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- EMDB-21985: Structure of MZT2/GCP-NHD and CDK5Rap2 at position 13 of the gamm... -

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Basic information

Entry
Database: EMDB / ID: EMD-21985
TitleStructure of MZT2/GCP-NHD and CDK5Rap2 at position 13 of the gamma-TuRC
Map dataFocused refinement %u03B3-TuRC density map surrounding positions 12-13
Sample
  • Complex: Focused refinement gamma-TuRC density map surrounding positions 12-13
    • Protein or peptide: Mitotic-spindle organizing protein 2A
    • Protein or peptide: Gamma-tubulin complex component 2
    • Protein or peptide: Centrosome protein Cep215
Keywordsgamma-TuRC / MZT2 / GCP / CDK5Rap2 / STRUCTURAL PROTEIN
Function / homology
Function and homology information


microtubule organizing center organization / negative regulation of centriole replication / regulation of mitotic cell cycle spindle assembly checkpoint / gamma-tubulin ring complex / polar microtubule / microtubule plus-end / gamma-tubulin complex / meiotic spindle organization / mitotic spindle microtubule / microtubule nucleation ...microtubule organizing center organization / negative regulation of centriole replication / regulation of mitotic cell cycle spindle assembly checkpoint / gamma-tubulin ring complex / polar microtubule / microtubule plus-end / gamma-tubulin complex / meiotic spindle organization / mitotic spindle microtubule / microtubule nucleation / microtubule bundle formation / gamma-tubulin binding / non-motile cilium / centrosome cycle / regulation of neuron differentiation / pericentriolar material / mitotic spindle pole / cell leading edge / establishment of mitotic spindle orientation / microtubule organizing center / mitotic sister chromatid segregation / centriole replication / negative regulation of neuron differentiation / cytoplasmic microtubule / spindle assembly / cytoplasmic microtubule organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of microtubule polymerization / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / tubulin binding / mitotic spindle organization / AURKA Activation by TPX2 / ciliary basal body / condensed nuclear chromosome / meiotic cell cycle / neurogenesis / chromosome segregation / neuron migration / brain development / recycling endosome / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / spindle pole / Regulation of PLK1 Activity at G2/M Transition / apical part of cell / cell junction / mitotic cell cycle / protein-containing complex assembly / microtubule binding / microtubule / cytoskeleton / calmodulin binding / transcription cis-regulatory region binding / neuron projection / centrosome / protein-containing complex binding / protein kinase binding / GTP binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
CDK5 regulatory subunit-associated protein 2 / MOZART2 family / Mitotic-spindle organizing gamma-tubulin ring associated / Centrosomin, N-terminal motif 1 / Centrosomin N-terminal motif 1 / Gamma-tubulin complex component 6, N-terminal / Gamma-tubulin complex component 6 N-terminus / Gamma tubulin / Gamma tubulin complex component, C-terminal / Gamma-tubulin complex component, C-terminal domain superfamily ...CDK5 regulatory subunit-associated protein 2 / MOZART2 family / Mitotic-spindle organizing gamma-tubulin ring associated / Centrosomin, N-terminal motif 1 / Centrosomin N-terminal motif 1 / Gamma-tubulin complex component 6, N-terminal / Gamma-tubulin complex component 6 N-terminus / Gamma tubulin / Gamma tubulin complex component, C-terminal / Gamma-tubulin complex component, C-terminal domain superfamily / Gamma tubulin complex component C-terminal / Gamma-tubulin complex component protein / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component N-terminal / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Tubulin gamma-1 chain / CDK5 regulatory subunit-associated protein 2 / Mitotic-spindle organizing protein 2A / Gamma-tubulin complex component 6 / CDK5 regulatory subunit-associated protein 2 / Gamma-tubulin complex component 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsWieczorek M / Huang T-L
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Human Frontier Science Program (HFSP)
Ministry of Science and Technology (MoST, Taiwan)
Academia Sinica (Taiwan)
CitationJournal: Cell Rep / Year: 2020
Title: MZT Proteins Form Multi-Faceted Structural Modules in the γ-Tubulin Ring Complex.
Authors: Michal Wieczorek / Tzu-Lun Huang / Linas Urnavicius / Kuo-Chiang Hsia / Tarun M Kapoor /
Abstract: Microtubule organization depends on the γ-tubulin ring complex (γ-TuRC), a ∼2.3-MDa nucleation factor comprising an asymmetric assembly of γ-tubulin and GCP2-GCP6. However, it is currently ...Microtubule organization depends on the γ-tubulin ring complex (γ-TuRC), a ∼2.3-MDa nucleation factor comprising an asymmetric assembly of γ-tubulin and GCP2-GCP6. However, it is currently unclear how the γ-TuRC-associated microproteins MZT1 and MZT2 contribute to the structure and regulation of the holocomplex. Here, we report cryo-EM structures of MZT1 and MZT2 in the context of the native human γ-TuRC. MZT1 forms two subcomplexes with the N-terminal α-helical domains of GCP3 or GCP6 (GCP-NHDs) within the γ-TuRC "lumenal bridge." We determine the X-ray structure of recombinant MZT1/GCP6-NHD and find it is similar to that within the native γ-TuRC. We identify two additional MZT/GCP-NHD-like subcomplexes, one of which is located on the outer face of the γ-TuRC and comprises MZT2 and GCP2-NHD in complex with a centrosomin motif 1 (CM1)-containing peptide. Our data reveal how MZT1 and MZT2 establish multi-faceted, structurally mimetic "modules" that can expand structural and regulatory interfaces in the γ-TuRC.
History
DepositionMay 17, 2020-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.032
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  • Surface view with fitted model
  • Atomic models: PDB-6x0v
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6x0v
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21985.png

Downloads & links

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Map

FileDownload / File: emd_21985.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement %u03B3-TuRC density map surrounding positions 12-13
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 368 pix.
= 381.248 Å		1.04 Å/pix.
x 368 pix.
= 381.248 Å		1.04 Å/pix.
x 368 pix.
= 381.248 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.036 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032 / Movie #1: 0.032
Minimum - Maximum-0.10054987 - 0.12101965
Average (Standard dev.)-0.0001789894 (±0.004876101)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 381.24802 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0361.0361.036
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z381.248381.248381.248
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.1010.121-0.000

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Supplemental data

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Sample components

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Entire : Focused refinement gamma-TuRC density map surrounding positions 12-13

EntireName: Focused refinement gamma-TuRC density map surrounding positions 12-13
Components
  • Complex: Focused refinement gamma-TuRC density map surrounding positions 12-13
    • Protein or peptide: Mitotic-spindle organizing protein 2A
    • Protein or peptide: Gamma-tubulin complex component 2
    • Protein or peptide: Centrosome protein Cep215

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Supramolecule #1: Focused refinement gamma-TuRC density map surrounding positions 12-13

SupramoleculeName: Focused refinement gamma-TuRC density map surrounding positions 12-13
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mitotic-spindle organizing protein 2A

MacromoleculeName: Mitotic-spindle organizing protein 2A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.240576 KDa
SequenceString:
MAAQGVGPGP GSAAPPGLEA ARQKLALRRK KVLSTEEMEL YELAQAAGGG IDPDVFKILV DLLKLNVAPL AVFQMLKSMC AGQRLASEP QDPAAVSLPT SSVPETRGRD KGSAALGGVL ALAERSNHEG SSQRMPRQPS ATRLPKGGGP GKSPTQGST

UniProtKB: Mitotic-spindle organizing protein 2A

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Macromolecule #2: Gamma-tubulin complex component 2

MacromoleculeName: Gamma-tubulin complex component 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.765719 KDa
SequenceString: MSEFRIHHDV NELLSLLRVH GGDGAEVYID LLQKNRTPYV TTTVSAHSAK VKIAEFSRTP EDFLKKYDEL KSKNTRNLDP LVYLLSKLT EDKETLQYLQ QNAKERAELA AAAVGSSTTS INVPAAASKI SMQELEELRK QLGSVATGST LQQSLELKRK M LRDKQNKK ...String:
MSEFRIHHDV NELLSLLRVH GGDGAEVYID LLQKNRTPYV TTTVSAHSAK VKIAEFSRTP EDFLKKYDEL KSKNTRNLDP LVYLLSKLT EDKETLQYLQ QNAKERAELA AAAVGSSTTS INVPAAASKI SMQELEELRK QLGSVATGST LQQSLELKRK M LRDKQNKK NSGQHLPIFP AWVYERPALI GDFLIGAGIS TDTALPIVLL RWNLALSPRL KCSGVISAHC NLHLPGTLPL AS QESAVVE DLLYVLVGVD GRYVSAQPLA GRQSRTFLVD PNLDLSIREL VHRILPVAAS YSAVTRFIEE KSSFEYGQVN HAL AAAMRT LVKEHLILVS QLEQLHRQGL LSLQKLWFYI QPAMRTMDIL ASLATSVDKG ECLGGSTLSL LHDRSFSYTG DSQA QELCL YLTKAASAPY FEVLEKWIYR GIIHDPYSEF MVEEHELRKE RIQEDYNDKY WDQRYTIVQQ QIPSFLQKMA DKILS TGKY LNVVRECGHD VTCPVAKEII YTLKERAYVE QIEKAFNYAS KVLLDFLMEE KELVAHLRSI KRYFLMDQGD FFVHFM DLA EEELRKPVED ITPPRLEALL ELALRMSTAN TDPFKDDLKI DLMPHDLITQ LLRVLAIETK QEKAMAHADP TELALSG LE AFSFDYIVKW PLSLIINRKA LTRYQMLFRH MFYCKHVERQ LCSVWISNKT AKQHSLHSAQ WFAGAFTLRQ RMLNFVQN I QYYMMFEVME PTWHILEKNL KSASNIDDVL GHHTGFLDTC LKDCMLTNPE LLKVFSKLMS VCVMFTNCMQ KFTQSMKLD GELGGQTLEH STVLGLPAGA EERARKELAR KHLAEHADTV QLVSGFEATI NKFDKNFSAH LLDLLARLSI YSTSDCEHGM ASVISRLDF NGFYTERLER LSAERSQKAT PQVPVLRGPP APAPRVAVTA Q

UniProtKB: Gamma-tubulin complex component 2

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Macromolecule #3: Centrosome protein Cep215

MacromoleculeName: Centrosome protein Cep215 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 215.417359 KDa
SequenceString: MMDLVLEEDV TVPGTLSGCS GLVPSVPDDL DGINPNAGLG NGLLPNVSEE TVSPTRARNM KDFENQITEL KKENFNLKLR IYFLEERMQ QEFHGPTEHI YKTNIELKVE VESLKRELQE REQLLIKASK AVESLAEAGG SEIQRVKEDA RKKVQQVEDL L TKRILLLE ...String:
MMDLVLEEDV TVPGTLSGCS GLVPSVPDDL DGINPNAGLG NGLLPNVSEE TVSPTRARNM KDFENQITEL KKENFNLKLR IYFLEERMQ QEFHGPTEHI YKTNIELKVE VESLKRELQE REQLLIKASK AVESLAEAGG SEIQRVKEDA RKKVQQVEDL L TKRILLLE KDVTAAQAEL EKAFAGTETE KALRLRLESK LSEMKKMHEG DLAMALVLDE KDRLIEELKL SLKSKEALIQ CL KEEKSQM ACPDENVSSG ELRGLCAAPR EEKERETEAA QMEHQKERNS FQERIQALEE DLREKEREIA TEKKNSLKRD KAI QGLTMA LKSKEKKVEE LNSEIEKLSA AFAKAREALQ KAQTQEFQGS EDYETALSGK EALSAALRSQ NLTKSTENHR LRRS IKKIT QELSDLQQER ERLEKDLEEA HREKSKGDCT IRDLRNEVEK LRNEVNEREK AMENRYKSLL SESNKKLHNQ EQVIK HLTE STNQKDVLLQ KFNEKDLEVI QQNCYLMAAE DLELRSEGLI TEKCSSQQPP GSKTIFSKEK KQSSDYEELI QVLKKE QDI YTHLVKSLQE SDSINNLQAE LNKIFALRKQ LEQDVLSYQN LRKTLEEQIS EIRRREEESF SLYSDQTFYL SICLEEN NR FQVEHFSQEE LKKKVSDLIQ LVKELYTDNQ HLKKTIFDLS CMGFQGNGFP DRLASTEQTE LLASKEDEDT IKIGEDDE I NFLSDQHLQQ SNEIMKDLSK GGCKNGYLRH TESKISDCDG AHAPGCLEEG AFINLLAPLF NEKATLLLES RPDLLKVVR ELLLGQLFLT EQEVSGEHLD GKTEKTPKQK GELVHFVQTN SFSKPHDELK LSCEAQLVKA GEVPKVGLKD ASVQTVATEG DLLRFKHEA TREAWEEKPI NTALSAEHRP ENLHGVPGWQ AALLSLPGIT NREAKKSRLP ILIKPSRSLG NMYRLPATQE V VTQLQSQI LELQGELKEF KTCNKQLHQK LILAEAVMEG RPTPDKTLLN AQPPVGAAYQ DSPGEQKGIK TTSSVWRDKE MD SDQQRSY EIDSEICPPD DLASLPSCKE NPEDVLSPTS VATYLSSKSQ PSAKVSVMGT DQSESINTSN ETEYLKQKIH DLE TELEGY QNFIFQLQKH SQCSEAIITV LCGTEGAQDG LSKPKNGSDG EEMTFSSLHQ VRYVKHVKIL GPLAPEMIDS RVLE NLKQQ LEEQEYKLQK EQNLNMQLFS EIHNLQNKFR DLSPPRYDSL VQSQARELSL QRQQIKDGHG ICVISRQHMN TMIKA FEEL LQASDVDYCV AEGFQEQLNQ CAELLEKLEK LFLNGKSVGV EMNTQNELME RIEEDNLTYQ HLLPESPEPS ASHALS DYE TSEKSFFSRD QKQDNETEKT SVMVNSFSQD LLMEHIQEIR TLRKRLEESI KTNEKLRKQL ERQGSEFVQG STSIFAS GS ELHSSLTSEI HFLRKQNQAL NAMLIKGSRD KQKENDKLRE SLSRKTVSLE HLQREYASVK EENERLQKEG SEKERHNQ Q LIQEVRCSGQ ELSRVQEELK LRQQLLSQND KLLQSLRVEL KAYEKLDEEH RRLREASGEG WKGQDPFRDL HSLLMEIQA LRLQLERSIE TSSTLQSRLK EQLARGAEKA QEGALTLAVQ AVSIPEVPLQ PDKHDGDKYP MESDNSFDLF DSSQAVTPKS VSETPPLSG NDTDSLSCDS GSSATSTPCV SRLVTGHHLW ASKNGRHVLG LIEDYEALLK QISQGQRLLA EMDIQTQEAP S STSQELGT KGPHPAPLSK FVSSVSTAKL TLEEAYRRLK LLWRVSLPED GQCPLHCEQI GEMKAEVTKL HKKLFEQEKK LQ NTMKLLQ LSKRQEKVIF DQLVVTHKIL RKARGNLELR PGGAHPGTCS PSRPGS

UniProtKB: CDK5 regulatory subunit-associated protein 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137513
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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