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- EMDB-21060: Structures of GCP4 and GCP5 in the native human gamma-tubulin rin... -

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Basic information

Entry
Database: EMDB / ID: EMD-21060
TitleStructures of GCP4 and GCP5 in the native human gamma-tubulin ring complex
Map data
Sample
  • Complex: Native human gamma-tubulin ring complex
    • Protein or peptide: Gamma-tubulin complex component 5
    • Protein or peptide: Gamma-tubulin complex component 4
KeywordsGCP / GCP4 / GCP5 / gamma-tubulin ring complex / gTuRC / g-TuRC / microtubule / microtubule nucleation / single particle cryo-EM structure / STRUCTURAL PROTEIN
Function / homology
Function and homology information


gamma-tubulin complex / gamma-tubulin ring complex / microtubule nucleation / gamma-tubulin binding / spindle assembly / cytoplasmic microtubule organization / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / meiotic cell cycle / recycling endosome ...gamma-tubulin complex / gamma-tubulin ring complex / microtubule nucleation / gamma-tubulin binding / spindle assembly / cytoplasmic microtubule organization / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / meiotic cell cycle / recycling endosome / structural constituent of cytoskeleton / spindle pole / mitotic cell cycle / microtubule cytoskeleton / protein-containing complex assembly / microtubule binding / microtubule / cilium / ciliary basal body / centrosome / membrane / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Gamma-tubulin complex component 5 / Gamma-tubulin complex component 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWieczorek M / Urnavicius L
Funding support United States, France, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM130234 United States
Human Frontier Science Program (HFSP)LT000025/18-L1 France
CitationJournal: Cell / Year: 2020
Title: Asymmetric Molecular Architecture of the Human γ-Tubulin Ring Complex.
Authors: Michal Wieczorek / Linas Urnavicius / Shih-Chieh Ti / Kelly R Molloy / Brian T Chait / Tarun M Kapoor /
Abstract: The γ-tubulin ring complex (γ-TuRC) is an essential regulator of centrosomal and acentrosomal microtubule formation, yet its structure is not known. Here, we present a cryo-EM reconstruction of the ...The γ-tubulin ring complex (γ-TuRC) is an essential regulator of centrosomal and acentrosomal microtubule formation, yet its structure is not known. Here, we present a cryo-EM reconstruction of the native human γ-TuRC at ∼3.8 Å resolution, revealing an asymmetric, cone-shaped structure. Pseudo-atomic models indicate that GCP4, GCP5, and GCP6 form distinct Y-shaped assemblies that structurally mimic GCP2/GCP3 subcomplexes distal to the γ-TuRC "seam." We also identify an unanticipated structural bridge that includes an actin-like protein and spans the γ-TuRC lumen. Despite its asymmetric architecture, the γ-TuRC arranges γ-tubulins into a helical geometry poised to nucleate microtubules. Diversity in the γ-TuRC subunits introduces large (>100,000 Å) surfaces in the complex that allow for interactions with different regulatory factors. The observed compositional complexity of the γ-TuRC could self-regulate its assembly into a cone-shaped structure to control microtubule formation across diverse contexts, e.g., within biological condensates or alongside existing filaments.
History
DepositionDec 4, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseJan 1, 2020-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0196
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0196
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6v69
  • Surface level: 0.0196
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6v69
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21060.png

Downloads & links

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Map

FileDownload / File: emd_21060.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 368 pix.
= 491.28 Å		1.34 Å/pix.
x 368 pix.
= 491.28 Å		1.34 Å/pix.
x 368 pix.
= 491.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.335 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0196 / Movie #1: 0.0196
Minimum - Maximum-0.038092647 - 0.07599434
Average (Standard dev.)0.00006492295 (±0.0014523533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 491.28003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3351.3351.335
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z491.280491.280491.280
α/β/γ90.00090.00090.000
start NX/NY/NZ-51-35-11
NX/NY/NZ11110799
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.0380.0760.000

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Supplemental data

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Sample components

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Entire : Native human gamma-tubulin ring complex

EntireName: Native human gamma-tubulin ring complex
Components
  • Complex: Native human gamma-tubulin ring complex
    • Protein or peptide: Gamma-tubulin complex component 5
    • Protein or peptide: Gamma-tubulin complex component 4

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Supramolecule #1: Native human gamma-tubulin ring complex

SupramoleculeName: Native human gamma-tubulin ring complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gamma-tubulin complex component 5

MacromoleculeName: Gamma-tubulin complex component 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.467547 KDa
SequenceString: MARHGPPWSR LDAQQERDVR ELVRGVAGLQ DEADPNFQLA LNFAWSNFRF HRFLDVNSHK IEKTIEGIYE KFVIHSDLSK AASWKRLTE EFLNAPLPSI KEIKTDAHYS ILSLLLCLSD SPSNSSYVET PRNKEVEKKD DFDWGKYLME DEEMDIGPYM D TPNWSEES ...String:
MARHGPPWSR LDAQQERDVR ELVRGVAGLQ DEADPNFQLA LNFAWSNFRF HRFLDVNSHK IEKTIEGIYE KFVIHSDLSK AASWKRLTE EFLNAPLPSI KEIKTDAHYS ILSLLLCLSD SPSNSSYVET PRNKEVEKKD DFDWGKYLME DEEMDIGPYM D TPNWSEES EEENDQQPLS REDSGIQVDR TPLEEQDQNR KLDPCISWKD EPDDRSWLEH HVVHQYWTAR PSQFPHSLHL HS NLAAVWD QHLYSSDPLY VPDDRVLVTE TQVIRETLWL LSGVKKLFIF QLIDGKVTVR NNIIVTHLTH SCLRSVLEQI AAY GQVVFR LQEFIDEVMG HSSESMLPGS GSVPKKSTEA PFRTYQAFMW ALYKYFISFK EELAEIEKCI INNDTTITLA IVVD KLAPR LSQLKVLHKV FSTGVAEVPP DTRNVVRASH LLNTLYKAIL EYDNVGEASE QTVSLLFSLW VETVRPYLQT VDEWI VHGH LWDGAREFII QRNKNVPVNH RDFWYATYTL YSVSEKTENE EKMSDNASAS SGSDQGPSSR QHTMVSFLKP VLKQII MAG KSMQLLKNLQ CAESTTCQAG ARDAERKSLY TLFLESVQSR LRHGEDSTPQ VLTEQQATKE NLMKMQSIAE SHLELDD VH DPLLAINFAR MYLEQSDFHE KFAGGDVCVD RSSESVTCQT FELTLRSCLY PHIDKQYLDC CGNLMQTLKK DYRLVEYL Q AMRNFFLMEG GDTMYDFYTS IFDKIREKET WQNVSFLNVQ LQEAVGQRYP EDSSRLSISF ENVDTAKKKL PVHILDGLT LSYKVPWPVD IVISLECQKI YNQVFLLLLQ IKWAKYSLDV LLFGELVSTA EKPRLKEGLI HEQDTVAQFG PQKEPVRQQI HRMFLLRVK LMHFVNSLHN YIMTRILHST GLEFQHQVEE AKDLDQLIKI HYRYLSTIHD RCLLREKVSF VKEAIMKVLN L ALMFADGW QAGLGTWRME SIEKMESDFK NCHMFLVTIL NKAVCRGSFP HLESLALSLM AGMEQS

UniProtKB: Gamma-tubulin complex component 5

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Macromolecule #2: Gamma-tubulin complex component 4

MacromoleculeName: Gamma-tubulin complex component 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.179969 KDa
SequenceString: MIHELLLALS GYPGSIFTWN KRSGLQVSQD FPFLHPSETS VLNRLCRLGT DYIRFTEFIE QYTGHVQQQD HHPSQQGQGG LHGIYLRAF CTGLDSVLQP YRQALLDLEQ EFLGDPHLSI SHVNYFLDQF QLLFPSVMVV VEQIKSQKIH GCQILETVYK H SCGGLPPV ...String:
MIHELLLALS GYPGSIFTWN KRSGLQVSQD FPFLHPSETS VLNRLCRLGT DYIRFTEFIE QYTGHVQQQD HHPSQQGQGG LHGIYLRAF CTGLDSVLQP YRQALLDLEQ EFLGDPHLSI SHVNYFLDQF QLLFPSVMVV VEQIKSQKIH GCQILETVYK H SCGGLPPV RSALEKILAV CHGVMYKQLS AWMLHGLLLD QHEEFFIKQG PSSGNVSAQP EEDEEDLGIG GLTGKQLREL QD LRLIEEE NMLAPSLKQF SLRVEILPSY IPVRVAEKIL FVGESVQMFE NQNVNLTRKG SILKNQEDTF AAELHRLKQQ PLF SLVDFE QVVDRIRSTV AEHLWKLMVE ESDLLGQLKI IKDFYLLGRG ELFQAFIDTA QHMLKTPPTA VTEHDVNVAF QQSA HKVLL DDDNLLPLLH LTIEYHGKEH KADATQAREG PSRETSPREA PASGWAALGL SYKVQWPLHI LFTPAVLEKY NVVFK YLLS VRRVQAELQH CWALQMQRKH LKSNQTDAIK WRLRNHMAFL VDNLQYYLQV DVLESQFSQL LHQINSTRDF ESIRLA HDH FLSNLLAQSF ILLKPVFHCL NEILDLCHSF CSLVSQNLGP LDERGAAQLS ILVKGFSRQS SLLFKILSSV RNHQINS DL AQLLLRLDYN KYYTQAGGTL GSFGM

UniProtKB: Gamma-tubulin complex component 4

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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 K2 SUMMIT (4k 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Relion 3.0 initial model generation
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103172
Initial angle assignmentType: OTHER / Details: Relion 3.0
Final angle assignmentType: OTHER / Details: Relion 3.0

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