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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | CryoEM structure of Sec7 autoinhibited conformation | |||||||||
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![]() | GEF / Exchange Factor / Golgi / PROTEIN TRANSPORT | |||||||||
Function / homology | ![]() regulation of ARF protein signal transduction / guanyl-nucleotide exchange factor activity / protein transport / Golgi apparatus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Brownfield BA / Fromme JC | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Sec7 regulatory domains scaffold autoinhibited and active conformations. Authors: Bryce A Brownfield / Brian C Richardson / Steve L Halaby / J Christopher Fromme / ![]() Abstract: The late stages of Golgi maturation involve a series of sequential trafficking events in which cargo-laden vesicles are produced and targeted to multiple distinct subcellular destinations. Each of ...The late stages of Golgi maturation involve a series of sequential trafficking events in which cargo-laden vesicles are produced and targeted to multiple distinct subcellular destinations. Each of these vesicle biogenesis events requires activation of an Arf GTPase by the Sec7/BIG guanine nucleotide exchange factor (GEF). Sec7 localization and activity is regulated by autoinhibition, positive feedback, and interaction with other GTPases. Although these mechanisms have been characterized biochemically, we lack a clear picture of how GEF localization and activity is modulated by these signals. Here, we report the cryogenic electron microscopy structure of full-length Sec7 in its autoinhibited form, revealing the architecture of its multiple regulatory domains. We use functional experiments to determine the basis for autoinhibition and use structural predictions to produce a model for an active conformation of the GEF that is supported empirically. This study therefore elucidates the conformational transition that Sec7 undergoes to become active on the organelle membrane surface. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.5 KB 19.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() ![]() ![]() | 715.7 KB 715.3 KB 7.7 KB 16.9 KB | Display Display Display Display | ![]() |
Images | ![]() | 26.7 KB | ||
Filedesc metadata | ![]() | 7.4 KB | ||
Others | ![]() ![]() | 1.2 MB 1.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 327.5 KB | Display | ![]() |
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Full document | ![]() | 327.1 KB | Display | |
Data in XML | ![]() | 90.7 KB | Display | |
Data in CIF | ![]() | 234.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ucqMC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.7415 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #2
File | emd_42135_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_42135_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Sec7 homodimer
Entire | Name: Sec7 homodimer |
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Components |
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-Supramolecule #1: Sec7 homodimer
Supramolecule | Name: Sec7 homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 392.14 KDa |
-Macromolecule #1: SEC7 domain-containing protein
Macromolecule | Name: SEC7 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 215.563719 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MEQKLISEED LNSAVDHHHH HHRIPGLINS SLKFVVSSLD IIAAQAGRNK QLAELAEKAL AAIKENDQQL PDPEVVFAPL QLATKSGTI PLTTTALDCI GKLISYSYFS APSSSATQDG TEQTPLIERA IDTICDCFQG ETTLVEIQLQ IVKSLLAAVL N DKIIVHGA ...String: MEQKLISEED LNSAVDHHHH HHRIPGLINS SLKFVVSSLD IIAAQAGRNK QLAELAEKAL AAIKENDQQL PDPEVVFAPL QLATKSGTI PLTTTALDCI GKLISYSYFS APSSSATQDG TEQTPLIERA IDTICDCFQG ETTLVEIQLQ IVKSLLAAVL N DKIIVHGA GLLKAVRQVY NIFLLSRSTA NQQVAQGTLT QMVGTVFERV KTRLHMKEAR ANLGRLKASR SSLAVDRSDD QD SQAGKVD GEDATVETVS DATPSESVDK AGGGKLTLKD LEHRKSFDDS HMGDGPTMVS QVKPMKKASR SVSEQSLQES PQD ETPESL DAEDEAYIRD AYLVFRSFCN LSTKILPPDQ LYDLRGQPMR SKLISLHLIH TLLNNHITVF TSPLCTIRNT KNNE PTNFL QAIKYYLCLS ITRNGASSVD RVFDICCEIF WLMLKYMRSS FKNEIEVFLN EIYLALLARR NAPLSQKLTF VGILK RLCE DPRALVELYL NYDCNQNVDN IFQTIVEDLS RFATASVPIT PTQEQQYEES RSKSATAGEW QIKSVLPPPL SVALIA TNH EADTELPKEY VMKRTALDSL VETLRSLVHW SQPGRPELNG ASGDVQRRTS SDDLGDSIDP SMSETASRME VPIAPAT PV IDDDPDQLEK EKARKTAMTN AIKVFNFKPK HGIKLLIKEG FIPSDKPEDI ARFLLREERL DKAQIGEYLG EGDQKNVD I MHAFVDMMDF SKKRFVDALR EFLQAFRLPG EAQKIDRFML KFAHRYVTGN PNAFANADTP YVLAYSVIML NTDLHSSKV VKRMSKAEFI KNNRGINDNA DLPDEYLIGI YDDIASNEIV LKSEREAAAA AGTLPAQSTG LAGLGQAFSN VGRDLQREAY VQQSEEISL RSEQLFRDLY RSQRKSATKG GVKFISATSF KHVGPMFDAT WMSFFSTLSS LVQKTHNLDV NKLCLEGMKL A TKIACLFD LSTPREAFIS MLKNTANLNN PREMQAKNVE ALKVLLDLAQ TEGNYLKESW KDVLLCISQL DRLQLISGGV DE SAVPDVS RARFVPPPRT ETGESRKSTS SARRTRPRAH TGPQGVSLEI ALESRSDEVI KSVDRIFTNT ANLSRDAIIH FAR ALTEVS WDEIKVSGSN DSPRTYSLQK IVEISYYNMT RVRFEWSHIW DVLGEHFNRV GCHANTAIVF FALDSLRQLS MRFM EIEEL AGFKFQKDFL KPFEHVMSNS SNVTVKDMVL RCLIQMIQAR GENIRSGWRT MFGVFTVAAR EPYESIVNLA YENVT QVYK TRFGVVISQG AFTDLIVCLT EFSKNMRFQK KSLQAMETLK SVIPTMLKTP ECPLSQHKPT ATTASGSESH SKKAAV QQT RTSVEEGFWF PVLFAFHDVL MTGEDLEVRS NALNYFFETL LRYGGDFPPE FWDILWRQQL YPIFMVLRSR PEMTNAL NH EELSVWLSTT MIQALRNMIT LFTHYFDALE YMLDRFLELL ALCICQENDT IARIGSNCLQ QLILQNVTKF TAEHWAKI V GAFCELFERT TAYQLFSATT INSTASLSPP PSGLELGGPL SPTSATAPVD GKSLKINGVE TNGQTPGAEP ANGDADGNG TAAAAADASA PAATPQPQQG PAQQLEEFKP NNPLQQQPVV VTAARRRFFN RIISRCVLQL LMIETVNELF SNDAVYAQIP SAELLRLMA LLKKSFLFAK RFNADKDLRM RLWREGFMKQ PPNLLKQESG SAATYVAILF RMFGDTAPDR RGSRADVEAA L VPLCRDII RGYTALDDES QHRNIVAWRP VVVDVLEGYA AFPRDAFAAH IRSFYPLVVE LLGKDLGQDL RAALLLVLRR VG EVGLGIE GMGSGGAAAA AAAGAAAASS GQGNGNGAAA AAADSERRSS VLSVPSGPRH TPSMDSLNDD PSRQVMGKAE QKL ISEEDL NSAVDHHHHH H UniProtKB: A7bd1859-5d22-4ce8-aff3-d8d273e6acf0 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 8.0 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4474 / Average exposure time: 3.092 sec. / Average electron dose: 55.6 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 63000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Details | Phenix Real Space Refinement |
Refinement | Space: REAL / Protocol: OTHER |
Output model | ![]() PDB-8ucq: |