+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10497 | ||||||||||||
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Title | CryoEM structure of the binary DOCK2-ELMO1 complex | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | guanine nucleotide exchange factor / cytoskeleton / actin / cryoEM / SIGNALING PROTEIN | ||||||||||||
Function / homology | Function and homology information membrane raft polarization / alpha-beta T cell proliferation / myeloid dendritic cell activation involved in immune response / establishment of T cell polarity / macropinocytosis / immunological synapse formation / negative thymic T cell selection / guanyl-nucleotide exchange factor complex / myoblast fusion / positive thymic T cell selection ...membrane raft polarization / alpha-beta T cell proliferation / myeloid dendritic cell activation involved in immune response / establishment of T cell polarity / macropinocytosis / immunological synapse formation / negative thymic T cell selection / guanyl-nucleotide exchange factor complex / myoblast fusion / positive thymic T cell selection / Nef and signal transduction / regulation of small GTPase mediated signal transduction / small GTPase-mediated signal transduction / phagocytosis, engulfment / Rac protein signal transduction / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / T cell receptor binding / positive regulation of phagocytosis / RAC1 GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / actin filament organization / cell motility / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / VEGFA-VEGFR2 Pathway / SH3 domain binding / specific granule lumen / chemotaxis / Factors involved in megakaryocyte development and platelet production / cell migration / actin cytoskeleton organization / cytoskeleton / Neutrophil degranulation / apoptotic process / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.5 Å | ||||||||||||
Authors | Chang L / Yang J | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structure of the DOCK2-ELMO1 complex provides insights into regulation of the auto-inhibited state. Authors: Leifu Chang / Jing Yang / Chang Hwa Jo / Andreas Boland / Ziguo Zhang / Stephen H McLaughlin / Afnan Abu-Thuraia / Ryan C Killoran / Matthew J Smith / Jean-Francois Côté / David Barford / Abstract: DOCK (dedicator of cytokinesis) proteins are multidomain guanine nucleotide exchange factors (GEFs) for RHO GTPases that regulate intracellular actin dynamics. DOCK proteins share catalytic (DOCK) ...DOCK (dedicator of cytokinesis) proteins are multidomain guanine nucleotide exchange factors (GEFs) for RHO GTPases that regulate intracellular actin dynamics. DOCK proteins share catalytic (DOCK) and membrane-associated (DOCK) domains. The structurally-related DOCK1 and DOCK2 GEFs are specific for RAC, and require ELMO (engulfment and cell motility) proteins for function. The N-terminal RAS-binding domain (RBD) of ELMO (ELMO) interacts with RHOG to modulate DOCK1/2 activity. Here, we determine the cryo-EM structures of DOCK2-ELMO1 alone, and as a ternary complex with RAC1, together with the crystal structure of a RHOG-ELMO2 complex. The binary DOCK2-ELMO1 complex adopts a closed, auto-inhibited conformation. Relief of auto-inhibition to an active, open state, due to a conformational change of the ELMO1 subunit, exposes binding sites for RAC1 on DOCK2, and RHOG and BAI GPCRs on ELMO1. Our structure explains how up-stream effectors, including DOCK2 and ELMO1 phosphorylation, destabilise the auto-inhibited state to promote an active GEF. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10497.map.gz | 2.4 MB | EMDB map data format | |
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Header (meta data) | emd-10497-v30.xml emd-10497.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
Images | emd_10497.png | 106.7 KB | ||
Filedesc metadata | emd-10497.cif.gz | 7.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10497 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10497 | HTTPS FTP |
-Validation report
Summary document | emd_10497_validation.pdf.gz | 338.3 KB | Display | EMDB validaton report |
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Full document | emd_10497_full_validation.pdf.gz | 337.9 KB | Display | |
Data in XML | emd_10497_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_10497_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10497 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10497 | HTTPS FTP |
-Related structure data
Related structure data | 6tgbMC 6tgcC 6ukaC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10497.map.gz / Format: CCP4 / Size: 85.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Binary complex of DOCK2-ELMO1
Entire | Name: Binary complex of DOCK2-ELMO1 |
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Components |
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-Supramolecule #1: Binary complex of DOCK2-ELMO1
Supramolecule | Name: Binary complex of DOCK2-ELMO1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 550 KDa |
-Macromolecule #1: Dedicator of cytokinesis protein 2
Macromolecule | Name: Dedicator of cytokinesis protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 195.902516 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MAPWRKADKE RHGVAIYNFQ GSGAPQLSLQ IGDVVRIQET CGDWYRGYLI KHKMLQGIFP KSFIHIKEVT VEKRRNTENI IPAEIPLAQ EVTTTLWEWG SIWKQLYVAS KKERFLQVQS MMYDLMEWRS QLLSGTLPKD ELKELKQKVT SKIDYGNKIL E LDLIVRDE ...String: MAPWRKADKE RHGVAIYNFQ GSGAPQLSLQ IGDVVRIQET CGDWYRGYLI KHKMLQGIFP KSFIHIKEVT VEKRRNTENI IPAEIPLAQ EVTTTLWEWG SIWKQLYVAS KKERFLQVQS MMYDLMEWRS QLLSGTLPKD ELKELKQKVT SKIDYGNKIL E LDLIVRDE DGNILDPDNT SVISLFHAHE EATDKITERI KEEMSKDQP(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)GFPE IIMPGDVRND IYITLLQGDF DKYNKTTQRN VEVIMCVCAE DGKTLP NAI CVGAGDKPMN EYRSVVYYQV KQPRWMETVK VAVPIEDMQR IHLRFMFRHR SSLESKDKGE KNFAMSYVKL MKEDGTT LH DGFHDLVVLK GDSKKMEDAS AYLTLPSYRH HVENKGATLS RSSSSVGGLS VSSRDVFSIS TLVCST(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)IM MEH SQSDEY DILVFDALIY IIGLIADRKF Q(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)S SELVDFLMET FIMFKDLIGK NVYPGDWMAM SMVQNRVFLR AINKFAETMN QKFL EHTNF EFQLWNNYFH LAVAFITQDS LQLEQFSHAK YNKILNKYGD MRRLIGFSIR DMWYKLGQNK ICFIPGMVGP ILEMT LIPE AELRKATIPI FFDMMLCEYQ RSGDFKKFEN EIILKLDHEV EGGRGDEQYM QLLESILMEC AAEHPTIAKS VENFVN LVK GLLEKLLDYR GVMTDESKDN RMSCTVNLLN FYKDNNREEM YIRYLYKLRD LHLDCDNYTE AAYTLLLHTW LLKWSDE QC ASQVMQTGQQ HPQTHRQLKE TLYETIIGYF DKGKMWEEAI SLCKELAEQY EMEIFDYELL SQNLIQQAKF YESIMKIL R PKPDYFAVGY YGQGFPSFLR NKVFIYRGKE YERREDFQMQ LMTQFPNAEK MNTTSAPGDD VKNAPGQYIQ CFTVQPVLD EHPRFKNKPV PDQIINFYKS NYVQRFHYSR PVRRGTVDPE NEFASMWIER TSFVTAYKLP GILRWFEVVH MSQTTISPLE NAIETMSTA NEKILMMINQ YQSDETLPIN PLSMLLNGIV DPAVMGGFAK YEKAFFTEEY VRDHPEDQDK LTHLKDLIAW Q IPFLGAGI KIHEKRVSDN LRPFHDRMEE CFKNLKMKVE KEYGVREMPD FDDRRVGRPR SMLRSYRQMS IISLASMNSD CS TPSKPTS ESFDLELASP KTPRVEQEEP ISPGSTLPEV KLRRSKKRTK RSSVVFADEK AAAESDLKRL SRKHEFMSDT NLS EHAAIP LKASVLSQMS FASQSMPTIP ALALSVAGIP GLDEANTSPR LSQTFLQLSD GDKKTLTRKK VNQFFKTMLA SKSA EEGKQ IPDSLSTDL UniProtKB: Dedicator of cytokinesis protein 2 |
-Macromolecule #2: Engulfment and cell motility protein 1
Macromolecule | Name: Engulfment and cell motility protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 83.891328 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MPPPADIVKV AIEWPGAYPK LMEIDQKKPL SAIIKEVCDG WSLANHEYFA LQHADSSNFY ITEKNRNEIK NGTILRLTTS PAQNAQQLH ERIQSSSMDA KLEALKDLAS LSRDVTFAQE FINLDGISLL TQMVESGTEL YQKLQKIMKP CFGDMLSFTL T AFVELMDH ...String: MPPPADIVKV AIEWPGAYPK LMEIDQKKPL SAIIKEVCDG WSLANHEYFA LQHADSSNFY ITEKNRNEIK NGTILRLTTS PAQNAQQLH ERIQSSSMDA KLEALKDLAS LSRDVTFAQE FINLDGISLL TQMVESGTEL YQKLQKIMKP CFGDMLSFTL T AFVELMDH GIVSWDTFSV AFIKKIASFV NKSAIDISIL QRSLAILESM VLNSHDLYQK VAQEITIGQL IPHLQGSDQE IQ TYTIAVI NALFLKAPDE RRQEMANILA QKQLRSIILT HVIRAQRAIN NEMAHQLYVL QVLTFNLLED RMMTKMDPQD QAQ RDIIFE LRRIAFDAES EPNNSSGSME KRKSMYTRDY KKLGFINHVN PAMDFTQTPP GMLALDNMLY FAKHHQDAYI RIVL ENSSR EDKHECPFGR SSIELTKMLC EILKVGELPS ETCNDFHPMF FTHDRSFEEF FCICIQLLNK TWKEMRATSE DFNKV MQVV KEQVMRALTT KPSSLDQFKS KLQNLSYTEI LKIRQSERMN QEDFQSRPIL ELKEKIQPEI LELIKQQRLN RLVEGT CFR KLNARRRQDK FWYCRLSPNH KVLHYGDLEE SPQGEVPHDS LQDKLPVADI KAVVTGKDCP HMKEKGALKQ NKEVLEL AF SILYDSNCQL NFIAPDKHEY CIWTDGLNAL LGKDMMSDLT RNDLDTLLSM EIKLRLLDLE NIQIPDAPPP IPKEPSNY D FVYDCN UniProtKB: Engulfment and cell motility protein 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL Details: e2initialmodel.py from the EMAN2 package was used for generation of the initial model |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 154428 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-6tgb: |