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- EMDB-52730: NEDD1-bound native vertebrate gamma-tubulin ring complex from Xen... -

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Basic information

Entry
Database: EMDB / ID: EMD-52730
TitleNEDD1-bound native vertebrate gamma-tubulin ring complex from Xenopus laevis
Map dataLocal resolution-filtered map of the NEDD1-bound native vertebrate gamma-tubulin ring complex from Xenopus laevis
Sample
  • Complex: Tetramer of NEDD1 bound to the gamma-tubulin ring complex
    • Protein or peptide: Gamma-tubulin complex component
    • Protein or peptide: Gamma-tubulin complex component 3 homolog
    • Protein or peptide: Gamma-tubulin complex component
    • Protein or peptide: Gamma-tubulin complex component
    • Protein or peptide: Gamma-tubulin complex component 6
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: NEDD1 gamma-tubulin ring complex targeting factor L homeolog
    • Protein or peptide: Tubulin gamma-1 chain
    • Protein or peptide: Mitotic-spindle organizing protein 1
Keywordscytoskeleton / microtubule / microtubule nucleation / complex / template / cap / gamma-tubulin / gamma-tubulin ring complex / cell cycle / nedd1 / neural precursor cell-expressed developmentally down-regulated 1
Function / homology
Function and homology information


microtubule minus-end binding / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / microtubule nucleator activity / polar microtubule / interphase microtubule organizing center / gamma-tubulin complex / gamma-tubulin ring complex / mitotic spindle microtubule / meiotic spindle organization ...microtubule minus-end binding / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / microtubule nucleator activity / polar microtubule / interphase microtubule organizing center / gamma-tubulin complex / gamma-tubulin ring complex / mitotic spindle microtubule / meiotic spindle organization / dense body / microtubule nucleation / gamma-tubulin binding / mitotic sister chromatid segregation / mitotic spindle assembly / spindle assembly / cytoplasmic microtubule organization / centriole / tubulin binding / mitotic spindle organization / meiotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / spindle / spindle pole / mitotic cell cycle / actin cytoskeleton / microtubule / cytoskeleton / hydrolase activity / ciliary basal body / focal adhesion / centrosome / GTP binding / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / 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 ...: / Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / 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 / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Actin / Actin family / Actin / 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 / ATPase, nucleotide binding domain / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Gamma-tubulin complex component / NEDD1 gamma-tubulin ring complex targeting factor L homeolog / Gamma-tubulin complex component / Gamma-tubulin complex component 6 / Gamma-tubulin complex component 3 homolog / Actin, cytoplasmic 1 / Tubulin gamma-1 chain / Mitotic-spindle organizing protein 1 / Gamma-tubulin complex component
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsVermeulen BJA / Pfeffer S
Funding support Germany, 7 items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG Schi 295/4-4 Germany
German Research Foundation (DFG)DFG Schi 295/11-1 Germany
German Research Foundation (DFG)DFG PF 963/1-4 Germany
German Research Foundation (DFG)DFG PF 963/4-1 Germany
German Research Foundation (DFG)INST 35/1314-1 FUGG Germany
German Research Foundation (DFG)INST 35/1503-1 FUGG Germany
German Research Foundation (DFG)INST 35/1134-1 FUGG Germany
CitationJournal: Nat Commun / Year: 2025
Title: Structural mechanisms for centrosomal recruitment and organization of the microtubule nucleator γ-TuRC.
Authors: Qi Gao / Florian W Hofer / Sebastian Filbeck / Bram J A Vermeulen / Martin Würtz / Annett Neuner / Charlotte Kaplan / Maja Zezlina / Cornelia Sala / Hyesu Shin / Oliver J Gruss / Elmar ...Authors: Qi Gao / Florian W Hofer / Sebastian Filbeck / Bram J A Vermeulen / Martin Würtz / Annett Neuner / Charlotte Kaplan / Maja Zezlina / Cornelia Sala / Hyesu Shin / Oliver J Gruss / Elmar Schiebel / Stefan Pfeffer /
Abstract: The γ-tubulin ring complex (γ-TuRC) acts as a structural template for microtubule formation at centrosomes, associating with two main compartments: the pericentriolar material and the centriole ...The γ-tubulin ring complex (γ-TuRC) acts as a structural template for microtubule formation at centrosomes, associating with two main compartments: the pericentriolar material and the centriole lumen. In the pericentriolar material, the γ-TuRC is involved in microtubule organization, while the function of the centriole lumenal pool remains unclear. The conformational landscape of the γ-TuRC, which is crucial for its activity, and its centrosomal anchoring mechanisms, which determine γ-TuRC activity and turnover, are not understood. Using cryo-electron tomography, we analyze γ-TuRCs in human cells and purified centrosomes. Pericentriolar γ-TuRCs simultaneously associate with the essential adapter NEDD1 and the microcephaly protein CDK5RAP2. NEDD1 forms a tetrameric structure at the γ-TuRC base through interactions with four GCP3/MZT1 modules and GCP5/6-specific extensions, while multiple copies of CDK5RAP2 engage the γ-TuRC in two distinct binding patterns to promote γ-TuRC closure and activation. In the centriole lumen, the microtubule branching factor Augmin tethers a condensed cluster of γ-TuRCs to the centriole wall with defined directional orientation. Centriole-lumenal γ-TuRC-Augmin is protected from degradation during interphase and released in mitosis to aid chromosome alignment. This study provides a unique view on γ-TuRC structure and molecular organization at centrosomes and identifies an important cellular function of centriole-lumenal γ-TuRCs.
History
DepositionFeb 5, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52730.png

Downloads & links

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Map

FileDownload / File: emd_52730.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution-filtered map of the NEDD1-bound native vertebrate gamma-tubulin ring complex from Xenopus laevis
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 384 pix.
= 547.853 Å		1.43 Å/pix.
x 384 pix.
= 547.853 Å		1.43 Å/pix.
x 384 pix.
= 547.853 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4267 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0217
Minimum - Maximum-0.15211141 - 0.2761342
Average (Standard dev.)0.0001769711 (±0.00459369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 547.8528 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: OccuPy-weighted local resolution-filtered map of the NEDD1-bound native...

Fileemd_52730_additional_1.map
AnnotationOccuPy-weighted local resolution-filtered map of the NEDD1-bound native vertebrate gamma-tubulin ring complex from Xenopus laevis
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of the NEDD1-bound native vertebrate...

Fileemd_52730_half_map_1.map
AnnotationHalf map 1 of the NEDD1-bound native vertebrate gamma-tubulin ring complex from Xenopus laevis
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of the NEDD1-bound native vertebrate...

Fileemd_52730_half_map_2.map
AnnotationHalf map 2 of the NEDD1-bound native vertebrate gamma-tubulin ring complex from Xenopus laevis
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetramer of NEDD1 bound to the gamma-tubulin ring complex

EntireName: Tetramer of NEDD1 bound to the gamma-tubulin ring complex
Components
  • Complex: Tetramer of NEDD1 bound to the gamma-tubulin ring complex
    • Protein or peptide: Gamma-tubulin complex component
    • Protein or peptide: Gamma-tubulin complex component 3 homolog
    • Protein or peptide: Gamma-tubulin complex component
    • Protein or peptide: Gamma-tubulin complex component
    • Protein or peptide: Gamma-tubulin complex component 6
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: NEDD1 gamma-tubulin ring complex targeting factor L homeolog
    • Protein or peptide: Tubulin gamma-1 chain
    • Protein or peptide: Mitotic-spindle organizing protein 1

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Supramolecule #1: Tetramer of NEDD1 bound to the gamma-tubulin ring complex

SupramoleculeName: Tetramer of NEDD1 bound to the gamma-tubulin ring complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Gamma-tubulin complex component

MacromoleculeName: Gamma-tubulin complex component / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 103.468312 KDa
SequenceString: MSEFRIHHDV NELISLLHVF GLEGADVYID LLQKNRTPYV TTSVSTHSAK VKIAEFSRTP DDFLKKYEEL KSKNTRNLDP LVYLLSKLI EDKETLQYLQ QNAKDKAELA TSSVTSVSLP IAPNTSKISM QELEELRRQL ETATVAVSCS HQPVEVLRKF L RDKLNKKH ...String:
MSEFRIHHDV NELISLLHVF GLEGADVYID LLQKNRTPYV TTSVSTHSAK VKIAEFSRTP DDFLKKYEEL KSKNTRNLDP LVYLLSKLI EDKETLQYLQ QNAKDKAELA TSSVTSVSLP IAPNTSKISM QELEELRRQL ETATVAVSCS HQPVEVLRKF L RDKLNKKH TGHPVPVFPS WVYERPALTG DFMSFSNPST DVTVSIGTLP LPSQETCLVE DLLYILIGVD GRYISVQPLV GR QSRSFSV EQNLDSSVKE LVNRILPVAT NYSTVTRFVE ENSSFEYGQV NHALGAAMRT LGKEYMILIS QLEHLQRQGL LSL QKLWFY IQPTLRTMEV LASIATSLNK GECFGGATLS LLHDRTFGYT GDSQAQELCL YLTKAASAPY FDILERWIYR GIIN DPYSE FMVEEHELQK EKIQEDYNDK YWDQRYTIVQ QQIPSFLQKV ADKILSTGKY LNVVRECGHD VTCPDAKEIT YTLKE QAYV ERIEKAYNYA SKVLLDFLME EEELVAHLRS IKHYFLMDQG DFFVHFMDLT EEELKKPVDD IIPTRLEALL ELALRM STA NTDPFKDDLK IELMPHDLIT QLLRVLAIET HQEKALINSD PTELALSGLE SFSFDYIVKW PLSLIINRKA LTRYQML FR HMFYCKHVER LLCNVWISNK TAKQFSLHSA KWFAGAFTLR QRMLNFVQNI QYYMMFEVME PTWHILEKNL KSASNIDD V LSHHTSFLDN CLKDCMLTNP ELLKIFSKLM SVCVMFTNCL QRFTQSMQVQ TEMEHLTLEH GTMMGPPTQC ERTEEALKK KLTSKYLEEH IDKFPSSFGF ESTINNFDSN FSAHLMDLLD KLSMYSTSDC EHSMINIIYR LDFNGFYTER LKQLSSERNQ KSAPLLGPA QHAVSTK

UniProtKB: Gamma-tubulin complex component

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Macromolecule #2: Gamma-tubulin complex component 3 homolog

MacromoleculeName: Gamma-tubulin complex component 3 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 103.789352 KDa
SequenceString: MAVPDQKSPN VLLQNLCCRI LGKGEADVAQ QFQYAVRVIG SNFAPTVERD EFLVTEKIKK EFVRQRREAD GALFSELHRK LQSQGVLKN RWSILYLLLS LSEDPRKQPN KTSSFAALFA QALPRDAHST PYYYARPQSL PLSYQDRNVQ CAQNAASIGS S GISSIGMY ...String:
MAVPDQKSPN VLLQNLCCRI LGKGEADVAQ QFQYAVRVIG SNFAPTVERD EFLVTEKIKK EFVRQRREAD GALFSELHRK LQSQGVLKN RWSILYLLLS LSEDPRKQPN KTSSFAALFA QALPRDAHST PYYYARPQSL PLSYQDRNVQ CAQNAASIGS S GISSIGMY ALNGPTPQSI IQGQSNQTPN MGDALRQQLG SRLAWTLAAG QQPSQQSTTT KGLPNTVSRN VPRTRREGDS SG SVEITET SLVRDLLYVF QGIDGKFVKM CNSENCYKVD GKVAVSKSLK DITSKLSELG WLHNKIKKYT DQRSLDRAFG LVG QSFCAA LHQELKEYYR LLSVLHSQLQ VEDDQGVNLG VESSLTLRRL LVWTFDPKIR LKTLAALVDH CQGRKGGELA SAVH AYTKT GDPYMRSLVQ HILGLVAYPI LNFLYRWIYD GELEDTYHEF FVASDPVVKT DRLWHDKYSL RKSMIPSFMT MDQSR KVLL IGKSINFLHQ VCHDQTPASK AMAVGKSAES PKDAAELFTD LENAFQTKID AAYFDTSKYL LDVLNKNYNL LEHMQA MRR YLLLGQGDFI RHLMDLLKPE LVRPATTLYQ HNLTGILETA VRATNAQFDN PEILKRLDVR LLEVSPGDTG WDVFSLD YH VDGPIATVFT RECMSHYLRV FNFLWRAKRM EYILTDIWKG HMCNAKLLKG MPELSGVLHQ CHILASEMVH FIHQMQYY I TFEVLECSWD ELWNKVLKAQ DLDHIIAAHD VFLDTIISRC LLDSESRALL NQLRAVFDQI IEFQNAQDAL YRAALEELQ QRLQFEERKK ERESEGEWGV TAAEEDVENK RIQEFQESIP KMRSQLRILT HFYQGIVQQF LVLLTTSTDE SLRFLSFRLD FNEHYKARE PRLRVSMGTR GRRSFHV

UniProtKB: Gamma-tubulin complex component 3 homolog

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Macromolecule #3: Gamma-tubulin complex component

MacromoleculeName: Gamma-tubulin complex component / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 76.122961 KDa
SequenceString: MIHELLLALS GYPGSIFTWN KRTGLQVSQD IPFLHPGETS VLNRLCKLGT DYIRFTEFIE QYTGHVQQQD HHPSQQGQVG LHGIYLRAF CRGLDSILQP YRQALLDLEQ EFLADPHLSI SHINYSLDQF HLLFPSIMVV VEQIKSQKIH GCQILETVYK H SCGGLPPV ...String:
MIHELLLALS GYPGSIFTWN KRTGLQVSQD IPFLHPGETS VLNRLCKLGT DYIRFTEFIE QYTGHVQQQD HHPSQQGQVG LHGIYLRAF CRGLDSILQP YRQALLDLEQ EFLADPHLSI SHINYSLDQF HLLFPSIMVV VEQIKSQKIH GCQILETVYK H SCGGLPPV RSALEKTLAV CHGVMYKQLS AWMLHGLLLD QYEEFFVRQG SSSGNLAAAF EEEEDDLGIG GLTGKQLREL QD LRLIEEE NMLAPSLKQF SLRAEMLPSY IPVRVAEKIL FVGESVQMFE NQNVNMSRTG SILKNQEDTF AAELHRLKQQ PLF SLVDFE SVLDRIRSTV AEHLWKLMVE ESDLLGQLKI IKDFYLLGRG ELFQAFIDVA QNMLKTPPTA VTEHDVNVAF QLSA HKVLL DDDNLLPLLN LTIDYHGKEH KDTSQPREGP FRDMSPREAP TSGWAALGLS YKVQWPLHIL FTPAVLEKYN VVFKY LLSV RRVQSELQHC WALQMQRKHL ESNKTDAIKW RLQNHMAFLV DNLQYYLQVD VLESQFSQLL QQINSTRDFE SIRLAH DHF LSNLLAQSFI LLKPVFHCLN EILELCHSFC SLVSQNLGPL DERGAGQLDI LVKGFSCQSS LLFRILSSVR NHQINPD LA QLLLRLDYNK YYTQAGGTLG SFGL

UniProtKB: Gamma-tubulin complex component

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Macromolecule #4: Gamma-tubulin complex component

MacromoleculeName: Gamma-tubulin complex component / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 117.577633 KDa
SequenceString: MAHWTRFERD QEGDIKKLVS LMSGIQDDQD GNFQQALQFA WSNFRFHRYL DVSSHTVLRT LEGIFEKLVV HSDLEKAESW KRLTEEFLL LPLPNTEGTK TDSHFAVLSL LLCLSDSPSN HDYTEKPRKK ENDEQEPFDW GKYLREGEDI EFSPDADTPE W SEASEEED ...String:
MAHWTRFERD QEGDIKKLVS LMSGIQDDQD GNFQQALQFA WSNFRFHRYL DVSSHTVLRT LEGIFEKLVV HSDLEKAESW KRLTEEFLL LPLPNTEGTK TDSHFAVLSL LLCLSDSPSN HDYTEKPRKK ENDEQEPFDW GKYLREGEDI EFSPDADTPE W SEASEEED AQEPPSREDS GIQVDRTPLE DPEKKGAPPL VSWKVGEPDA RSWLEQHIVH QYWTSRAPRF SHSSHLHSNL SA IWDQHLY TTDPLYTPDD KTIVTETQVI RETLWLLSGV KKLLIFQLND GKVNVRNDII VTHMTQNCLR SVLEQIAAYG QVV FRLQKF IDEITGHGSE VPLPGTLPTA KKTTEAPFRT YQAFMWALYK YFISFKEELT EIEKCIINKD ETVTLAIVLD KLAP RLAQL KVLHRVFSTG IAEVPPDTRN VVRASHLLNT LYKAILDYDN VGEASEQTVS LLFCLWVETV RPYLEIVDEW IVHGN LFDP AKEFIIQRNK DVPFNHRDFW YATYTLYSVS EKTENEDKMS DNASASSGSD QAPAGRQHTM VSFLKPVLKQ IIMAGK SMQ LLKNLKCRTA LQQDSSRDSD RKSLYTLFLE SVQSRLQHGN DSVPDIITEQ QVNKLSLIKM QSIVAKHLEL DEVHDPL LA INFVRLYLEQ SDFLETFTCN EVCVDRSSES VTCQSFELTL RSCLYPHIGK QYLECCGNLM YTLKKDYRLV EYLQAMRN F FLLEAGDTMY DFYTPIFDKI REKEPWLNLS YLNVQIQEAV GQRYPDDSTR LSVSFESVDL AKKKLPVHTL DGLILSYKV PWPVDIVISS ECQKIYNQVF LLLLLIKWAK YSLDVLQFNE LGNASENEST KEGATVEPFP LPPLTSPSEP KGQQIHRMFL LRVKLMHFV NSLHNYLMTR ILHSTGLEFQ HQVEEAKDLD QLIKIHYRYL STIHDRCLLR EKVSSVKEAI MKVLNVVLMF A DRWHAGLG AWKKESIVKM ESDFTNCHKF LVKVLNKAVC RGSFPHLESL ALSLMAGMEQ S

UniProtKB: Gamma-tubulin complex component

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Macromolecule #5: Gamma-tubulin complex component 6

MacromoleculeName: Gamma-tubulin complex component 6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 193.069141 KDa
SequenceString: MDSITKLFGD LCESHMVGFP WRTALNSRKH SKNRTKQTLK KLAYDTLFVH LFQDEARKLQ PNCTRLPVKN KIIMLSFNLR ICGMSSEAD RLEELVEYLE QSNGIQISDL HAVLELLVEL SGTGPPQLLP PKRDYFKNNK YVGRNVKYQG YDYYDVQVFE A DLGTTVAY ...String:
MDSITKLFGD LCESHMVGFP WRTALNSRKH SKNRTKQTLK KLAYDTLFVH LFQDEARKLQ PNCTRLPVKN KIIMLSFNLR ICGMSSEAD RLEELVEYLE QSNGIQISDL HAVLELLVEL SGTGPPQLLP PKRDYFKNNK YVGRNVKYQG YDYYDVQVFE A DLGTTVAY QELEISTTIQ RTLQIMEAAP GTGLPALSFF SQNDLSTDKF EKETRGSLFG ALVHSRTNDM DIKLDMPPVP EN ADLSGLA IKVPQSIDQS EDEGFQSASN MTPDSQSEPS MTPDIDVWEA VLTYGPSKRR CWERIGCPPG KREEPYVTEA GRE AFDKLY KLHEGGLQIL SATTLQPQLV LLEETDLVKA VLNVLIGVVS STFSYNQALQ SFAVKQGVYI SGTSPDNVSS LLTQ VAEYG TYYTRLSHFS LLTVLDSSHS NGLVFQAFTS GLRKYLQYYR ACVLSTPASL TLLTISFLFR KLGRQLRYLA ELCCI GTLV TSATRGISTA FPTGVKLLSY LYKEALENSS NENYPVLLSL LKTSCEPYTR FIYDWVYSGV FRDVCGEFMI QVNEDY LGF RDKRYWTHGY VLISKEVEDC VPVFLKHVAN EIYICGKTIN LLKLCCPKHY ICWSDIPVPR ISVTFSLEEL KEMEKDC AV YVARMERIAR HSCISKEQKA LQTEIARQEL IIQARETTEK VFETFKDRKL AEKLSLDTKK RELFQKLKDQ YEKEQERR L TTKQEEADDD FSYAREIRDR EKRLKALEEE LELKTRQELI EHYSRLSEEA TRKEQRALWK LQRHKLETIR LKFFLEEQK RMQDLVANFP VDICEENLGV LPDGEISHQT DNTNDAGLGN IENEKSVPEQ HALHNNNDEV YTAQNCISKS ESLCVDVTLP TENVHSQTS NASVLGVPSF DSNLCTPDVD IIDFLPTLPS ENQEVAVVQS LVDDALISIG SDLNTDTKDK ESLCALKSDL Q ESSTGSEY DFKTILKPIA CTQVSQGHIK IGEYSSNVQP ARPRWSTHGH SSDSNIKIGN YVSDINVHQP KHSQHGHSSD SN INISDHM SDVEPRLPRL NLHGHISTGH IKVGEYASDV EPSTPRHSVH GHASQGNIKI GENVSDVKLS RPRWNIHGHV SDA NIKIGE NTSEIAPLRP RWNIHGHASQ SHIKIGELVS DIEPSQPRRT PFGHPSQSSI PIGDQPVEKY AQKSESEVHS SNST IQHLL YSNIPDKNKD TGGTLTDSPV PVPDQGNSND DTEKRSSTLE QRVQAADSVC DGEASPNTAQ SLPCMSDTLD FGTNG EENV GNDDHTWEKQ QEYLKGLAEK YCLEKYQDSY ELMSHPPVLH LYSNVMPNRF SFPTDSDIKS ATDETTVQLI ELLSLP VLM KYSVTAPMVS HVYLVNKAIV DYYFVELKME RHFEAMRHFL LMEDGEFAQS LSDMLFEKLG SGQTPSELLN PLVLNSI LN KALQYSLHGD SSLASNLTFA LKYLPEVFTP TAPDALSCLE LKYKVDWPLN IVITDTCMNK YSRIFSFLLQ LKHMVWTL R DVWFHLKRTA LVNQASNSVQ YRQLQLYRHE MQHFVKVIQG YIANQILHVT WCEFRNKLSA VSNLEEIYKT HADYLNKAL FRGLLTEKAA PLMNIIHSIF SLILKFRLQL ISQSWICDTG KQMAVHPNFG LMQQSYNTFK YYSDFLFEVV SKLVNRGYQP HLEDFLLRI NFNSYYKQS

UniProtKB: Gamma-tubulin complex component 6

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Macromolecule #6: Actin, cytoplasmic 1

MacromoleculeName: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 41.812684 KDa
SequenceString: MEDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG ...String:
MEDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TYNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #7: NEDD1 gamma-tubulin ring complex targeting factor L homeolog

MacromoleculeName: NEDD1 gamma-tubulin ring complex targeting factor L homeolog
type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 73.215234 KDa
SequenceString: MESRGGGGRV RLPGTTMQDN IRFVSAGDDV KIWDYSSMTT VEQFNPHSAS HPVSSLCWSS NNHFLVTASG SGDKIVVSSC KSKPVPLLE LAEGKKQTCV NLNSSSQYVV SGGLDNTVNI WDLKSKRLHR SLKDHKDEVT CVTFNANDCY VASGSMSGEI I LHNVTTNL ...String:
MESRGGGGRV RLPGTTMQDN IRFVSAGDDV KIWDYSSMTT VEQFNPHSAS HPVSSLCWSS NNHFLVTASG SGDKIVVSSC KSKPVPLLE LAEGKKQTCV NLNSSSQYVV SGGLDNTVNI WDLKSKRLHR SLKDHKDEVT CVTFNANDCY VASGSMSGEI I LHNVTTNL SSTPFGHGSS QPIRHLKYSY VKKSLLGTVS DSGSVTLWDA NSQNPYHVFE SAHKAPASGI CFSPVNDLLL VT VGLDKRI ICYDVSSKIL LQTVVAESPL TAVDFMPDGA TLAVGSSRGK IYLYDLRMLS SPVKTVSAHK TSVQCIQFQH SNI YKSSKG PSSKSSILST AVNKKPSTKT AAGGTQSANI TKDLPPSAIS SLPQPVMPVD SKVLRVNDDK SGFPRSTSLD IIPS KETDF AKTSDYKSID SFGRSSLGDI FSPVRDDASH FRGAEDLSCK GNDLDYLPQF STIPSSRRNP VGANTQGIHG SPLHL IIES PIKEEDESQD SELKTRKPQL LKQDFRESSS KPASVDQNNL NNSPINSVTR TPEAIEKTGH QILSQLKSDV PAHGTK IAS PKVAATMSTQ LASSLSEKIA DTLASDRTGA PLTAIQINFI KNMIEETLDD FREACHRDIV NLQVEMIKQF HIQSSEI QM LLERYSLNES LVSEIEKLRE ENKRLRANF

UniProtKB: NEDD1 gamma-tubulin ring complex targeting factor L homeolog

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Macromolecule #8: Tubulin gamma-1 chain

MacromoleculeName: Tubulin gamma-1 chain / type: protein_or_peptide / ID: 8 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 51.226719 KDa
SequenceString: MPREIITLQL GQCGNQIGFE FWKQLCAEHG ISPEGIVEEF ATEGTDRKDV FFYQADDEHY IPRAVLLDLE PRVIHSILNS PYANLYNPE NIYLSEHGGG AGNNWASGFS QGEKIHEDIF DIIDREADGS DSLEGFVLCH SIAGGTGSGL GSYLLERLND R YPKKLVQT ...String:
MPREIITLQL GQCGNQIGFE FWKQLCAEHG ISPEGIVEEF ATEGTDRKDV FFYQADDEHY IPRAVLLDLE PRVIHSILNS PYANLYNPE NIYLSEHGGG AGNNWASGFS QGEKIHEDIF DIIDREADGS DSLEGFVLCH SIAGGTGSGL GSYLLERLND R YPKKLVQT YSVFPNQDEM SHVVVQPYNS LLTLKRLTQN ADCVVVLDNT ALNRIATDRL HIQNPSFSQI NQLVSTIMSA ST TTLRYPG YMNNDLIGLI ASLIPTPRLH FLMTGYTPLT TDQSVASVRK TTVLDVMRRL LQPKNVMVST GRDRQTNHCY IAI LNIIQG EVDPTQVHKS LQRIRERKLA NFIPWGPASI QVALSRKSPY LPSAHRVSGL MMANHTNISS LFERTCRQYD KLRK REAFL EQFRKEDIFK DNFDELDNSR EIVQQLIDEY HAATRPDYIS WGTQDK

UniProtKB: Tubulin gamma-1 chain

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Macromolecule #9: Mitotic-spindle organizing protein 1

MacromoleculeName: Mitotic-spindle organizing protein 1 / type: protein_or_peptide / ID: 9 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 7.749854 KDa
SequenceString:
MANASGNMSA VRETMDVLLE ISRLLNTGLD METLSICVRL CEQGINPEAL SSVIKELRRA SDTLKASEST AS

UniProtKB: Mitotic-spindle organizing protein 1

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

10491


Details: The reference contains no density for the NEDD1/N-GCP/MZT1 grapnel and density for the GRIP2 domains and gamma-tubulins at spokes 5 and 6 was removed
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 299022
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9i8n:
NEDD1-bound native vertebrate gamma-tubulin ring complex from Xenopus laevis

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