+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4104 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Negative stain reconstruction of the ROD(1-1250):Zwilch:ZW10 | |||||||||
Map data | Negative stain 3D reconstruction of ROD1-1250:Zwilch:ZW10 complex | |||||||||
Sample |
| |||||||||
Method | single particle reconstruction / negative staining / Resolution: 26.0 Å | |||||||||
Authors | Mosalaganti S | |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4104.map.gz | 7.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4104-v30.xml emd-4104.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_4104.png | 8.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4104 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4104 | HTTPS FTP |
-Validation report
Summary document | emd_4104_validation.pdf.gz | 179.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4104_full_validation.pdf.gz | 178.8 KB | Display | |
Data in XML | emd_4104_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4104 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4104 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_4104.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Negative stain 3D reconstruction of ROD1-1250:Zwilch:ZW10 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Heterotrimeric complex of Zw10, Zwilch and ROD with a C-terminal ...
Entire | Name: Heterotrimeric complex of Zw10, Zwilch and ROD with a C-terminal truncation of 759 amino acids |
---|---|
Components |
|
-Supramolecule #1: Heterotrimeric complex of Zw10, Zwilch and ROD with a C-terminal ...
Supramolecule | Name: Heterotrimeric complex of Zw10, Zwilch and ROD with a C-terminal truncation of 759 amino acids type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Molecular weight | Experimental: 710 KDa |
-Macromolecule #1: ROD(1-1250)
Macromolecule | Name: ROD(1-1250) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Sequence | String: 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 |
-Macromolecule #2: Zw10
Macromolecule | Name: Zw10 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
---|---|
Sequence | String: 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 |
-Macromolecule #3: Zwilch
Macromolecule | Name: Zwilch / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
---|---|
Sequence | String: MWERLNCAAE DFYSRLLQKF NEEKKGIRKD PFLYEADVQV QLISKGQPNP LKNILNENDI VFIVEKVPL EKEETSHIEE LQSEETAISD FSTGENVGPL ALPVGKARQL IGLYTMAHNP N MTHLKINL PVTALPPLWV RCDSSDPEGT CWLGAELITT NNSITGIVLY ...String: MWERLNCAAE DFYSRLLQKF NEEKKGIRKD PFLYEADVQV QLISKGQPNP LKNILNENDI VFIVEKVPL EKEETSHIEE LQSEETAISD FSTGENVGPL ALPVGKARQL IGLYTMAHNP N MTHLKINL PVTALPPLWV RCDSSDPEGT CWLGAELITT NNSITGIVLY VVSCKADKNY SV NLENLKN LHKKRHHLST VTSKGFAQYE LFKSSALDDT ITASQTAIAL DISWSPVDEI LQI PPLSST ATLNIKVESG EPRGPLNHLY RELKFLLVLA DGLRTGVTEW LEPLEAKSAV ELVQ EFLND LNKLDGFGDS TKKDTEVETL KHDTAAVDRS VKRLFKVRSD LDFAEQLWCK MSSSV ISYQ DLVKCFTLII QSLQRGDIQP WLHSGSNSLL SKLIHQSYHG TMDTVSLSGT IPVQML LEI GLDKLKKDYI SFFIGQELAS LNHLEYFIAP SVDIQEQVYR VQKLHHILEI LVSCMPF IK SQHELLFSLT QICIKYYKQN PLDEQHIFQL PVRPTAVKNL YQSEKPQKWR VEIYSGQK K IKTVWQLSDS SPIDHLNFHK PDFSELTLNG SLEERIFFTN MVTCSQVHFK |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8.5 |
---|---|
Staining | Type: NEGATIVE / Material: Uranyl Formate |
-Electron microscopy
Microscope | JEOL 1200 |
---|---|
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 19.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 3424 |
---|---|
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |