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- EMDB-25387: Cryo-EM structure of the human augmin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-25387
TitleCryo-EM structure of the human augmin complex
Map dataStructure of a Protein Complex in Cell Division
Sample
  • Complex: Holocomplex of the Homologous to Augment Subunits Complex
    • Protein or peptide: HAUS augmin-like complex subunit 1
    • Protein or peptide: HAUS augmin-like complex subunit 2
    • Protein or peptide: HAUS augmin-like complex subunit 3
    • Protein or peptide: Isoform 4 of HAUS augmin-like complex subunit 4
    • Protein or peptide: HAUS augmin-like complex subunit 5
    • Protein or peptide: HAUS augmin-like complex subunit 6
    • Protein or peptide: HAUS augmin-like complex subunit 7
    • Protein or peptide: HAUS augmin-like complex subunit 8
Function / homology
Function and homology information


HAUS complex / microtubule minus-end binding / regulation of microtubule nucleation / nuclear microtubule / mitotic spindle microtubule / microtubule nucleation / thioesterase binding / centrosome cycle / spindle assembly / Loss of Nlp from mitotic centrosomes ...HAUS complex / microtubule minus-end binding / regulation of microtubule nucleation / nuclear microtubule / mitotic spindle microtubule / microtubule nucleation / thioesterase binding / centrosome cycle / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / mitotic spindle / microtubule cytoskeleton organization / spindle pole / Regulation of PLK1 Activity at G2/M Transition / microtubule binding / cell division / centrosome / nucleolus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
HAUS augmin-like complex subunit 2, metazoa / HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 N-terminus / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 4, metazoa / HAUS complex subunit 5, metazoa / HAUS augmin-like complex subunit 1 ...HAUS augmin-like complex subunit 2, metazoa / HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 N-terminus / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 4, metazoa / HAUS complex subunit 5, metazoa / HAUS augmin-like complex subunit 1 / HAUS augmin-like complex subunit 5 / HAUS augmin-like complex subunit 4 / HAUS augmin-like complex subunit 4 / HAUS augmin-like complex subunit 5 / HAUS augmin-like complex subunit 3 / HAUS augmin-like complex subunit 3, N-terminal / HAUS augmin-like complex subunit 3
Similarity search - Domain/homology
HAUS augmin-like complex subunit 5 / HAUS augmin-like complex subunit 3 / HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 1 / HAUS augmin-like complex subunit 7 / HAUS augmin-like complex subunit 8 / HAUS augmin-like complex subunit 4 / HAUS augmin-like complex subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsGabel CA / Chang L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Molecular architecture of the augmin complex.
Authors: Clinton A Gabel / Zhuang Li / Andrew G DeMarco / Ziguo Zhang / Jing Yang / Mark C Hall / David Barford / Leifu Chang /
Abstract: Accurate segregation of chromosomes during mitosis depends on the correct assembly of the mitotic spindle, a bipolar structure composed mainly of microtubules. The augmin complex, or homologous to ...Accurate segregation of chromosomes during mitosis depends on the correct assembly of the mitotic spindle, a bipolar structure composed mainly of microtubules. The augmin complex, or homologous to augmin subunits (HAUS) complex, is an eight-subunit protein complex required for building robust mitotic spindles in metazoa. Augmin increases microtubule density within the spindle by recruiting the γ-tubulin ring complex (γ-TuRC) to pre-existing microtubules and nucleating branching microtubules. Here, we elucidate the molecular architecture of augmin by single particle cryo-electron microscopy (cryo-EM), computational methods, and crosslinking mass spectrometry (CLMS). Augmin's highly flexible structure contains a V-shaped head and a filamentous tail, with the head existing in either extended or contracted conformational states. Our work highlights how cryo-EM, complemented by computational advances and CLMS, can elucidate the structure of a challenging protein complex and provides insights into the function of augmin in mediating microtubule branching nucleation.
History
DepositionNov 5, 2021-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateOct 5, 2022-
Current statusOct 5, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25387.png

Downloads & links

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Map

FileDownload / File: emd_25387.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of a Protein Complex in Cell Division
Voxel sizeX=Y=Z: 1.384 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum0.0 - 0.19346383
Average (Standard dev.)9.074064e-05 (±0.00195876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 664.31995 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Holocomplex of the Homologous to Augment Subunits Complex

EntireName: Holocomplex of the Homologous to Augment Subunits Complex
Components
  • Complex: Holocomplex of the Homologous to Augment Subunits Complex
    • Protein or peptide: HAUS augmin-like complex subunit 1
    • Protein or peptide: HAUS augmin-like complex subunit 2
    • Protein or peptide: HAUS augmin-like complex subunit 3
    • Protein or peptide: Isoform 4 of HAUS augmin-like complex subunit 4
    • Protein or peptide: HAUS augmin-like complex subunit 5
    • Protein or peptide: HAUS augmin-like complex subunit 6
    • Protein or peptide: HAUS augmin-like complex subunit 7
    • Protein or peptide: HAUS augmin-like complex subunit 8

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Supramolecule #1: Holocomplex of the Homologous to Augment Subunits Complex

SupramoleculeName: Holocomplex of the Homologous to Augment Subunits Complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 378 kDa/nm

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Macromolecule #1: HAUS augmin-like complex subunit 1

MacromoleculeName: HAUS augmin-like complex subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.910348 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEPQEERETQ VAAWLKKIFG DHPIPQYEVN PRTTEILHHL SERNRVRDRD VYLVIEDLKQ KASEYESEAK YLQDLLMESV NFSPANLSS TGSRYLNALV DSAVALETKD TSLASFIPAV NDLTSDLFRT KSKSEEIKIE LEKLEKNLTA TLVLEKCLQE D VKKAELHL ...String:
MEPQEERETQ VAAWLKKIFG DHPIPQYEVN PRTTEILHHL SERNRVRDRD VYLVIEDLKQ KASEYESEAK YLQDLLMESV NFSPANLSS TGSRYLNALV DSAVALETKD TSLASFIPAV NDLTSDLFRT KSKSEEIKIE LEKLEKNLTA TLVLEKCLQE D VKKAELHL STERAKVDNR RQNMDFLKAK SEEFRFGIKA AEEQLSARGM DASLSHQSLV ALSEKLARLK QQTIPLKKKL ES YLDLMPN PSLAQVKIEE AKRELDSIEA ELTRRVDMME L

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Macromolecule #2: HAUS augmin-like complex subunit 2

MacromoleculeName: HAUS augmin-like complex subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.487453 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHHHP QLAMWSHPQF EKGGGSGGGS GGGSWSHPQF EKENLYFQSM AAANPWDPAS APNGAGLVLG HFIASGMVNQ EMLNMSKKT VSCFVNFTRL QQITNIQAEI YQKNLEIELL KLEKDTADVV HPFFLAQKCH TLQSMNNHLE AVLKEKRSLR Q RLLKPMCQ ...String:
MHHHHHHHHP QLAMWSHPQF EKGGGSGGGS GGGSWSHPQF EKENLYFQSM AAANPWDPAS APNGAGLVLG HFIASGMVNQ EMLNMSKKT VSCFVNFTRL QQITNIQAEI YQKNLEIELL KLEKDTADVV HPFFLAQKCH TLQSMNNHLE AVLKEKRSLR Q RLLKPMCQ ENLPIEAVYH RYMVHLLELA VTFIERLETH LETIRNIPHL AANLKKMNQA LAKMDILVTE TEELAENILK WR KQQNEVS SCIPKILAEE SYLYKHDIIM PPLPFTSKVH VQTINAK

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Macromolecule #3: HAUS augmin-like complex subunit 3

MacromoleculeName: HAUS augmin-like complex subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.74018 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSCGNEFVET LKKIGYPKAD NLNGEDFDWL FEGVEDESFL KWFCGNVNEQ NVLSERELEA FSILQKSGKP ILEGAALDEA LKTCKTSDL KTPRLDDKEL EKLEDEVQTL LKLKNLKIQR RNKCQLMASV TSHKSLRLNA KEEEATKKLK QSQGILNAMI T KISNELQA ...String:
MSCGNEFVET LKKIGYPKAD NLNGEDFDWL FEGVEDESFL KWFCGNVNEQ NVLSERELEA FSILQKSGKP ILEGAALDEA LKTCKTSDL KTPRLDDKEL EKLEDEVQTL LKLKNLKIQR RNKCQLMASV TSHKSLRLNA KEEEATKKLK QSQGILNAMI T KISNELQA LTDEVTQLMM FFRHSNLGQG TNPLVFLSQF SLEKYLSQEE QSTAALTLYT KKQFFQGIHE VVESSNEDNF QL LDIQTPS ICDNQEILEE RRLEMARLQL AYICAQHQLI HLKASNSSMK SSIKWAEESL HSLTSKAVDK ENLDAKISSL TSE IMKLEK EVTQIKDRSL PAVVRENAQL LNMPVVKGDF DLQIAKQDYY TARQELVLNQ LIKQKASFEL LQLSYEIELR KHRD IYRQL ENLVQELSQS NMMLYKQLEM LTDPSVSQQI NPRNTIDTKD YSTHRLYQVL EGENKKKELF LTHGNLEEVA EKLKQ NISL VQDQLAVSAQ EHSFFLSKRN KDVDMLCDTL YQGGNQLLLS DQELTEQFHK VESQLNKLNH LLTDILADVK TKRKTL ANN KLHQMEREFY VYFLKDEDYL KDIVENLETQ SKIKAVSLED

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Macromolecule #4: Isoform 4 of HAUS augmin-like complex subunit 4

MacromoleculeName: Isoform 4 of HAUS augmin-like complex subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.269805 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASGDFCSPG EGMEILQQVC SKQLPPCNLS KEDLLQNPYF SKLLLNLSQH VDESGLSLTL AKEQAQAWKE VRLHKTTWLR SEILHRVIQ ELLVDYYVKI QDTNVTSEDK KDFVWMRARL QQEVEEQLKK KCFTLLCYYD PNSDADSETV KAAKVWKLAE V LVGEQQQC ...String:
MASGDFCSPG EGMEILQQVC SKQLPPCNLS KEDLLQNPYF SKLLLNLSQH VDESGLSLTL AKEQAQAWKE VRLHKTTWLR SEILHRVIQ ELLVDYYVKI QDTNVTSEDK KDFVWMRARL QQEVEEQLKK KCFTLLCYYD PNSDADSETV KAAKVWKLAE V LVGEQQQC QDAKSQQKEQ MLLLEKKSAA YSQVLLRCLT LLQRLLQEHR LKTQSELDRI NAQYLEVKCG AMILKLRMEE LK ILSDTYT VEKVEVHRLI RDRLEGAIHL QEQDMENSRQ VLNSYEVLGE EFDRLVKEYT VLKQATENKR WALQEFSKVY R

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Macromolecule #5: HAUS augmin-like complex subunit 5

MacromoleculeName: HAUS augmin-like complex subunit 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.783406 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MELAQEAREL GCWAVEEMGV PVAARAPEST LRRLCLGQGA DIWAYILQHV HSQRTVKKIR GNLLWYGHQD SPQVRRKLEL EAAVTRLRA EIQELDQSLE LMERDTEAQD TAMEQARQHT QDTQRRALLL RAQAGAMRRQ QHTLRDPMQR LQNQLRRLQD M ERKAKVDV ...String:
MELAQEAREL GCWAVEEMGV PVAARAPEST LRRLCLGQGA DIWAYILQHV HSQRTVKKIR GNLLWYGHQD SPQVRRKLEL EAAVTRLRA EIQELDQSLE LMERDTEAQD TAMEQARQHT QDTQRRALLL RAQAGAMRRQ QHTLRDPMQR LQNQLRRLQD M ERKAKVDV TFGSLTSAAL GLEPVVLRDV RTACTLRAQF LQNLLLPQAK RGSLPTPHDD HFGTSYQQWL SSVETLLTNH PP GHVLAAL EHLAAEREAE IRSLCSGDGL GDTEISRPQA PDQSDSSQTL PSMVHLIQEG WRTVGVLVSQ RSTLLKERQV LTQ RLQGLV EEVERRVLGS SERQVLILGL RRCCLWTELK ALHDQSQELQ DAAGHRQLLL RELQAKQQRI LHWRQLVEET QEQV RLLIK GNSASKTRLC RSPGEVLALV QRKVVPTFEA VAPQSRELLR CLEEEVRHLP HILLGTLLRH RPGELKPLPT VLPSI HQLH PASPRGSSFI ALSHKLGLPP GKASELLLPA AASLRQDLLL LQDQRSLWCW DLLHMKTSLP PGLPTQELLQ IQASQE KQQ KENLGQALKR LEKLLKQALE RIPELQGIVG DWWEQPGQAA LSEELCQGLS LPQWRLRWVQ AQGALQKLCS

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Macromolecule #6: HAUS augmin-like complex subunit 6

MacromoleculeName: HAUS augmin-like complex subunit 6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.250039 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSSASVTAFE KEHLWMYLQA LGFEPGPATI ACGKIVSHTH LGVNMFDKLN RDAFHIISYF LFQVLDQSLT KEVFKFCWPP FDQKSDTEF RKHCCEWIKR ISGECGSSFP QVVGSLFLSP GGPKFIHLMY HFARFVAMKY IKSNSKNSSH HFVETFNIKP Q DLHKCIAR ...String:
MSSASVTAFE KEHLWMYLQA LGFEPGPATI ACGKIVSHTH LGVNMFDKLN RDAFHIISYF LFQVLDQSLT KEVFKFCWPP FDQKSDTEF RKHCCEWIKR ISGECGSSFP QVVGSLFLSP GGPKFIHLMY HFARFVAMKY IKSNSKNSSH HFVETFNIKP Q DLHKCIAR CHFARSRFLQ ILQRQDCVTQ KYQENAQLSV KQVRNLRSEC IGLENQIKKM EPYDDHSNME EKIQKVRSLW AS VNETLMF LEKEREVVSS VLSLVNQYAL DGTNVAINIP RLLLDKIEKQ MFQLHIGNVY EAGKLNLLTV IQLLNEVLKV MKY ERCQAD QARLTVDLHY LEKETKFQKE RLSDLKHMRY RIKDDLTTIR HSVVEKQGEW HKKWKEFLGL SPFSLIKGWT PSVD LLPPM SPLSFDPASE EVYAKSILCQ YPASLPD

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Macromolecule #7: HAUS augmin-like complex subunit 7

MacromoleculeName: HAUS augmin-like complex subunit 7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.819152 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGGARLGARN MAGQDAGCGR GGDDYSEDEG DSSVSRAAVE VFGKLKDLNC PFLEGLYITE PKTIQELLCS PSEYRLEILE WMCTRVWPS LQDRFSSLKG VPTEVKIQEM TKLGHELMLC APDDQELLKG CACAQKQLHF MDQLLDTIRS LTIGCSSCSS L MEHFEDTR ...String:
MGGARLGARN MAGQDAGCGR GGDDYSEDEG DSSVSRAAVE VFGKLKDLNC PFLEGLYITE PKTIQELLCS PSEYRLEILE WMCTRVWPS LQDRFSSLKG VPTEVKIQEM TKLGHELMLC APDDQELLKG CACAQKQLHF MDQLLDTIRS LTIGCSSCSS L MEHFEDTR EKNEALLGEL FSSPHLQMLL NPECDPWPLD MQPLLNKQSD DWQWASASAK SEEEEKLAEL ARQLQESAAK LH ALRTEYF AQHEQGAAAG AADISTLDQK LRLVTSDFHQ LILAFLQVYD DELGECCQRP GPDLHPCGPI IQATHQNLTS YSQ LLQVVM AVADTSAKAV ETVKKQQGEQ ICWGGSSSVM SLATKMNELM EK

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Macromolecule #8: HAUS augmin-like complex subunit 8

MacromoleculeName: HAUS augmin-like complex subunit 8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.92243 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MADSSGRGAG KPATGPTNSS SAKKKDKRVQ GGRVIESRYL QYEKKTTQKA PAGDGSQTRG KMSEGGRKSS LLQKSKADSS GVGKGDLQS TLLEGHGTAP PDLDLSAIND KSIVKKTPQL AKTISKKPES TSFSAPRKKS PDLSEAMEMM ESQTLLLTLL S VKMENNLA ...String:
MADSSGRGAG KPATGPTNSS SAKKKDKRVQ GGRVIESRYL QYEKKTTQKA PAGDGSQTRG KMSEGGRKSS LLQKSKADSS GVGKGDLQS TLLEGHGTAP PDLDLSAIND KSIVKKTPQL AKTISKKPES TSFSAPRKKS PDLSEAMEMM ESQTLLLTLL S VKMENNLA EFERRAEKNL LIMCKEKEKL QKKAHELKRR LLLSQRKREL ADVLDAQIEM LSPFEAVATR FKEQYRTFAT AL DTTRHEL PVRSIHLEGD GQQLLDALQH ELVTTQRLLG ELDVGDSEEN VQVLDLLSEL KDVTAKKDLE LRRSFAQVLE LSA EASKEA ALANQEVWEE TQGMAPPSRW YFNQDSACRE SGGAPKNTPL SEDDNPGASS APAQATFISP SEDFSSSSQA EVPP SLSRS GRDLS

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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

Concentration0.05 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
200.0 mMNaClSodium chloridesodium chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine
1.0 % (v/v)GlycerolGlycerol
GridModel: Quantifoil R2/2 / Material: GOLD / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2000000
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER
Details: Generated by ab initial reconstruction in cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 447000

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