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- EMDB-4103: Structure of the human Rod-Zw10-Zwilch (RZZ) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4103
TitleStructure of the human Rod-Zw10-Zwilch (RZZ) complex
Map dataCryo-EM structure of RZZ complex
Sample
  • Complex: Dimer of heterotrimer of ROD, Zw10 and Zwilch
    • Protein or peptide: Rough Deal (ROD)
    • Protein or peptide: Zw10
    • Protein or peptide: Zwilch
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.4 Å
AuthorsMosalaganti S / Keller J
CitationJournal: J Cell Biol / Year: 2017
Title: Structure of the RZZ complex and molecular basis of its interaction with Spindly.
Authors: Shyamal Mosalaganti / Jenny Keller / Anika Altenfeld / Michael Winzker / Pascaline Rombaut / Michael Saur / Arsen Petrovic / Annemarie Wehenkel / Sabine Wohlgemuth / Franziska Müller / ...Authors: Shyamal Mosalaganti / Jenny Keller / Anika Altenfeld / Michael Winzker / Pascaline Rombaut / Michael Saur / Arsen Petrovic / Annemarie Wehenkel / Sabine Wohlgemuth / Franziska Müller / Stefano Maffini / Tanja Bange / Franz Herzog / Herbert Waldmann / Stefan Raunser / Andrea Musacchio /
Abstract: Kinetochores are macromolecular assemblies that connect chromosomes to spindle microtubules (MTs) during mitosis. The metazoan-specific ≈800-kD ROD-Zwilch-ZW10 (RZZ) complex builds a fibrous corona ...Kinetochores are macromolecular assemblies that connect chromosomes to spindle microtubules (MTs) during mitosis. The metazoan-specific ≈800-kD ROD-Zwilch-ZW10 (RZZ) complex builds a fibrous corona that assembles on mitotic kinetochores before MT attachment to promote chromosome alignment and robust spindle assembly checkpoint signaling. In this study, we combine biochemical reconstitutions, single-particle electron cryomicroscopy, cross-linking mass spectrometry, and structural modeling to build a complete model of human RZZ. We find that RZZ is structurally related to self-assembling cytosolic coat scaffolds that mediate membrane cargo trafficking, including Clathrin, Sec13-Sec31, and αβ'ε-COP. We show that Spindly, a dynein adaptor, is related to BicD2 and binds RZZ directly in a farnesylation-dependent but membrane-independent manner. Through a targeted chemical biology approach, we identify ROD as the Spindly farnesyl receptor. Our results suggest that RZZ is dynein's cargo at human kinetochores.
History
DepositionAug 22, 2016-
Header (metadata) releaseOct 12, 2016-
Map releaseMar 22, 2017-
UpdateJun 7, 2017-
Current statusJun 7, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4103.png

Downloads & links

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Map

FileDownload / File: emd_4103.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of RZZ complex
Voxel sizeX=Y=Z: 2.28 Å
Density
Contour LevelBy AUTHOR: 2.12 / Movie #1: 2.12
Minimum - Maximum-2.0304322 - 8.658478000000001
Average (Standard dev.)0.012069275 (±0.22623411)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 684.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.282.282.28
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z684.000684.000684.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-2.0308.6580.012

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Supplemental data

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Sample components

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Entire : Dimer of heterotrimer of ROD, Zw10 and Zwilch

EntireName: Dimer of heterotrimer of ROD, Zw10 and Zwilch
Components
  • Complex: Dimer of heterotrimer of ROD, Zw10 and Zwilch
    • Protein or peptide: Rough Deal (ROD)
    • Protein or peptide: Zw10
    • Protein or peptide: Zwilch

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Supramolecule #1: Dimer of heterotrimer of ROD, Zw10 and Zwilch

SupramoleculeName: Dimer of heterotrimer of ROD, Zw10 and Zwilch / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Ascalapha odorata (black witch) / Recombinant cell: TnaO38 / Recombinant plasmid: pACEbac1 and pFL
Molecular weightExperimental: 810 KDa

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Macromolecule #1: Rough Deal (ROD)

MacromoleculeName: Rough Deal (ROD) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MWNDIELLTN DDTGSGYLSV GSRKEHGTAL YQVDLLVKIS SEKASLNPKI QACSLSDGFI IVADQSVIL LDSICRSLQL HLVFDTEVDV VGLCQEGKFL LVGERSGNLH LIHVTSKQTL L TNAFVQKA NDENRRTYQN LVIEKDGSNE GTYYMLLLTY SGFFCITNLQ ...String:
MWNDIELLTN DDTGSGYLSV GSRKEHGTAL YQVDLLVKIS SEKASLNPKI QACSLSDGFI IVADQSVIL LDSICRSLQL HLVFDTEVDV VGLCQEGKFL LVGERSGNLH LIHVTSKQTL L TNAFVQKA NDENRRTYQN LVIEKDGSNE GTYYMLLLTY SGFFCITNLQ LLKIQQAIEN VD FSTAKKL QGQIKSSFIS TENYHTLGCL SLVAGDLASE VPVIIGGTGN CAFSKWEPDS SKK GMTVKN LIDAEIIKGA KKFQLIDNLL FVLDTDNVLS LWDIYTLTPV WNWPSLHVEE FLLT TEADS PSSVTWQGIT NLKLIALTAS ANKKMKNLMV YSLPTMEILY SLEVSSVSSL VQTGI STDT IYLLEGVCKN DPKLSEDSVS VLVLRCLTEA LPENRLSRLL HKHRFAEAES FAIQFG LDV ELVYKVKSNH ILEKLALSSV DASEQTEWQQ LVDDAKENLH KIQDDEFVVN YCLKAQW IT YETTQEMLNY AKTRLLKKED KTALIYSDGL KEVLRAHAKL TTFYGAFGPE KFSGSSWI E FLNNEDDLKD IFLQLKEGNL VCAQYLWLRH RANFESRFDV KMLESLLNSM SASVSLQKL CPWFKNDVIP FVRRTVPEGQ IILAKWLEQA ARNLELTDKA NWPENGLQLA EIFFTAEKTD ELGLASSWH WISLKDYQNT EEVCQLRTLV NNLRELITLH RKYNCKLALS DFEKENTTTI V FRMFDKVL APELIPSILE KFIRVYMREH DLQEEELLLL YIEDLLNRCS SKSTSLFETA WE AKAMAVI ACLSDTDLIF DAVLKIMYAA VVPWSAAVEQ LVKQHLEMDH PKVKLLQESY KLM EMKKLL RGYGIREVNL LNKEIMRVVR YILKQDVPSS LEDALKVAQA FMLSDDEIYS LRII DLIDR EQGEDCLLLL KSLPPAEAEK TAERVIIWAR LALQEEPDHS KEGKAWRMSV AKTSV DILK ILCDIQKDNL QKKDECEEML KLFKEVASLQ ENFEVFLSFE DYSNSSLVAD LREQHI KAH EVAQAKHKPG STPEPIAAEV RSPSMESKLH RQALALQMSK QELEAELTLR ALKDGNI KT ALKKCSDLFK YHCNADTGKL LFLTCQKLCQ MLADNVPVTV PVGLNLPSMI HDLASQAA T ICSPDFLLDA LELCKHTLMA VELSRQCQMD DCGILMKASF GTHKDPYEEW SYSDFFSED GIVLESQMVL PVIYELISSL VPLAESKRYP LESTSLPYCS LNEGDGLVLP VINSISALLQ NLQESSQWE LALRFVVGSF GTCLQHSVSN FMNATLSEKL FGETTLVKSR HVVMELKEKA V IFIRENAT TLLHKVFNCR LVDLDLALGY CTLLPQKDVF ENLWKLIDKA WQNYDKILAI SL VGSELAS LYQEIEMGLK FRELSTDAQW GIRLGKLGIS FQPVFRQHFL TKKDLIKALV ENI DMDTSL ILEYCSTFQL DCDAVLQLFI ETLLHNTNAG QGQGDASMDS AKRRHPKLLA KALE MVPLL TSTKDLVISL SGILHKLDPY DYEMIEVVLK VIERADEKIT NININQALSI LKHLK SYRR ISPPVDLEYQ YMLEHVITLP SAAQTRLPFH LIFFGTAQNF WKILSTELSE ESFPTL LLI SKLMKFSLDT LYVSTAKHVF EKKLKPKLLK LTQAKSSTLI NKEITKITQT IESCLLS IV NPEWAVAIAI SLAQDIPEGS FKISALKFCL YLAERWLQNI PSQDEKREKA EALLKKLH I QYRRSGTEAV LIAHKLNTEE YLRVIGKPAH LIVSLYEHPS INQRIQNSSG TDYPDIHAA AKEIAEVNEI NLEKVWDMLL EKWLCPSTKP GEKPSELFEL QEDEALRRVQ YLLLSRPIDY SSRMLFVFA TSTTTTLGMH QLTFAHRTRA LQCLFYLADK ETIESLFKKP IEEVKSYLRC I TFLASFET LNIPITYELF CSSPKEGMIK GLWKNHSHES MAVRLVTELC LEYKIYDLQL WN GLLQKLL GFNMIPYLRK VLKAISSIHS LWQVPYFSKA WQRVIQIPLL SASCPLSPDQ LSD CSESLI AVLECPVSGD LDLIGVARQY IQLELPAFAL ACLMLMPHSE KRHQQIKNFL GSCD PQVIL KQLEEHMNTG QLAGFSHQIR SLILNNIINK KEFGILAKTK YFQMLKMHAM NTNNI TELV NYLANDLSLD EASVLITEYS KHCGKPVPPD TAPCEILKMF LSGLS

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Macromolecule #2: Zw10

MacromoleculeName: Zw10 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: MASFVTEVLA HSGRLEKEDL GTRISRLTRR VEEIKGEVCN MISKKYSEFL PSMQSAQGLI TQVDKLSED IDLLKSRIES EVRRDLHVST GEFTDLKQQL ERDSVVLSLL KQLQEFSTAI E EYNCALTE KKYVTGAQRL EEAQKCLKLL KSRKCFDLKI LKSLSMELTI ...String:
MASFVTEVLA HSGRLEKEDL GTRISRLTRR VEEIKGEVCN MISKKYSEFL PSMQSAQGLI TQVDKLSED IDLLKSRIES EVRRDLHVST GEFTDLKQQL ERDSVVLSLL KQLQEFSTAI E EYNCALTE KKYVTGAQRL EEAQKCLKLL KSRKCFDLKI LKSLSMELTI QKQNILYHLG EE WQKLIVW KFPPSKDTSS LESYLQTELH LYTEQSHKEE KTPMPPISSV LLAFSVLGEL HSK LKSFGQ MLLKYILRPL ASCPSLHAVI ESQPNIVIIR FESIMTNLEY PSPSEVFTKI RLVL EVLQK QLLDLPLDTD LENEKTSTVP LAEMLGDMIW EDLSECLIKN CLVYSIPTNS SKLQQ YEEI IQSTEEFENA LKEMRFLKGD TTDLLKYARN INSHFANKKC QDVIVAARNL MTSEIH NTV KIIPDSKINV PELPTPDEDN KLEVQKVSNT QYHEVMNLEP ENTLDQHSFS LPTCRIS ES VKKLMELAYQ TLLEATTSSD QCAVQLFYSV RNIFHLFHDV VPTYHKENLQ KLPQLAAI H HNNCMYIAHH LLTLGHQFRL RLAPILCDGT ATFVDLVPGF RRLGTECFLA QMRAQKGEL LERLSSARNF SNMDDEENYS AASKAVRQVL HQLKRLGIVW QDVLPVNIYC KAMGTLLNTA ISEVIGKIT ALEDISTEDG DRLYSLCKTV MDEGPQVFAP LSEESKNKKY QEEVPVYVPK W MPFKELMM MLQASLQEIG DRWADGKGPL AAAFSSSEVK ALIRALFQNT ERRAAALAKI K

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Macromolecule #3: Zwilch

MacromoleculeName: Zwilch / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
SequenceString: MAHNPNMTHL KINLPVTALP PLWVRCDSSD PEGTCWLGAE LITTNNSITG IVLYVVSCKA DKNYSVNLE NLKNLHKKRH HLSTVTSKGF AQYELFKSSA LDDTITASQT AIALDISWSP V DEILQIPP LSSTATLNIK VESGEPRGPL NHLYRELKFL LVLADGLRTG ...String:
MAHNPNMTHL KINLPVTALP PLWVRCDSSD PEGTCWLGAE LITTNNSITG IVLYVVSCKA DKNYSVNLE NLKNLHKKRH HLSTVTSKGF AQYELFKSSA LDDTITASQT AIALDISWSP V DEILQIPP LSSTATLNIK VESGEPRGPL NHLYRELKFL LVLADGLRTG VTEWLEPLEA KS AVELVQE FLNDLNKLDG FGDSTKKDTE VETLKHDTAA VDRSVKRLFK VRSDLDFAEQ LWC KMSSSV ISYQDLVKCF TLIIQSLQRG DIQPWLHSGS NSLLSKLIHQ SYHGTMDTVS LSGT IPVQM LLEIGLDKLK KDYISFFIGQ ELASLNHLEY FIAPSVDIQE QVYRVQKLHH ILEIL VSCM PFIKSQHELL FSLTQICIKY YKQNPLDEQH IFQLPVRPTA VKNLYQSEKP QKWRVE IYS GQKKIKTVWQ LSDSSPIDHL NFHKPDFSEL TLNGSLEERI FFTNMVTCSQ VHFK

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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: 8.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 39.0 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

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX / Number images used: 11666
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: NOT APPLICABLE

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