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- EMDB-10498: CryoEM structure of the ternary DOCK2-ELMO1-RAC1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-10498
TitleCryoEM structure of the ternary DOCK2-ELMO1-RAC1 complex
Map data
Sample
  • Complex: Ternary complex of DOCK2-ELMO1-RAC1
    • Protein or peptide: Dedicator of cytokinesis protein 2
    • Protein or peptide: Engulfment and cell motility protein 1
    • Protein or peptide: Ras-related C3 botulinum toxin substrate 1
Keywordsguanine nucleotide exchange factor / cytoskeleton / actin / cryoEM / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of vasculogenesis / guanyl nucleotide exchange factor activator activity / myeloid dendritic cell activation involved in immune response / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of fibroblast migration / ruffle assembly ...regulation of vasculogenesis / guanyl nucleotide exchange factor activator activity / myeloid dendritic cell activation involved in immune response / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of fibroblast migration / ruffle assembly / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / regulation of hydrogen peroxide metabolic process / Rac protein signal transduction / macropinocytosis / engulfment of apoptotic cell / guanyl-nucleotide exchange factor complex / superoxide anion generation / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / respiratory burst / motor neuron axon guidance / ruffle organization / myoblast fusion / positive regulation of bicellular tight junction assembly / GTP-dependent protein binding / midbrain dopaminergic neuron differentiation / regulation of lamellipodium assembly / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate CIT / regulation of nitric oxide biosynthetic process / regulation of small GTPase mediated signal transduction / Nef and signal transduction / Activation of RAC1 / PCP/CE pathway / hepatocyte growth factor receptor signaling pathway / RHO GTPases activate KTN1 / forebrain development / sphingosine-1-phosphate receptor signaling pathway / DCC mediated attractive signaling / MET activates RAP1 and RAC1 / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / lamellipodium assembly / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of neutrophil chemotaxis / Wnt signaling pathway, planar cell polarity pathway / positive regulation of ruffle assembly / phagocytosis, engulfment / regulation of receptor signaling pathway via JAK-STAT / NRAGE signals death through JNK / Rho GDP-dissociation inhibitor binding / small GTPase-mediated signal transduction / Activation of RAC1 downstream of NMDARs / positive regulation of Rho protein signal transduction / pericentriolar material / establishment or maintenance of cell polarity / semaphorin-plexin signaling pathway / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / SRC activates STAT3 in a quantitative manner, through Cadherin-11 (CDH11), RAC1 and gp130 (IL6ST) / EPH-ephrin mediated repulsion of cells / regulation of postsynapse assembly / ficolin-1-rich granule membrane / RHOA GTPase cycle / RAC2 GTPase cycle / positive regulation of focal adhesion assembly / RHO GTPases Activate NADPH Oxidases / positive regulation of substrate adhesion-dependent cell spreading / anatomical structure morphogenesis / positive regulation of stress fiber assembly / regulation of synaptic vesicle endocytosis / RHO GTPases Activate WASPs and WAVEs / substrate adhesion-dependent cell spreading / positive regulation of lamellipodium assembly / cell-matrix adhesion / RHO GTPases activate IQGAPs / GPVI-mediated activation cascade / RHO GTPases activate PKNs / T cell receptor binding / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / phagocytic cup / actin filament polymerization / RAC1 GTPase cycle / EPHB-mediated forward signaling / regulation of cell migration / positive regulation of endothelial cell migration / positive regulation of phagocytosis / guanyl-nucleotide exchange factor activity / GTPase activator activity / Activation of STAT3 by cadherin engagement / cell motility / actin filament organization
Similarity search - Function
Dedicator of cytokinesis protein 2 / : / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / : / DOCK N-terminus / Dedicator of cytokinesis (DOCK) TPR region / ELMO protein N-terminal Ras-binding domain / ELMO domain / ELMO, armadillo-like helical domain ...Dedicator of cytokinesis protein 2 / : / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / : / DOCK N-terminus / Dedicator of cytokinesis (DOCK) TPR region / ELMO protein N-terminal Ras-binding domain / ELMO domain / ELMO, armadillo-like helical domain / : / ELMO/CED-12 family / ELMO, armadillo-like helical domain / ELMO domain profile. / Pleckstrin homology domain / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / DHR-2, Lobe C / DHR-2, Lobe B / C2 DOCK-type domain profile. / DOCKER domain profile. / Variant SH3 domain / Small GTPase Rho / Small GTPase Rho domain profile. / C2 domain superfamily / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Src homology 3 domains / Rab subfamily of small GTPases / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ras-related C3 botulinum toxin substrate 1 / Engulfment and cell motility protein 1 / Dedicator of cytokinesis protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsChang L / Yang J
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
Marie Sklodowska-Curie Actions, FragNET ITN657725European Union
CitationJournal: 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
DepositionNov 15, 2019-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
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  • Surface view colored by radius
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-6tgc
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tgc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10498.png

Downloads & links

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Map

FileDownload / File: emd_10498.map.gz / Format: CCP4 / Size: 85.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 282 pix.
= 403.26 Å		1.43 Å/pix.
x 282 pix.
= 403.26 Å		1.43 Å/pix.
x 282 pix.
= 403.26 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.07212933 - 0.17415883
Average (Standard dev.)-0.000120875775 (±0.003674054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions282282282
Spacing282282282
CellA=B=C: 403.25998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z282282282
origin x/y/z0.0000.0000.000
length x/y/z403.260403.260403.260
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS282282282
D min/max/mean-0.0720.174-0.000

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Supplemental data

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Additional map: #1

Fileemd_10498_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of DOCK2-ELMO1-RAC1

EntireName: Ternary complex of DOCK2-ELMO1-RAC1
Components
  • Complex: Ternary complex of DOCK2-ELMO1-RAC1
    • Protein or peptide: Dedicator of cytokinesis protein 2
    • Protein or peptide: Engulfment and cell motility protein 1
    • Protein or peptide: Ras-related C3 botulinum toxin substrate 1

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Supramolecule #1: Ternary complex of DOCK2-ELMO1-RAC1

SupramoleculeName: Ternary complex of DOCK2-ELMO1-RAC1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: Dedicator of cytokinesis protein 2

MacromoleculeName: Dedicator of cytokinesis protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 195.902516 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #2: Engulfment and cell motility protein 1

MacromoleculeName: Engulfment and cell motility protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.891328 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #3: Ras-related C3 botulinum toxin substrate 1

MacromoleculeName: Ras-related C3 botulinum toxin substrate 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.478113 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MQAIKCVVVG DGAVGKTCLL ISYTTNAFPG EYIPTVFDNY SANVMVDGKP VNLGLWDTAG QEDYDRLRPL SYPQTDVFLI CFSLVSPAS FENVRAKWYP EVRHHCPNTP IILVGTKLDL RDDKDTIEKL KEKKLTPITY PQGLAMAKEI GAVKYLECSA L TQRGLKTV ...String:
MQAIKCVVVG DGAVGKTCLL ISYTTNAFPG EYIPTVFDNY SANVMVDGKP VNLGLWDTAG QEDYDRLRPL SYPQTDVFLI CFSLVSPAS FENVRAKWYP EVRHHCPNTP IILVGTKLDL RDDKDTIEKL KEKKLTPITY PQGLAMAKEI GAVKYLECSA L TQRGLKTV FDEAIRAVLC PPPVKKRKRK CLLL

UniProtKB: Ras-related C3 botulinum toxin substrate 1

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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

Concentration0.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHepes
200.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Details: e2initialmodel.py from the EMAN2 package was used for generation of the initial model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 245763
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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