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- EMDB-54161: D. melanogaster Augmin TII N-clamp (GST-fusion) bound to a microt... -

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Basic information

Entry
Database: EMDB / ID: EMD-54161
TitleD. melanogaster Augmin TII N-clamp (GST-fusion) bound to a microtubule, well-defined subset of particles
Map data
Sample
  • Complex: Microtubule decorated with D. melanogaster N-clamp
    • Complex: Heterotetrameric Augmin TII N-clamp complex
    • Organelle or cellular component: Microtubule
    • Protein or peptide: Augmin complex subunit dgt4
    • Protein or peptide: Augmin complex subunit dgt6
    • Protein or peptide: Augmin complex subunit msd5,Green fluorescent protein,Glutathione S-transferase class-mu 26 kDa isozyme
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Tubulin alpha-1A chain
Keywordsaugmin / N-clamp / TII / microtubule / branching / nucleation / HAUS / HAUS augmin-like complex subunit / HAUS6 / HAUS7 / HAUS2 / HAUS8 / Dgt6 / Msd5 / Dgt4 / Msd1 / Drosophila melanogaster / complex / CH domain / calponin homology domain / CELL CYCLE / MAP / cell division
Function / homology
Function and homology information


mitotic spindle-templated microtubule nucleation / HAUS complex / mitotic spindle microtubule / motile cilium / regulation of mitotic nuclear division / glutathione transferase / centrosome duplication / glutathione transferase activity / mitotic spindle assembly / glutathione metabolic process ...mitotic spindle-templated microtubule nucleation / HAUS complex / mitotic spindle microtubule / motile cilium / regulation of mitotic nuclear division / glutathione transferase / centrosome duplication / glutathione transferase activity / mitotic spindle assembly / glutathione metabolic process / bioluminescence / mitotic spindle organization / generation of precursor metabolites and energy / kinetochore / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / neuron migration / spindle pole / mitotic cell cycle / protein-macromolecule adaptor activity / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / cell division / GTPase activity / centrosome / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 6 N-terminus / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 6 N-terminus / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Green fluorescent protein, GFP / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Green fluorescent protein-related / Green fluorescent protein / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Green fluorescent protein / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Tubulin alpha-1A chain / Tubulin beta chain / Glutathione S-transferase class-mu 26 kDa isozyme / Green fluorescent protein / Augmin complex subunit dgt6 / Augmin complex subunit msd5 / Augmin complex subunit dgt4
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly) / Sus scrofa (pig) / Schistosoma japonicum (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsWuertz M / Vermeulen BJA / Tonon G / Pfeffer S
Funding support Germany, 9 items
OrganizationGrant numberCountry
German Research Foundation (DFG)Sch Baden-Wuerttemberg 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
German Research Foundation (DFG)DFG Schi 295/4-4 Germany
German Research Foundation (DFG)SCHI 295/11-1 Germany
German Research Foundation (DFG)SCHI 295/9-1 Germany
German Research Foundation (DFG)DFG PF 963/1-4 Germany
German Research Foundation (DFG)DFG PF 963/4-1 Germany
CitationJournal: To Be Published / Year: 2025
Title: Structural insights into the augmin-microtubule interaction reveal a conserved function of the HAUS6 CH domain in orienting augmin on microtubules
Authors: Wuertz M / Tonon G / Vermeulen BJA / Gao Q / Zezlina M / Neuner A / Seidl A / Koenig M / Harkenthal M / Eustermann S / Erhardt S / Lolicato F / Schiebel E / Pfeffer S
History
DepositionJun 24, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_54161.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.069 Å
Density
Contour LevelBy AUTHOR: 0.00846
Minimum - Maximum-0.012607779 - 0.025806485
Average (Standard dev.)0.00015531038 (±0.0019867958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.664 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Microtubule decorated with D. melanogaster N-clamp

EntireName: Microtubule decorated with D. melanogaster N-clamp
Components
  • Complex: Microtubule decorated with D. melanogaster N-clamp
    • Complex: Heterotetrameric Augmin TII N-clamp complex
    • Organelle or cellular component: Microtubule
    • Protein or peptide: Augmin complex subunit dgt4
    • Protein or peptide: Augmin complex subunit dgt6
    • Protein or peptide: Augmin complex subunit msd5,Green fluorescent protein,Glutathione S-transferase class-mu 26 kDa isozyme
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Tubulin alpha-1A chain

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Supramolecule #1: Microtubule decorated with D. melanogaster N-clamp

SupramoleculeName: Microtubule decorated with D. melanogaster N-clamp / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Supramolecule #2: Heterotetrameric Augmin TII N-clamp complex

SupramoleculeName: Heterotetrameric Augmin TII N-clamp complex / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Supramolecule #3: Microtubule

SupramoleculeName: Microtubule / type: organelle_or_cellular_component / ID: 3 / Parent: 1
Source (natural)Organism: Sus scrofa (pig) / Organ: Brain

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Macromolecule #1: Augmin complex subunit dgt4

MacromoleculeName: Augmin complex subunit dgt4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 12.246828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
METPPTPTTT TPPSLTTEGT MDDIQYLLHL EAMRRFQEDS RNVKRQVEEQ VRIWLDAKCE YQRDFGRLAR LLKCGALQAA VDAHRVSDV NQVDQAAKDI ASLRSKLGS

UniProtKB: Augmin complex subunit dgt4

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Macromolecule #2: Augmin complex subunit dgt6

MacromoleculeName: Augmin complex subunit dgt6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 32.382451 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDRTIIAPWK AEEKEQSEKL HRKLQGLALV HPLPDELRKL IAWDMFLKPN QVAFVHVMHY LFRLLDPAEF KRRFFWPITD KKSEANFRS STVEYLKHLN EKHQLHWANI KSYLVVMPGG MRFINFLLEF VGFVIQELIK QREKSLGLEA GTPNVSAKVM A RQNAVMKE ...String:
MDRTIIAPWK AEEKEQSEKL HRKLQGLALV HPLPDELRKL IAWDMFLKPN QVAFVHVMHY LFRLLDPAEF KRRFFWPITD KKSEANFRS STVEYLKHLN EKHQLHWANI KSYLVVMPGG MRFINFLLEF VGFVIQELIK QREKSLGLEA GTPNVSAKVM A RQNAVMKE YASSYVVNLE ENTALLRDKT QKIRRLMADL SADMGVPEEQ LADDGFLDEF EATAALGVER VITQPTERKF DL EASLCGL KEAIDLFQVK QAENNQSKEA VEKALRGMRV LFD

UniProtKB: Augmin complex subunit dgt6

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Macromolecule #3: Augmin complex subunit msd5,Green fluorescent protein,Glutathione...

MacromoleculeName: Augmin complex subunit msd5,Green fluorescent protein,Glutathione S-transferase class-mu 26 kDa isozyme
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: glutathione transferase
Source (natural)Organism: Schistosoma japonicum (invertebrata)
Molecular weightTheoretical: 76.561094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: METNVDFSSI SSKLYRKYAQ HVRNLKDVCV SKTVMKPGAF FDSLQQMMEE EAAATTPPRD LSSVADYAEL FKTLEEYPAN LQKMPKKRE LQRTNSTLLR GADESVAMGI NTSNVSLSLT RLEEQRSAVD VYNDFKGFQR KLAKIYDEAA ALDTTESIYK Q KLTQLHGF ...String:
METNVDFSSI SSKLYRKYAQ HVRNLKDVCV SKTVMKPGAF FDSLQQMMEE EAAATTPPRD LSSVADYAEL FKTLEEYPAN LQKMPKKRE LQRTNSTLLR GADESVAMGI NTSNVSLSLT RLEEQRSAVD VYNDFKGFQR KLAKIYDEAA ALDTTESIYK Q KLTQLHGF AQQLEKLMPT GLSGENLYFQ GGSAGSAAGS GEFMVSKGEE LFTGVVPILV ELDGDVNGHK FSVSGEGEGD AT YGKLTLK FICTTGKLPV PWPTLVTTLT YGVQCFSRYP DHMKQHDFFK SAMPEGYVQE RTIFFKDDGN YKTRAEVKFE GDT LVNRIE LKGIDFKEDG NILGHKLEYN YNSHNVYIMA DKQKNGIKVN FKIRHNIEDG SVQLADHYQQ NTPIGDGPVL LPDN HYLST QSALSKDPNE KRDHMVLLEF VTAAGITLGM DELYKLEVLM SPILGYWKIK GLVQPTRLLL EYLEEKYEEH LYERD EGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKERA EISMLEGAVL DIRYGVSRIA YSKDFE TLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL DVVLYMDPMC LDAFPKLVCF KKRIEAIPQI DKYLKSS KY IAWPLQGWQA TFGGGDHPPK GPHHHHHHHH

UniProtKB: Augmin complex subunit msd5, Green fluorescent protein, Glutathione S-transferase class-mu 26 kDa isozyme

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Macromolecule #4: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 49.90777 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEGEEDEA

UniProtKB: Tubulin beta chain

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Macromolecule #5: Tubulin alpha-1A chain

MacromoleculeName: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 50.121266 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFSVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFSVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRAHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YEPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1A chain

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 6.8
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: 40.4 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Synthetic reference provided under https://github.com/moores-lab/MiRPv2/tree/main/data/protofilament_sorting_references
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 117870
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9rpd:
D. melanogaster Augmin TII N-clamp (GST-fusion) bound to a microtubule, well-defined subset of particles

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