[English] 日本語
Yorodumi
- EMDB-0051: Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0051
TitleCore Centromere Binding Factor 3 (CBF3) with monomeric Ndc10
Map dataReconstruction of the CBF3CCdeltaN (Core complex of CBF3 comprising the homodimer of Cep3deltaN and the heterodimer of Skp1-Ctf13) in complex with domains 1-2 of Ndc10
Sample
  • Complex: Core CBF3 in complex with Ndc10 D1-2
    • Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit B
    • Protein or peptide: Suppressor of kinetochore protein 1
    • Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit C
    • Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit A
KeywordsCentromere / CDEIII-binding / LRR domain / DNA BINDING PROTEIN
Function / homology
Function and homology information


RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / septin ring assembly / mitotic spindle elongation / centromeric DNA binding ...RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / septin ring assembly / mitotic spindle elongation / centromeric DNA binding / regulation of exit from mitosis / kinetochore assembly / condensed chromosome, centromeric region / vacuolar acidification / positive regulation of D-glucose transmembrane transport / protein neddylation / regulation of metabolic process / mitochondrial fusion / mitotic intra-S DNA damage checkpoint signaling / spindle pole body / silent mating-type cassette heterochromatin formation / DNA binding, bending / exit from mitosis / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / mitotic spindle assembly checkpoint signaling / Orc1 removal from chromatin / DNA replication origin binding / cullin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / regulation of protein-containing complex assembly / subtelomeric heterochromatin formation / endomembrane system / spindle midzone / negative regulation of cytoplasmic translation / regulation of mitotic cell cycle / chromosome segregation / kinetochore / spindle / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / DNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Ndc10 N-terminal domain / Transcription activator GCR1-like domain / Ndc10, domain 2 / Ndc10, domain 2 superfamily / Transcriptional activator of glycolytic enzymes / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / : / Centromere DNA-binding protein complex CBF3 subunit B ...: / Ndc10 N-terminal domain / Transcription activator GCR1-like domain / Ndc10, domain 2 / Ndc10, domain 2 superfamily / Transcriptional activator of glycolytic enzymes / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / : / Centromere DNA-binding protein complex CBF3 subunit B / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Integrase/recombinase, N-terminal / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Centromere DNA-binding protein complex CBF3 subunit A / Centromere DNA-binding protein complex CBF3 subunit C / Centromere DNA-binding protein complex CBF3 subunit B / Suppressor of kinetochore protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsZhang WJ / Lukoynova N
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J007595/1 United Kingdom
CitationJournal: Cell Rep / Year: 2018
Title: Insights into Centromere DNA Bending Revealed by the Cryo-EM Structure of the Core Centromere Binding Factor 3 with Ndc10.
Authors: Wenjuan Zhang / Natalya Lukoyanova / Shomon Miah / Jonathan Lucas / Cara K Vaughan /
Abstract: The centromere binding factor 3 (CBF3) complex binds the third centromere DNA element in organisms with point centromeres, such as S. cerevisiae. It is an essential complex for assembly of the ...The centromere binding factor 3 (CBF3) complex binds the third centromere DNA element in organisms with point centromeres, such as S. cerevisiae. It is an essential complex for assembly of the kinetochore in these organisms, as it facilitates genetic centromere specification and allows association of all other kinetochore components. We determined high-resolution structures of the core complex of CBF3 alone and in association with a monomeric construct of Ndc10, using cryoelectron microscopy (cryo-EM). We identify the DNA-binding site of the complex and present a model in which CBF3 induces a tight bend in centromeric DNA, thus facilitating assembly of the centromeric nucleosome.
History
DepositionJun 13, 2018-
Header (metadata) releaseJul 4, 2018-
Map releaseAug 1, 2018-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0051.png

Downloads & links

-
Map

FileDownload / File: emd_0051.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the CBF3CCdeltaN (Core complex of CBF3 comprising the homodimer of Cep3deltaN and the heterodimer of Skp1-Ctf13) in complex with domains 1-2 of Ndc10
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0174
Minimum - Maximum-0.02745911 - 0.09228461
Average (Standard dev.)0.00013709656 (±0.0042895144)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Core CBF3 in complex with Ndc10 D1-2

EntireName: Core CBF3 in complex with Ndc10 D1-2
Components
  • Complex: Core CBF3 in complex with Ndc10 D1-2
    • Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit B
    • Protein or peptide: Suppressor of kinetochore protein 1
    • Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit C
    • Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit A

-
Supramolecule #1: Core CBF3 in complex with Ndc10 D1-2

SupramoleculeName: Core CBF3 in complex with Ndc10 D1-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The truncated CBF3 complex, recombinantly expressed in Saccharomyces cerevisiae. It comprises a Cep3 homodimer, in which the binuclear zinc cluster domains are truncated, full length ...Details: The truncated CBF3 complex, recombinantly expressed in Saccharomyces cerevisiae. It comprises a Cep3 homodimer, in which the binuclear zinc cluster domains are truncated, full length heterodimer of Skp1 and Ctf13, and a monomeric construct Ndc10 comprising domains 1-2.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 286 KDa

-
Macromolecule #1: Centromere DNA-binding protein complex CBF3 subunit B

MacromoleculeName: Centromere DNA-binding protein complex CBF3 subunit B / type: protein_or_peptide / ID: 1
Details: N-terminal polyhistidine purification tagTruncation of the binuclear zinc cluster domain
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 68.454125 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGGSSHHHHH HSSGLVPRGS HMKLITASSS KEYLPDLLLF WQNYEYWITN IGLYKTKQRD LTRTPANLDT DTEECMFWMN YLQKDQSFQ LMNFAMENLG ALYFGSIGDI SELYLRVEQY WDRRADKNHS VDGKYWDALI WSVFTMCIYY MPVEKLAEIF S VYPLHEYL ...String:
MGGSSHHHHH HSSGLVPRGS HMKLITASSS KEYLPDLLLF WQNYEYWITN IGLYKTKQRD LTRTPANLDT DTEECMFWMN YLQKDQSFQ LMNFAMENLG ALYFGSIGDI SELYLRVEQY WDRRADKNHS VDGKYWDALI WSVFTMCIYY MPVEKLAEIF S VYPLHEYL GSNKRLNWED GMQLVMCQNF ARCSLFQLKQ CDFMAHPDIR LVQAYLILAT TTFPYDEPLL ANSLLTQCIH TF KNFHVDD FRPLLNDDPV ESIAKVTLGR IFYRLCGCDY LQSGPRKPIA LHTEVSSLLQ HAAYLQDLPN VDVYREENST EVL YWKIIS LDRDLDQYLN KSSKPPLKTL DAIRRELDIF QYKVDSLEED FRSNNSRFQK FIALFQISTV SWKLFKMYLI YYDT ADSLL KVIHYSKVII SLIVNNFHAK SEFFNRHPMV MQTITRVVSF ISFYQIFVES AAVKQLLVDL TELTANLPTI FGSKL DKLV YLTERLSKLK LLWDKVQLLD SGDSFYHPVF KILQNDIKII ELKNDEMFSL IKGLGSLVPL NKLRQESLLE EEDENN TEP SDFRTIVEEF QSEYNISDIL S

UniProtKB: Centromere DNA-binding protein complex CBF3 subunit B

-
Macromolecule #2: Suppressor of kinetochore protein 1

MacromoleculeName: Suppressor of kinetochore protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.558451 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGVTSNVVLV SGEGERFTVD KKIAERSLLL KNYLNDMHDS NLQNNSDSES DSDSETNHKS KDNNNGDDDD EDDDEIVMPV PNVRSSVLQ KVIEWAEHHR DSNFPDEDDD DSRKSAPVDS WDREFLKVDQ EMLYEIILAA NYLNIKPLLD AGCKVVAEMI R GRSPEEIR ...String:
MGVTSNVVLV SGEGERFTVD KKIAERSLLL KNYLNDMHDS NLQNNSDSES DSDSETNHKS KDNNNGDDDD EDDDEIVMPV PNVRSSVLQ KVIEWAEHHR DSNFPDEDDD DSRKSAPVDS WDREFLKVDQ EMLYEIILAA NYLNIKPLLD AGCKVVAEMI R GRSPEEIR RTFNIVNDFT PEEEAAIRRE NEWAEDRGS

UniProtKB: Suppressor of kinetochore protein 1

-
Macromolecule #3: Centromere DNA-binding protein complex CBF3 subunit C

MacromoleculeName: Centromere DNA-binding protein complex CBF3 subunit C / type: protein_or_peptide / ID: 3 / Details: C-terminal CBP purification tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 60.899961 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGPSFNPVRF LELPIDIRKE VYFHLDGNFC GAHPYPIDIL YKSNDVELPG KPSYKRSKRS KKLLRYMYPV FATYLNIFEY SPQLIEKWL EYAFWLRYDC LVLDCFKVNH LYDGTLIDAL EWTYLDNELR LAYFNKASML EVWYTFKEYK KWVIDSVAFD E LDLLNVSN ...String:
MGPSFNPVRF LELPIDIRKE VYFHLDGNFC GAHPYPIDIL YKSNDVELPG KPSYKRSKRS KKLLRYMYPV FATYLNIFEY SPQLIEKWL EYAFWLRYDC LVLDCFKVNH LYDGTLIDAL EWTYLDNELR LAYFNKASML EVWYTFKEYK KWVIDSVAFD E LDLLNVSN IQFNIDNLTP QLVDKCLSIL EQKDLFATIG EVQFGQDEEV GEEKDVDVSG ANSDENSSPS STIKNKKRSA SK RSHSDNG NVGATHNQLT SISVIRTIRS MESMKSLRKI TVRGEKLYEL LINFHGFRDN PGKTISYIVK RRINEIRLSR MNQ ISRTGL ADFTRWDNLQ KLVLSRVAYI DLNSIVFPKN FKSLTMKRVS KIKWWNIEEN ILKELKVDKR TFKSLYIKED DSKF TKFFN LRHTRIKELD KSEINQITYL RCQAIVWLSF RTLNHIKLQN VSEVFNNIIV PRALFDSKRV EIYRCEKISQ VLVIG SRSG SENLYFQGSK RRWKKNFIAV SAANRFKKIS SSGAL

UniProtKB: Centromere DNA-binding protein complex CBF3 subunit C

-
Macromolecule #4: Centromere DNA-binding protein complex CBF3 subunit A

MacromoleculeName: Centromere DNA-binding protein complex CBF3 subunit A / type: protein_or_peptide / ID: 4
Details: Domains 1-2 of Ndc10 with a non-cleavable C-terminal StrepII tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 66.159578 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGRSSILFLL KLMKIMDVQQ QQEAMSSEDR FQELVDSLKP RTAHQYKTYY TKYIQWCQLN QIIPTPEDNS VNSVPYKDLP ISAELIHWF LLDTLITDDK PGEKREETED LDEEEENSFK IATLKKIIGS LNFLSKLCKV HENPNANIDT KYLESVTKLH T HWIDSQKA ...String:
MGRSSILFLL KLMKIMDVQQ QQEAMSSEDR FQELVDSLKP RTAHQYKTYY TKYIQWCQLN QIIPTPEDNS VNSVPYKDLP ISAELIHWF LLDTLITDDK PGEKREETED LDEEEENSFK IATLKKIIGS LNFLSKLCKV HENPNANIDT KYLESVTKLH T HWIDSQKA ITTNETNNTN TQVLCPPLLK VSLNLWNPET NHLSEKFFKT CSEKLRFLVD FQLRSYLNLS FEERSKIRFG SL KLGKRDR DAIIYHKVTH SAEKKDTPGH HQLLALLPQD CPFICPQTTL AAYLYLRFYG IPSVSKGDGF PNLNADENGS LLQ DIPILR GKSLTTYPRE ETFSNYYTTV FRYCHLPYKR REYFNKCNLV YPTWDEDTFR TFFNEENHGN WLEQPEAFAF PDKI PFDFK KIMNFKSPYT SYSTNAKKDP FPPPKDLLVQ IFPEIDEYKR HDYEGLSQNS RDFLDLMEVL RERFLSNLPW IYKFF PNHD IFQDPIFGNS DFQSYFNDKT IHSKGSPILS FDILPGFNKI YKNKTNFYSL LIERPSQLTF ASSHNPDTHP WSHPQF EK

UniProtKB: Centromere DNA-binding protein complex CBF3 subunit A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.15 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
15.0 mMTris base
2.0 mMDTT
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I
DetailsThe sample is homogeneous and well-dispersed on grids.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2003 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsThe selected images were high-pass filtered and normalized.
Particle selectionNumber selected: 214608
Details: Number of particles after selection by 2D classification
Startup modelType of model: OTHER
Details: Cryosparc was used to generate a startup model from a smaller dataset collected in-house. This was then low pass filtered to 60 Angstroms
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 56509
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Details"Fit in map" function used to place 6FE8 and 4ACO with out further refinement or model building
Output model

PDB-6gsa:
Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more