPVKD LVKYQNSSLK LNDHKKNQFL KMTTFNNKNI FQSTMLTEAT TSNSSLDISA IKPNKDGLKN KANYESPGKI FLRMKEKVLR DKQEQP

UniProtKB: Mis18-binding protein 1

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: 2% Uranyl acetate

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 24.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2042
FSC plot (resolution estimation)

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