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- EMDB-51017: Structure of the Partially-assembled gamma-Tubulin Ring Complex f... -

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Basic information

Entry
Database: EMDB / ID: EMD-51017
TitleStructure of the Partially-assembled gamma-Tubulin Ring Complex from Pig Brain
Map data
Sample
  • Complex: Gamma-Tubulin Ring Complex in native pig brain
    • Protein or peptide: Mitotic spindle organizing protein 1
    • Protein or peptide: Gamma-tubulin complex component
    • Protein or peptide: Gamma-tubulin complex component 3
    • Protein or peptide: Gamma-tubulin complex component
    • Protein or peptide: Gamma-tubulin complex component
    • Protein or peptide: Tubulin gamma chain
KeywordsTubulin Complex / STRUCTURAL PROTEIN
Function / homology
Function and homology information


microtubule minus-end binding / microtubule nucleation by interphase microtubule organizing center / Recruitment of mitotic centrosome proteins and complexes / gamma-tubulin complex localization / equatorial microtubule organizing center / gamma-tubulin ring complex / interphase microtubule organizing center / polar microtubule / gamma-tubulin complex / microtubule nucleation ...microtubule minus-end binding / microtubule nucleation by interphase microtubule organizing center / Recruitment of mitotic centrosome proteins and complexes / gamma-tubulin complex localization / equatorial microtubule organizing center / gamma-tubulin ring complex / interphase microtubule organizing center / polar microtubule / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / Recruitment of NuMA to mitotic centrosomes / pericentriolar material / cytoplasmic microtubule / mitotic spindle assembly / spindle assembly / cytoplasmic microtubule organization / centriole / meiotic cell cycle / spindle microtubule / neuron migration / brain development / spindle / spindle pole / mitotic cell cycle / microtubule binding / microtubule / centrosome / GTP binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / 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 ...Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / 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 chain / Mitotic spindle organizing protein 1 / Gamma-tubulin complex component / Gamma-tubulin complex component / Gamma-tubulin complex component 3 / Gamma-tubulin complex component
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsMunoz-Hernandez H / Wieczorek M
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science FoundationTMSGI3_211309 Switzerland
Swiss National Science Foundation310030_208120 Switzerland
CitationJournal: Dev Cell / Year: 2024
Title: Partial closure of the γ-tubulin ring complex by CDK5RAP2 activates microtubule nucleation.
Authors: Yixin Xu / Hugo Muñoz-Hernández / Rościsław Krutyhołowa / Florina Marxer / Ferdane Cetin / Michal Wieczorek /
Abstract: Microtubule nucleation is templated by the γ-tubulin ring complex (γ-TuRC), but its structure deviates from the geometry of α-/β-tubulin in the microtubule, explaining the complex's poor ...Microtubule nucleation is templated by the γ-tubulin ring complex (γ-TuRC), but its structure deviates from the geometry of α-/β-tubulin in the microtubule, explaining the complex's poor nucleating activity. Several proteins may activate the γ-TuRC, but the mechanisms underlying activation are not known. Here, we determined the structure of the porcine γ-TuRC purified using CDK5RAP2's centrosomin motif 1 (CM1). We identified an unexpected conformation of the γ-TuRC bound to multiple protein modules containing MZT2, GCP2, and CDK5RAP2, resulting in a long-range constriction of the γ-tubulin ring that brings it in closer agreement with the 13-protofilament microtubule. Additional CDK5RAP2 promoted γ-TuRC decoration and stimulated the microtubule-nucleating activities of the porcine γ-TuRC and a reconstituted, CM1-free human complex in single-molecule assays. Our results provide a structural mechanism for the control of microtubule nucleation by CM1 proteins and identify conformational transitions in the γ-TuRC that prime it for microtubule nucleation.
History
DepositionJul 12, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51017.png

Downloads & links

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Map

FileDownload / File: emd_51017.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 384 pix.
= 542.707 Å		1.41 Å/pix.
x 384 pix.
= 542.707 Å		1.41 Å/pix.
x 384 pix.
= 542.707 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4133 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.27518514 - 0.8954884
Average (Standard dev.)0.0027232966 (±0.032947302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 542.7072 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51017_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51017_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Gamma-Tubulin Ring Complex in native pig brain

EntireName: Gamma-Tubulin Ring Complex in native pig brain
Components
  • Complex: Gamma-Tubulin Ring Complex in native pig brain
    • Protein or peptide: Mitotic spindle organizing protein 1
    • Protein or peptide: Gamma-tubulin complex component
    • Protein or peptide: Gamma-tubulin complex component 3
    • Protein or peptide: Gamma-tubulin complex component
    • Protein or peptide: Gamma-tubulin complex component
    • Protein or peptide: Tubulin gamma chain

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Supramolecule #1: Gamma-Tubulin Ring Complex in native pig brain

SupramoleculeName: Gamma-Tubulin Ring Complex in native pig brain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Mitotic spindle organizing protein 1

MacromoleculeName: Mitotic spindle organizing protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 8.285489 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString:
MAGNSGSGAA AAANLNAVRE TMDVLLEISR ILNTGLDMET LSICVRLCEQ GINPEALSSV IKELRKATEA LKAAENMTS

UniProtKB: Mitotic spindle organizing protein 1

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Macromolecule #2: Gamma-tubulin complex component

MacromoleculeName: Gamma-tubulin complex component / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 102.609703 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString: MSEFRIHHDV NELLSLLRVH GGDGAEVYID LLQKNRTPYV TTTVSAHSAK VKIAEFSRTP EDFLKKYDEL KSKNTRNLDP LVYLLSKLM EDRETLQYLQ QNAKERAELA ASAAASSTAS FGASATASKI SMQELEELRK QLGSVATGPT WQQSLELTRK M LRDKQSKK ...String:
MSEFRIHHDV NELLSLLRVH GGDGAEVYID LLQKNRTPYV TTTVSAHSAK VKIAEFSRTP EDFLKKYDEL KSKNTRNLDP LVYLLSKLM EDRETLQYLQ QNAKERAELA ASAAASSTAS FGASATASKI SMQELEELRK QLGSVATGPT WQQSLELTRK M LRDKQSKK NSGQRLPVLP AWVYERPALL GDFLPGTGGS ADTAVPIGSL PLASQEAAVV EDLLYVLVGV DGRYISAQPL TG RQGRTFL VDPNLDLSIR ELVSRILPVA ASYSTVTRFI EEKSSFEYGQ VNHALAAAMR TLVKEYLVLV TQLEQLQRQG LLS LQKLWF YIQPAMRSLD ILASLATSVD KGECIGGATL SLLHDRSFSY TGDSQAQELC LHLTKAASTP YFEILEKWIY RGII DDPYS EFMVEEHELR KEKIQEDYND KYWDQRYTVV QRQIPSFLQK MAGKVLSTGK YLNVVRECGH DVTCPVAKEV VYTLK ERAY VEQIEKAFSY ASKVLLDFLM GEKELLAHLR SIKRYFLMDQ GDFFVHFMDL TEEELKKPVD DITPTRLEAL LELALR MST ANTDPFKDDL KIDLMPHDLI TQLLRVLAIE TQQEKAMVHA DPTELTLSGL EAFSFDYVVT WPLSLIINRK ALTRYQM LF RHMFYCKHVE RQLCSVWISN KAAKRFSLHS AKWFAGAFTL RQRMLNFVQN IQSYMMFEVM EPTWHVLEQN LRSASNID D VLGHHASFLD NCLKDCMLTN PELLRVFSKL MSVCVMFTNC LQRFTQSMKL DSELGHPALE PGAMLGPPTE AERAEERAR KELARKCLAE HVDAPQLASS FEATITKFDK NFSAHLLDLL ARLSIYSTSD CEHGMASVIS RLDFNGFYTE RLERLSAERS QKAAPPVPG PRGPPALVPR VAVTAQ

UniProtKB: Gamma-tubulin complex component

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Macromolecule #3: Gamma-tubulin complex component 3

MacromoleculeName: Gamma-tubulin complex component 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 103.172477 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString: MATPDQKSPN VLLQNLCCRI LGKSEADVAQ QFQYAVRVIG SNFAPTVERD EFLVAEKIKK ELTRQRREAD AALFSELHRK LHSQGVLKN KWSILYLLLS LSEDPRKQPS KVSGYAALFA QALPRDAHST PYYYARPQSL PLNYQERGAP SAQSAGSAGS S GVSSLGTY ...String:
MATPDQKSPN VLLQNLCCRI LGKSEADVAQ QFQYAVRVIG SNFAPTVERD EFLVAEKIKK ELTRQRREAD AALFSELHRK LHSQGVLKN KWSILYLLLS LSEDPRKQPS KVSGYAALFA QALPRDAHST PYYYARPQSL PLNYQERGAP SAQSAGSAGS S GVSSLGTY ALNGPTPPPP PPALLPGQPL PAPGVGDGLR QQLGSRLAWT LTASQPSLPS TTSKAVPSSG SRGAARPRRE GD AAAGAVE VTEAALVRDI LYVFQGIDGK HVKMSNADNC YTVEGKANLS KSLRDTAVRL AELGWLHNKI RKYTDQRSLD RSF GLVGQS FCAALHQELR EYYRLLSVLH SQLQLEDDQG VNLGLESSLT LRRLLVWTYD PKMRLKTLAA LVDHCQGRKG GELA SAVHA YTKTGDPYAR SLVQHILSLV SHPVLSFLYR WIYDGELEDT YHEFFVASDP AVKADRLWHD KYALRKPMIP SFMTM DQCR KVLLIGKSIN FLHQVCHDQT PTTKMIAVTK SAESPQDAAD LFTDLENAFQ GKIDAAYFET SKYLLDVLNK KYSLLD HMQ AMRRYLLLGQ GDFIRHLMDL LKPELVRPAT TLYQHNLTGI LETAVRATNA QFDSPEILKR LDVRLLEVSP GDTGWDV FS LDYHVDGPIA TVFTRECMSH YLRAFNFLWR AKRVEYILTD IRKGHMCNAR LLRSMPEFSG VLHHCHILAS EMVHFIHQ M QYYVTFEVLE CSWDELWNRV QRAQDLDHII AAHEAFLGTV ISRCLLDSDS RALLNQLRAV FDQIIELQNT QDAIYRAAL EELQRRLQFE EKKKQREAEG QWGVSAAEEE QEKRRVQEFQ ESIPKMCSQL RILTHFYQGV VQQFLVSLTT SSDESLRFLS FRLDFNEHY RAREPRLRVS LGTRGRRSSH T

UniProtKB: Gamma-tubulin complex component 3

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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: Sus scrofa (pig)
Molecular weightTheoretical: 76.104867 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString: MIHELLLALS GYPGSIFTWN KRGGLQVSQD FPFLHPSETS VLNRLCRLGT DYIRFTEFIE QYTGHVQQQD HHPSQQGQGG LHGIYLRAF CTGLDSVLQP YRQALLDLEQ EFLADPHLSI SHINYSLDQF QLLFPSVMVV VEQIKSQKIH GCQILETVYK H SCGGLPPV ...String:
MIHELLLALS GYPGSIFTWN KRGGLQVSQD FPFLHPSETS VLNRLCRLGT DYIRFTEFIE QYTGHVQQQD HHPSQQGQGG LHGIYLRAF CTGLDSVLQP YRQALLDLEQ EFLADPHLSI SHINYSLDQF QLLFPSVMVV VEQIKSQKIH GCQILETVYK H SCGGLPPV RSALEKILAV CHGVMYKQLS AWMLHGLLLD QHEEFFIKQG PSSGNVSAQP EEDEEDLGIG GLTGKQLREL QD LRLIEEE NMLAPSLKQF SLRVEILPSY IPVRVAEKIL FVGESVQMFE NQNVNLTRKG SILKDQEDTF AAELHRLKQQ PLF SLVDFE QVVDRIRSTV AEHLWKLMVE ESDLLGQLKI IKDFYLLGRG ELFQAFIDTA QHMLKTPPTA VTEHDVNVAF QQSA HKVLL DDDNLLPLLH LTIEYHGKEH KADATQAREG PSRETSPREA PASGWAALGL SYKVQWPLHI LFTPAVLEKY NVVFK YLLS VRRVQAELQH CWALQMQRKH LKSNQTDAVK WRLRNHMAFL VDNLQYYLQV DVLESQFSQL LHQINSTRDF ESIRLA HDH FLSNLLAQSF ILLKPVFHCL NEILDLCHSF CSLVSQNLGP LDERGAAQLS ILVKGFSRQS SLLFKILSSV RNHQINS DL AQLLLRLDYN KYYTQAGGTL GSFGM

UniProtKB: Gamma-tubulin complex component

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Macromolecule #5: Gamma-tubulin complex component

MacromoleculeName: Gamma-tubulin complex component / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 122.040344 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString: MASPAPSWTR LDPQQERDVR ELIRLVSGVQ DEADPNFQLA LHFAWSNFRF HRFLDVNSHK VEKTIEGIYE KFIIHSDLSK AASWKRLTD EFLNASLPSI KEIKTDAHYS ILSLLLCLSD SPSNSNYVET PRNKEVEKKD DFDWGKYLME GEEIDLGPNV D TPNWSEES ...String:
MASPAPSWTR LDPQQERDVR ELIRLVSGVQ DEADPNFQLA LHFAWSNFRF HRFLDVNSHK VEKTIEGIYE KFIIHSDLSK AASWKRLTD EFLNASLPSI KEIKTDAHYS ILSLLLCLSD SPSNSNYVET PRNKEVEKKD DFDWGKYLME GEEIDLGPNV D TPNWSEES EDEDDPQPLS REDSGIQVDR TPLEEQDQSR KPASRVSWKV DEPDARSWLE QHVVRQYWTT RSSKFPHSLH LH SNLAAVW DQHLYSSDPL YVPDDRVSVT ETQVIRETLW LLSGVKKLFI FQLIDGKVAV RNNIMVTHLT HSCLRSVLEQ IAA YGQVVF RLQEFIDEVM GHSSESTLPG NGSVPKKSTD APFRTYQAFM WALYKYFISF KEELSEIEKC IINNDTTVTL AIVV DKLSP RLAQLKVLHK VFSTGVAEVP PDTRNVVRAS HLLNTLYKAI LEYDNVGEAS EQTVSLLFSL WVETVRPYLQ IVDEW IVHG HLCDGAREFI IQRNKNVPVN HRDFWYATYT LYSVSEKTEN EEKMSDNASA SSGSDQGPSS RQHTMVSFLK PVLKQI IMA GKSMQLLKNL QCAESTTCQA MARDAERKSL YTLFLESVQS RLRHGEDATA QALTEQQATR ETLIKMQSIA ERHLELD DV HDPLLAINFA RLYLEQSDFH EKFAGGDICV DRSSESVTCQ TFELTLRSCL YPHIDKQYLD CCGNLMRTLK KDYRLVEY L QAMRNFFLME GGDTMYDFYT SIFDKIREKE TWQNVSFLNV QLQEAVGQRY PEDSSRLSIS FENTDTAKKK LPVHTLDGL TLSYKVPWPV DIVISLECQK IYNQVFLLLL QIKWAKYSLD VLLFGELASS AEKPQSKEGL LSGQDTAAQF GPQKEPVRQQ IHRMFLLRV KLMHFVNSLH NYIMTRILHS TGLEFQHQVE EAKDLDQLIK IHYRYLSTIH DRCLLREKVS FVKEAIMKVL N LALMFADG WQAGLGAWQM ESIEKMESDF KNCHMFLVTI LNKAVCRGSF PHLESLALSL MAGMEQKRED DLFNHTWGQG DL PNYTCAV RLLGVRKGGG TRPK

UniProtKB: Gamma-tubulin complex component

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Macromolecule #6: Tubulin gamma chain

MacromoleculeName: Tubulin gamma chain / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 51.135562 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString: MPREIITLQL GQCGNQIGFE FWKQLCAEHG ISPEGIVEEF ATEGTDRKDV FFYQADDEHY IPRAVLLDLE PRVIHSILNS PYAKLYNPE NIYLSEHGGG AGNNWASGFS QGEKIHEDIF DIIDREADGS DSLEGFVLCH SIAGGTGSGL GSYLLERLND R YPKKLVQT ...String:
MPREIITLQL GQCGNQIGFE FWKQLCAEHG ISPEGIVEEF ATEGTDRKDV FFYQADDEHY IPRAVLLDLE PRVIHSILNS PYAKLYNPE NIYLSEHGGG AGNNWASGFS QGEKIHEDIF DIIDREADGS DSLEGFVLCH SIAGGTGSGL GSYLLERLND R YPKKLVQT YSVFPNQDEM SDVVVQPYNS LLTLKRLTQN ADCVVVLDNT ALNRIATDRL HIQNPSFSQI NQLVSTIMSA ST TTLRYPG YMNNDLIGLI ASLIPTPRLH FLMTGYTPLT TDQSVASVRK TTVLDVMRRL LQPKNVMVST GRDRQTNHCY IAI LNIIQG EVDPTQVHKS LQRIRERKLA NFIPWGPASI QVALSRKSPY LPSAHRVSGL MMANHTSISS LFESSCQQYD KLRK REAFL EQFRKEDIFK ENFDELDRSR EVVQELIDEY HAATRPDYIS WGTQEQ

UniProtKB: Tubulin gamma chain

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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
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29893
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-9g3x:
Structure of the Partially-assembled gamma-Tubulin Ring Complex from Pig Brain

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