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- EMDB-6827: Cryo-EM Structure of the Exocyst Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-6827
TitleCryo-EM Structure of the Exocyst Complex
Map dataCryo-EM map of the yeast Exocyst complex overall structure at 5.5A resolution
Sample
  • Complex: Cryo-EM map of the Yeast Exocyst complex overall structure at 5.5A resolution
    • Complex: Cryo-EM map of the yeast Exocyst complex head-part structure at 6.7A resolution
      • Protein or peptide: Exocyst complex component SEC3Exocyst
      • Protein or peptide: Exocyst complex component SEC5Exocyst
      • Protein or peptide: Exocyst complex component SEC6Exocyst
      • Protein or peptide: Exocyst complex component SEC8Exocyst
    • Complex: Cryo-EM map of the yeast Exocyst complex top head-part structure at 6.2A resolution
    • Complex: Cryo-EM map of the yeast Exocyst complex bottom leg-part structure at 4.6A resolution
      • Protein or peptide: Exocyst complex component SEC10Exocyst
      • Protein or peptide: Exocyst complex component SEC15Exocyst
      • Protein or peptide: Exocyst complex component EXO70Exocyst
      • Protein or peptide: Exocyst complex component EXO84Exocyst
    • Complex: Cryo-EM map of the yeast Exocyst complex body-part structure at 4.4A resolution
    • Complex: Cryo-EM map mask for the Yeast Exocyst complex overall structure at 5.5A resolution
    • Complex: Cryo-EM map mask for the Yeast Exocyst complex head structure at 6.7A resolution
    • Complex: Cryo-EM map mask for the yeast Exocyst complex top head-part structure at 6.2A resolution
    • Complex: Cryo-EM map mask for the yeast Exocyst complex bottom leg-part structure at 4.6A resolution
    • Complex: Cryo-EM map mask for the yeast Exocyst complex body-part structure at 4.4A resolution
Keywordsexocyst / coiled-coil / EXOCYTOSIS
Function / homology
Function and homology information


vesicle tethering involved in exocytosis / exocyst assembly / exocyst localization / negative regulation of SNARE complex assembly / Insulin processing / endoplasmic reticulum inheritance / exocyst / prospore membrane / Golgi inheritance / incipient cellular bud site ...vesicle tethering involved in exocytosis / exocyst assembly / exocyst localization / negative regulation of SNARE complex assembly / Insulin processing / endoplasmic reticulum inheritance / exocyst / prospore membrane / Golgi inheritance / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / cellular bud neck / mating projection tip / spliceosomal complex assembly / exocytosis / Rho protein signal transduction / transport vesicle / phosphatidylinositol-4,5-bisphosphate binding / SNARE binding / cell periphery / intracellular protein transport / protein localization / small GTPase binding / protein transport / plasma membrane / cytoplasm
Similarity search - Function
Exocyst complex subunit Sec15, C-terminal / : / : / : / : / Exocyst complex component EXOC6/Sec15, N-terminal / Exocyst complex component Sec8 C-terminal / Exocyst complex component Sec10, N-terminal / Exocyst complex component EXOC6/Sec15 / Exocyst complex component Sec10-like ...Exocyst complex subunit Sec15, C-terminal / : / : / : / : / Exocyst complex component EXOC6/Sec15, N-terminal / Exocyst complex component Sec8 C-terminal / Exocyst complex component Sec10, N-terminal / Exocyst complex component EXOC6/Sec15 / Exocyst complex component Sec10-like / Exocyst complex component EXOC6/Sec15, C-terminal, domain 1 / Exocyst complex component EXOC3/Sec6, C-terminal domain / Exocyst complex subunit Sec15 C-terminal / Exocyst complex component Sec10-like, alpha-helical bundle / Exocyst complex component Sec8, N-terminal / Exocyst complex component EXOC3/Sec6 / Exocyst complex component EXOC2/Sec5 / Exocyst complex component EXOC2/Sec5, N-terminal domain / Exocyst complex component Sec8/EXOC4 / Exocyst complex component Sec8 N-terminal / Exocyst complex component Sec6 / Exocyst complex component Sec5 / Exocyst component Exo84, C-terminal / Exocyst complex component Exo84 / Exocyst component Exo84, C-terminal, subdomain 2 / Exocyst component Exo84, C-terminal, subdomain 1 / Exocyst component 84 C-terminal / Exocyst complex component Exo70 N-terminal / Exocyst complex subunit Exo70, C-terminal / Exocyst complex component Sec3, C-terminal / Exocyst complex component Sec3, PIP2-binding N-terminal domain / : / Vps51/EXO84/COG1 N-terminal / Exocyst complex component Sec3, coiled-coil / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Exocyst complex component Sec3, C-terminal / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Exocyst complex component Exo70 / EXOC6/PINT-1/Sec15/Tip20, C-terminal, domain 2 / Exo70 exocyst complex subunit C-terminal / Cullin repeat-like-containing domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Exocyst complex component EXO70 / Exocyst complex component SEC15 / Exocyst complex component SEC6 / Exocyst complex component SEC8 / Exocyst complex component SEC3 / Exocyst complex component EXO84 / Exocyst complex component SEC5 / Exocyst complex component SEC10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsMei K / Li Y
Funding support China, United States, 4 items
OrganizationGrant numberCountry
National Science Foundation of China31530018 China
Beijing Municipal Science & Technology CommissionZ161100000116034 China
National Key Research and Development Program of MOST2016YFA0501100 China
National Institute of HealthR01GM111128 United States
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Cryo-EM structure of the exocyst complex.
Authors: Kunrong Mei / Yan Li / Shaoxiao Wang / Guangcan Shao / Jia Wang / Yuehe Ding / Guangzuo Luo / Peng Yue / Jun-Jie Liu / Xinquan Wang / Meng-Qiu Dong / Hong-Wei Wang / Wei Guo /
Abstract: The exocyst is an evolutionarily conserved octameric protein complex that mediates the tethering of post-Golgi secretory vesicles to the plasma membrane during exocytosis and is implicated in many ...The exocyst is an evolutionarily conserved octameric protein complex that mediates the tethering of post-Golgi secretory vesicles to the plasma membrane during exocytosis and is implicated in many cellular processes such as cell polarization, cytokinesis, ciliogenesis and tumor invasion. Using cryo-EM and chemical cross-linking MS (CXMS), we solved the structure of the Saccharomyces cerevisiae exocyst complex at an average resolution of 4.4 Å. Our model revealed the architecture of the exocyst and led to the identification of the helical bundles that mediate the assembly of the complex at its core. Sequence analysis suggests that these regions are evolutionarily conserved across eukaryotic systems. Additional cell biological data suggest a mechanism for exocyst assembly that leads to vesicle tethering at the plasma membrane.
History
DepositionSep 21, 2017-
Header (metadata) releaseDec 13, 2017-
Map releaseJan 31, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0203
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0203
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5yfp
  • Surface level: 0.0203
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6827.png

emd_6827_1.png

emd_6827_2.png

emd_6827_3.png

emd_6827_4.png

emd_6827_5.png

Downloads & links

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Map

FileDownload / File: emd_6827.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the yeast Exocyst complex overall structure at 5.5A resolution
Voxel sizeX=Y=Z: 1.30654 Å
Density
Contour LevelBy AUTHOR: 0.0203 / Movie #1: 0.0203
Minimum - Maximum-0.021267172 - 0.08846979
Average (Standard dev.)0.00026629618 (±0.0029179268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 470.3544 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.30653888888891.30653888888891.3065388888889
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z470.354470.354470.354
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0210.0880.000

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Supplemental data

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Mask #1

Fileemd_6827_msk_1.map
Projections & Slices
AxesZYX

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Mask #2

Fileemd_6827_msk_2.map
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Mask #3

Fileemd_6827_msk_3.map
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Mask #4

Fileemd_6827_msk_4.map
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Mask #5

Fileemd_6827_msk_5.map
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Additional map: Cryo-EM map of the yeast Exocyst complex head-part...

Fileemd_6827_additional_1.map
AnnotationCryo-EM map of the yeast Exocyst complex head-part structure at 6.7A resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryo-EM map of the yeast Exocyst complex top...

Fileemd_6827_additional_2.map
AnnotationCryo-EM map of the yeast Exocyst complex top head-part structure at 6.2A resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryo-EM map of the yeast Exocyst complex bottom...

Fileemd_6827_additional_3.map
AnnotationCryo-EM map of the yeast Exocyst complex bottom leg-part structure at 4.6A resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryo-EM map of the yeast Exocyst complex body-part...

Fileemd_6827_additional_4.map
AnnotationCryo-EM map of the yeast Exocyst complex body-part structure at 4.4A resolution
Projections & Slices
AxesZYX

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Sample components

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Entire : Cryo-EM map of the Yeast Exocyst complex overall structure at 5.5...

EntireName: Cryo-EM map of the Yeast Exocyst complex overall structure at 5.5A resolution
Components
  • Complex: Cryo-EM map of the Yeast Exocyst complex overall structure at 5.5A resolution
    • Complex: Cryo-EM map of the yeast Exocyst complex head-part structure at 6.7A resolution
      • Protein or peptide: Exocyst complex component SEC3Exocyst
      • Protein or peptide: Exocyst complex component SEC5Exocyst
      • Protein or peptide: Exocyst complex component SEC6Exocyst
      • Protein or peptide: Exocyst complex component SEC8Exocyst
    • Complex: Cryo-EM map of the yeast Exocyst complex top head-part structure at 6.2A resolution
    • Complex: Cryo-EM map of the yeast Exocyst complex bottom leg-part structure at 4.6A resolution
      • Protein or peptide: Exocyst complex component SEC10Exocyst
      • Protein or peptide: Exocyst complex component SEC15Exocyst
      • Protein or peptide: Exocyst complex component EXO70Exocyst
      • Protein or peptide: Exocyst complex component EXO84Exocyst
    • Complex: Cryo-EM map of the yeast Exocyst complex body-part structure at 4.4A resolution
    • Complex: Cryo-EM map mask for the Yeast Exocyst complex overall structure at 5.5A resolution
    • Complex: Cryo-EM map mask for the Yeast Exocyst complex head structure at 6.7A resolution
    • Complex: Cryo-EM map mask for the yeast Exocyst complex top head-part structure at 6.2A resolution
    • Complex: Cryo-EM map mask for the yeast Exocyst complex bottom leg-part structure at 4.6A resolution
    • Complex: Cryo-EM map mask for the yeast Exocyst complex body-part structure at 4.4A resolution

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Supramolecule #1: Cryo-EM map of the Yeast Exocyst complex overall structure at 5.5...

SupramoleculeName: Cryo-EM map of the Yeast Exocyst complex overall structure at 5.5A resolution
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: overall map of Yeast Exocyst complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c / Location in cell: cytoplasm
Molecular weightTheoretical: 844 KDa

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Supramolecule #2: Cryo-EM map of the yeast Exocyst complex head-part structure at 6...

SupramoleculeName: Cryo-EM map of the yeast Exocyst complex head-part structure at 6.7A resolution
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Details: Map acquired from mask refinement against the head-part of the overall Yeast Exocyst complex map
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c / Location in cell: cytoplasm

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Supramolecule #3: Cryo-EM map of the yeast Exocyst complex top head-part structure ...

SupramoleculeName: Cryo-EM map of the yeast Exocyst complex top head-part structure at 6.2A resolution
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#4
Details: Map acquired from mask refinement against the top part of the Yeast Exocyst complex head-part map
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c / Location in cell: cytoplasm

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Supramolecule #4: Cryo-EM map of the yeast Exocyst complex bottom leg-part structur...

SupramoleculeName: Cryo-EM map of the yeast Exocyst complex bottom leg-part structure at 4.6A resolution
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5-#8
Details: Map acquired from mask refinement against the bottom leg-part of the overall Yeast Exocyst complex map
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c / Location in cell: cytoplasm

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Supramolecule #5: Cryo-EM map of the yeast Exocyst complex body-part structure at 4...

SupramoleculeName: Cryo-EM map of the yeast Exocyst complex body-part structure at 4.4A resolution
type: complex / ID: 5 / Parent: 1 / Macromolecule list: all
Details: Map acquired from mask refinement against the body-part of the overall Yeast Exocyst complex map
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c / Location in cell: cytoplasm

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Supramolecule #6: Cryo-EM map mask for the Yeast Exocyst complex overall structure ...

SupramoleculeName: Cryo-EM map mask for the Yeast Exocyst complex overall structure at 5.5A resolution
type: complex / ID: 6 / Parent: 1 / Macromolecule list: all
Details: The mask was generated by relion_image_handler against the overall final half map. The threshold was set to 0.0046, extending binary map with 6 pixels and a soft-edge of 6 pixels was added.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c / Location in cell: cytoplasm

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Supramolecule #7: Cryo-EM map mask for the Yeast Exocyst complex head structure at ...

SupramoleculeName: Cryo-EM map mask for the Yeast Exocyst complex head structure at 6.7A resolution
type: complex / ID: 7 / Parent: 1 / Macromolecule list: #1-#4
Details: The mask was made by relion_image_handler against the head part of overall final half map. Map threshold was set to 0.0046, extending binary map with 6 pixels and a soft-edge of 6 pixels was applied.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c / Location in cell: cytoplasm

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Supramolecule #8: Cryo-EM map mask for the yeast Exocyst complex top head-part stru...

SupramoleculeName: Cryo-EM map mask for the yeast Exocyst complex top head-part structure at 6.2A resolution
type: complex / ID: 8 / Parent: 1 / Macromolecule list: #1-#4
Details: The mask was made by relion_image_handler against the top head part of the head masked final half map. Map threshold was set to 0.0046, extending binary map with 6 pixels and a soft-edge of 6 pixels was applied.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c / Location in cell: cytoplasm

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Supramolecule #9: Cryo-EM map mask for the yeast Exocyst complex bottom leg-part st...

SupramoleculeName: Cryo-EM map mask for the yeast Exocyst complex bottom leg-part structure at 4.6A resolution
type: complex / ID: 9 / Parent: 1 / Macromolecule list: #5-#8
Details: The mask was made by relion_image_handler against the bottom leg part of overall final half map. Map threshold was set to 0.0046, extending binary map with 6 pixels and a soft-edge of 6 pixels was applied.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c / Location in cell: cytoplasm

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Supramolecule #10: Cryo-EM map mask for the yeast Exocyst complex body-part structur...

SupramoleculeName: Cryo-EM map mask for the yeast Exocyst complex body-part structure at 4.4A resolution
type: complex / ID: 10 / Parent: 1 / Macromolecule list: all
Details: The mask was made by relion_image_handler against the body part of the overall final half map. Map threshold was set to 0.0046, extending binary map with 6 pixels and a soft-edge of 6 pixels was applied.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c / Location in cell: cytoplasm

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Macromolecule #1: Exocyst complex component SEC3

MacromoleculeName: Exocyst complex component SEC3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 154.889547 KDa
SequenceString: MRSSKSPFKR KSHSRETSHD ENTSFFHKRT ISGSSAHHSR NVSQGAVPSS APPVSGGNYS HKRNVSRASN SSQTSNFLAE QYERDRKAI INCCFSRPDH KTGEPPNNYI THVRIIEDSK FPSSRPPPDS KLENKKKRLL ILSAKPNNAK LIQIHKAREN S DGSFQIGR ...String:
MRSSKSPFKR KSHSRETSHD ENTSFFHKRT ISGSSAHHSR NVSQGAVPSS APPVSGGNYS HKRNVSRASN SSQTSNFLAE QYERDRKAI INCCFSRPDH KTGEPPNNYI THVRIIEDSK FPSSRPPPDS KLENKKKRLL ILSAKPNNAK LIQIHKAREN S DGSFQIGR TWQLTELVRV EKDLEISEGF ILTMSKKYYW ETNSAKERTV FIKSLITLYI QTFEGHVPEL VNWDLSLFYL DE RSYQRAV ITNRPGSVSP IKSPTSNFTT NTTQSVGSVP FSAPTERTRR SETESVNPVS TPASVEYHAG MKSLNKAPYS SNS TLNEVN KRYELEQQQQ QEEAELRRLE EQKRLQLQKE NEMKRLEEER RIKQEERKRQ MELEHQRQLE EEERKRQMEL EAKK QMELK RQRQFEEEQR LKKERELLEI QRKQREQETA ERLKKEEQEA LAKKEEEEKS KRNKVDNESY TQEINGKVDN LLEDL NAVL AEETETTPTM QNGTYVPERS TARAHDQLKK PLNIAKVESL GGSDLNDSIS LSDEIAGLNT SNLSGEDQDE KNDLSF EKG DEVRYSNNFE GEAPHVYHEV SIIQEEAPAV SQKLILPEEN NESEALIESK EEIKTMENID DEVLLEILTD INWSIED DA DSMIERIDLR LAETEYLFNQ NLLSLQKIGP NIRPYEDKVN DECHRIIPTL SLFLMEMSNF SNDIENVESQ DNGLQVES A NKKLLWNTLD ELLKTVSLDE ISLNQLLECP IREKNLPWME NQLNLLLKAF QAIGSDGNEV EYNLREISGL KQRLQFYEK VTKIFLNRIV EEMQKKFSNI RGQDISHDQM IRILTTLLIF SPLILFCKEI SQKSYQAIVE NWNVSIQPVY MELWTKKISQ LQGIDTNDE KMNELSLSQL LNEWDTFRKE RKTNDINPVF KNSFSLLTEC LQTMRQECIV YQNFVEVFFH ISSKHNFEEY I KHFNDPDA PPILLDTVKV MQSDREAAVI ETQLVSRIFQ PIVTRLSSYF VELVKAEPTV APALTFYLEN EIKSLESSNH EF LLSAVTR MYTQIKQVWS DNVEEQVLHF ERISNATTNG EILPGILDLP VGLKNSEDLF QFAKRSMDIK DTDEGYESIE LMN SSFRKL SIAATRSITH KEVNSSINPN LSDTAALNND YMETISLLVN SNWLTEMLSM LNFNKDGIFD TSLQNVKKVF DVEK ESYAS FLLRDTMPKL TAFVYGVSNI IENTNNVNMT NPSRWAAYSR QNLENILLAY TSHEIETLVK RLHTHMVNDF GYHQE NAIN NVLCDKLWSC IQGQTVSLYL KLYTVIDKHY RGTNIRFTKN DIISAFEEYK NA

UniProtKB: Exocyst complex component SEC3

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Macromolecule #2: Exocyst complex component SEC5

MacromoleculeName: Exocyst complex component SEC5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 112.236875 KDa
SequenceString: MDRFQIGDEQ LLRFYQLKTI NPTHSWAQDS SKLNNEEATS NELGVETSFD ILKDFKYGNQ ISIDKESRAY LNDESLSYIR DPLNGQEMS KELQHLPNDS MRLNYLVNSK QFNVKAFLRD MHKQDSFNDL NNSLDRLDSD IQDQSIHLKQ LVGKNFTKYV K IKNKLDQI ...String:
MDRFQIGDEQ LLRFYQLKTI NPTHSWAQDS SKLNNEEATS NELGVETSFD ILKDFKYGNQ ISIDKESRAY LNDESLSYIR DPLNGQEMS KELQHLPNDS MRLNYLVNSK QFNVKAFLRD MHKQDSFNDL NNSLDRLDSD IQDQSIHLKQ LVGKNFTKYV K IKNKLDQI YKEFDEKTNE KNQCDSPKEN QINVESLNKK VDEVIRTTTF KLKPLMDNYQ KILNYQATKK FIELNKFYFN LP KSLKRCL TNNDFNEFII EYSKGLTLRR RFNQSSDASQ SLVIKRIWTQ IENLLVTYKD LIWNSLINSN FNIDQPQETI LSL FSKLLN LENFINNNQR ESESGNKNTT SSSNENPILR WMSIKMNGFQ NELNELSGHM ISKIIHSQRL ILQNNTNQDK SQGC VELSY YLKINQLFQI ISDTGKDSEG LKSTVEPNKV NTISGTSYLN LNCQPSSQGL TDSPTIIEMW LLILKYINDL WKICD QFIE FWEHIEKFLD GTYQNSIINE KRKENILIGD SNIIESYQKS LILKEEQINE VRLKGEEFIT SVSQNLISFF TSSQSS LPS SLKDSTGDIT RSNKDSGSPL DYGFIPPNCN GLSCLRYLPK IVEPILKFST ELAQLNITTN GITICRNTLS TIINRCV GA ISSTKLRDIS NFYQLENWQV YETVTFSSKS QDSSKNLTFE YGVTQFPEIV TSFQEVSIKT TRDLLFAYEK LPIINGIS V VSYPSKQLLT GIEIQQIISM EAVLEAILKN AAKDKDNPRN SHTILTLTNL QYFRECAFPN ILQYFDDAFE WNLASKNLE LFSLLSKMES SIFGNYLSDL KINLRDTLEE KFHEINWPMY TSNSFRVGDY IIEALMILIV VHSECFRIGP QLIHKILIET QIFIARYLF EAFKPYVGNL SNDGSLQIIV DLEFFQKVMG PLLEKDTEAT LRACLQNCFQ NDTNRLQKCI NEINPIVSAN L KRTAIQFA AFS

UniProtKB: Exocyst complex component SEC5

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Macromolecule #3: Exocyst complex component SEC6

MacromoleculeName: Exocyst complex component SEC6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 93.539703 KDa
SequenceString: MSSDPLQQVC DLIKGDLSLE RVRDIKEQLL KEKSVVEYQL NKESDKYYGE VEESLKLLNL SKNSVTSIKQ QINEVNKLGN DNRFAINRY DILFRATKLY ETVNTTSSIY DRIYNFVALM EHIERLLVAE LAEDALETGC PHLLEIHFLL TSARDFQEQV V VMAKEATE ...String:
MSSDPLQQVC DLIKGDLSLE RVRDIKEQLL KEKSVVEYQL NKESDKYYGE VEESLKLLNL SKNSVTSIKQ QINEVNKLGN DNRFAINRY DILFRATKLY ETVNTTSSIY DRIYNFVALM EHIERLLVAE LAEDALETGC PHLLEIHFLL TSARDFQEQV V VMAKEATE DAQRTVMKLF SRLSGIISKF DKLLDGLTYD IVEMARAEQI SLAIRLFKIY DLEEREDLRI EAIRNIIKKK EI EIEKSSI KKLPNSKNTA RLQDETPKVI EYPTNKGLYQ EIMSGTISTR TAPRGYKHFL INGINNSISE MFGEMREKYV GDQ KFDVLD NMDWIFNELI IVKEHIANCC PPHWNIFEVY FDQYYKELHS LITDLVESEP ETIIILDILA FDKTFQDTLK QDFG FTKSE VKSVIGDKEK ETLFKDYLNL IVVKMTEWIG NLEKAEFDVF LERSTPPHSD SDGLLFLDGT KTCFQMFTQQ VEVAA GTNQ AKILVGVVER FSDLLTKRQK NWISKISEEI KKQINYNHKY DIDPESITPE DECPGGLVEY LIAVSNDQMK AADYAV AIS SKYGKLVSKV YEKQITNHLE GTLDGFAEVA QCSSLGLITL MFDDLRKPYQ EIFSKTWYMG SQAQQIADTL DEYLLDI KP QMNSVLFVNF IDNVIGETII KFLTALSFEH SFKNKNNKFL EAMKRDFEIF YQLFVKVLDG NESKDTLITQ NFTVMEFF M DLSCEPIDSI LDIWQKYLEV YWDSRIDLLV GILKCRKDVS SSERKKIVQQ ATEMLHEYRR NMEANGVDRE PTLMRRFVL EFEKQ

UniProtKB: Exocyst complex component SEC6

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Macromolecule #4: Exocyst complex component SEC8

MacromoleculeName: Exocyst complex component SEC8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 122.367109 KDa
SequenceString: MDYLKPAQKG RRRGLSINSL SETQQSAMNS SLDHLQNDLN RINLQWNRIL SDNTNPLELA LAFLDDTSVG LGHRYEEFNQ LKSQIGSHL QDVVNEHSQV FNTNVASYGK AVSSIMQAQE QTLNLKNCLK EANEKITTDK GSLQELNDNN LKYTKMIDVL V NIEELLQI ...String:
MDYLKPAQKG RRRGLSINSL SETQQSAMNS SLDHLQNDLN RINLQWNRIL SDNTNPLELA LAFLDDTSVG LGHRYEEFNQ LKSQIGSHL QDVVNEHSQV FNTNVASYGK AVSSIMQAQE QTLNLKNCLK EANEKITTDK GSLQELNDNN LKYTKMIDVL V NIEELLQI PEKIEENIRK ENFHQVQILL ERGFILMNNK SLKTVEILKP INQQLELQEH LLFNNLIEEI HDIMYSKSNK TN FTRVTNN DIFKIISISH NGFTSLENYL YNIVNIDIME HSKTINKNLE QFIHDQSLNK GNIMLQENAA TQAPLAPSRN QEN EGFNRI GFLLKTINNI NKLPVAFNII TERAKEEIHN IIVKSTESIR SKHPSLLKMA TSLKNDNHFG LPVQDILSII LREC FWEIF LKLLYAIQCH RAIFEMSNIL QPTSSAKPAF KFNKIWGKLL DEIELLLVRY INDPELISSN NGSIKPINGA TNNAP TLPK RKNPKIFSLE YNIEDNSSVK DQAFELKALL KDIFPGFSVS SNMDLDSIYV KDESFEQDEP LVPPSVFNMK VILDPF LLF TQSTSTIVPS VLTQNTISSL TFFDDYMNKS FLPKIQMTMD YLFTVEVESN NPYALELSDE NHNIFKTALD FQRLFYN LL NVFNTANTFR EKISYCILDL LNHFYNYYLG LFNSLIGTSD RHLTRKIITA WLQNGILMDQ EQKILNGDET LFHEESIE L FKEIPHFYQA GKGLSKSDLF NNLTLDTILQ FSASVLWILN WLPGLKKAIN IDEVSQEPML DADRLRSSWT FSESMDLNY SNPSSSPNSL GNLKILLDDK ASKKFDETID GFKTLKFKLI TILRFNIRAL CIYDIGSFFQ NTKIWNMDVG SIELDQNIAS LISELRRTE SKLKQQLPEK EKNSIFIGLD IVNNYALIKG AKSIKVLNHN GIKKMLRNVN VLQHAYRNLS SEPSKINMNV T MNFYSLCG SSEAELFEYI KDNELPHCSV EDLKTILRLQ FSEEMHRQLK RQSTSSTKGS IKPSNKRYTE ALEKLSNLEK EQ SKEGART KIGKLKSKLN AVHTANEK

UniProtKB: Exocyst complex component SEC8

+
Macromolecule #5: Exocyst complex component SEC10

MacromoleculeName: Exocyst complex component SEC10 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 100.459578 KDa
SequenceString: MNSLYELDPK WKKLLKTDNF LGGLTVNEFV QELSKDHRND VLIDANTKNL PTNEKDQDAI REAIWKQLDP KPYIRTFEST LKELKNLNE ETLNKRQYFS EQVATQEVIH SENVIKLSKD LHTTLLTFDK LDDRLTNVTQ VVSPLGDKLE TAIKKKQNYI Q SVELIRRY ...String:
MNSLYELDPK WKKLLKTDNF LGGLTVNEFV QELSKDHRND VLIDANTKNL PTNEKDQDAI REAIWKQLDP KPYIRTFEST LKELKNLNE ETLNKRQYFS EQVATQEVIH SENVIKLSKD LHTTLLTFDK LDDRLTNVTQ VVSPLGDKLE TAIKKKQNYI Q SVELIRRY NDFYSMGKSD IVEQLRLSKN WKLNLKSVKL MKNLLILSSK LETSSIPKTI NTKLVIEKYS EMMENELLEN FN SAYRENN FTKLNEIAII LNNFNGGVNV IQSFINQHDY FIDTKQIDLE NEFENVFIKN VKFKEQLIDF ENHSVIIETS MQN LINDVE TVIKNESKIV KRVFEEKATH VIQLFIQRVF AQKIEPRFEV LLRNSLSISN LAYVRILHGL FTLFGKFTKS LIDY FQLLE IDDSNQILST TLEQCFADLF SHYLYDRSKY FGIEKRSLEA ILVDMTSKFT VNYDKEINKR VLLDKYKEKL STNVD AFMH SPRGNTHSRQ DSTSRSKLSQ FNSFLKTHLD KDHLSLNRTN TLSDSFNNSS SSTQYDVANN SSSLVNSSFT ASDIDN SPN SPANYSLNDV DSMLKCVVES TARVMELIPN KAHLYILEIL KIMFLGIVDS YMEIALEVAY WKICKVDINK TAGVVNL NF LKFISMSTEI LDLLSISIKS IFLPLLNNSP EIKAQIIEMT NSQIQKMEIL INIILQETIT VISTKFSAIL CKQKKKDF V PKSQELLDQD TLPAIEIVNI LNLIFEQSSK FLKGKNLQTF LTLIGEELYG LLLSHYSHFQ VNSIGGVVVT KDIIGYQTA IEDWGVASLI DKFATLRELA NLFTVQPELL ESLTKEGHLA DIGRDIIQSY ISNREDFNHD NFINSVKLNF R

UniProtKB: Exocyst complex component SEC10

+
Macromolecule #6: Exocyst complex component SEC15

MacromoleculeName: Exocyst complex component SEC15 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 105.166641 KDa
SequenceString: MDQEGQPLLS KDFQQVLLAT ASGNNSSWTE RAVLNNESTD AVKHEPALGQ NDVFDLDPLS FDKWVPFLRR ALDKNQLDPV IDELENSIE DNFQGLELQL LQDSQMNDKL ETSIDEIANI QGMVQDTLSS EISKFQIRLS ESANELIVKK QMYVNNKKIS L KISEATIL ...String:
MDQEGQPLLS KDFQQVLLAT ASGNNSSWTE RAVLNNESTD AVKHEPALGQ NDVFDLDPLS FDKWVPFLRR ALDKNQLDPV IDELENSIE DNFQGLELQL LQDSQMNDKL ETSIDEIANI QGMVQDTLSS EISKFQIRLS ESANELIVKK QMYVNNKKIS L KISEATIL ITKVVRILEL SSKCQELITE RKFFKVLQNL DSLEKLYLQE FKNYNFQFLI EIYNSIPFLQ KVTKDECINL IR NSLNLNL GKNLIKVGQE FVAIYENELL PQWLETRSKM KLTNFKFNSP IEISMRDESF LAKLNLGEFF QLDDFHDSIM IFQ NLNELS VLSGEFNKEY ELRKTKLMYP LIWKKNKTAA YQMDSLLRGT GTTPGSTAHD VSTDDPFTQS LSLHFLQDYF LKIL GFLLY DINLNKATEF ILVDNNYNST NEFWDGLMDR LSPYLSYFID EKLKTEEDMI KLKDFLCIYV AILENFKLNI EPLYK ILVS IFEKFCSVSL RAFDDEFQIL LNDDDFMPLS INDKTLYEKV LKICWMKEGE HLSLPDPTNG EPFAVTLPFS PLYPMT CTL AKKTYSKITA FLSIFYRHEL HTLNNILVKT MDDIFNDIVN KKIRSKLEST SREEIAQILV NLDYFIIAAK EFSNFMT RE NILQNPDMEI RLSSIKYLAE SRKLAETKLI ELIDSKISDI LETIEIDWQI TEVRQDPDIS IIDLAQFLEM MFASTLQN L PYSVQTLLIF REFDSLTRQF MGLLLHDTPS TITHESIMNF EVDVNYLESI IPRIFPSTPG TIDSNGYQSP MTPSTPTFP NANGVDAPTL FENNIKSLEA TFMELKQCIE LLKTQGKDYN EPEIRLRKYS RIRQEDAALL LSKIQHFVSS VEGANGDDTS VMDSSSIFN SESASVIDSN TSRIAKFFNR R

UniProtKB: Exocyst complex component SEC15

+
Macromolecule #7: Exocyst complex component EXO70

MacromoleculeName: Exocyst complex component EXO70 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 71.382328 KDa
SequenceString: MPAEIDIDEA DVLVLSQELQ KTSKLTFEIN KSLKKIAATS NQSSQLFTPI LARNNVLTTL QRNIESTLNS VASVKDLANE ASKYEIILQ KGINQVGLKQ YTQVVHKLDD MLEDIQSGQA NREENSEFHG ILTHLEQLIK RSEAQLRVYF ISILNSIKPF D PQINITKK ...String:
MPAEIDIDEA DVLVLSQELQ KTSKLTFEIN KSLKKIAATS NQSSQLFTPI LARNNVLTTL QRNIESTLNS VASVKDLANE ASKYEIILQ KGINQVGLKQ YTQVVHKLDD MLEDIQSGQA NREENSEFHG ILTHLEQLIK RSEAQLRVYF ISILNSIKPF D PQINITKK MPFPYYEDQQ LGALSWILDY FHGNSEGSII QDILVGERSK LILKCMAFLE PFAKEISTAK NAPYEKGSSG MN SYTEALL GFIANEKSLV DDLYSQYTES KPHVLSQILS PLISAYAKLF GANLKIVRSN LENFGFFSFE LVESINDVKK SLR GKELQN YNLLQDCTQE VRQVTQSLFR DAIDRIIKKA NSISTIPSNN GVTEATVDTM SRLRKFSEYK NGCLGAMDNI TREN WLPSN YKEKEYTLQN EALNWEDHNV LLSCFISDCI DTLAVNLERK AQIALMPNQE PDVANPNSSK NKHKQRIGFF ILMNL TLVE QIVEKSELNL MLAGEGHSRL ERLKKRYISY MVSDWRDLTA NLMDSVFIDS SGKKSKDKEQ IKEKFRKFNE GFEDLV SKT KQYKLSDPSL KVTLKSEIIS LVMPMYERFY SRYKDSFKNP RKHIKYTPDE LTTVLNQLVR

UniProtKB: Exocyst complex component EXO70

+
Macromolecule #8: Exocyst complex component EXO84

MacromoleculeName: Exocyst complex component EXO84 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 85.649672 KDa
SequenceString: MVEFSLKKAR NNWKHVKKSA SSPAKQKTPP SPAKPKQKTK KNPYSDLKDP ATSYTLPTIN ARERSRVATS MQRRLSIHNT NYAPPTLDY SMPLPDMPNM IVPNDNVDSS HNNSSFTTEN ESVSSKGPSN SLNLSTADLS LNDSSYNKVP ARSAMRNTVN P SGSNDPFN ...String:
MVEFSLKKAR NNWKHVKKSA SSPAKQKTPP SPAKPKQKTK KNPYSDLKDP ATSYTLPTIN ARERSRVATS MQRRLSIHNT NYAPPTLDY SMPLPDMPNM IVPNDNVDSS HNNSSFTTEN ESVSSKGPSN SLNLSTADLS LNDSSYNKVP ARSAMRNTVN P SGSNDPFN NSTSLRKMLA NPHFNAKDFV HDKLGNASAI TIDKFTSNLT DLSIQVQEEV KLNINKSYNE IMTVNNDLNV AM LELKRVR ANINDLNEVL DQCTKIAEKR LQLQDQIDQE RQGNFNNVES HSNSPALLPP LKAGQNGNLM RRDRSSVLIL EKF WDTELD QLFKNVEGAQ KFINSTKGRH ILMNSANWME LNTTTGKPLQ MVQIFILNDL VLIADKSRDK QNDFIVSQCY PLKD VTVTQ EEFSTKRLLF KFSNSNSSLY ECRDADECSR LLDVIRKAKD DLCDIFHVEE ENSKRIRESF RYLQSTQQTP GRENN RSPN KNKRRSMGGS ITPGRNVTGA MDQYLLQNLT LSMHSRPRSR DMSSTAQRLK FLDEGVEEID IELARLRFES AVETLL DIE SQLEDLSERI SDEELMLLNL ISLKIEQRRE AISSKLSQSI LSSNEIVHLK SGTENMIKLG LPEQALDLFL QNRSNFI QD LILQIGSVDN PTNYLTQLAV IRFQTIKKTV EDFQDIFKEL GAKISSILVD WCSDEVDNHF KLIDKQLLND EMLSPGSI K SSRKQIDGLK AVGLDFVYKL DEFIKKNSDK IR

UniProtKB: Exocyst complex component EXO84

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Experimental details

+
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

+
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
10.0 mMC8H18N204SHEPES
2.0 mMDTT

Details: Solutions were freshly prepared from stock and filtered with 0.22um membrane to avoid microbial contamination.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: Purchased Quantifoil R1.2/1.3 gold grid was directly glow discharged 60 seconds before use. Before glow discharge, the sample chamber was vacuumed by an air bump for 2 minutes.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 301 K / Instrument: FEI VITROBOT MARK IV
Details: Protein sample was applied onto a Quantifoil R1.2/1.3 golden grid and hold for 60 seconds, then blot for 2.5 seconds before plunging..
DetailsThis sample was mono-disperse.

+
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.2 µm / Calibrated defocus min: 1.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 113.0 K / Max: 123.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 0-31 / Number grids imaged: 11 / Number real images: 6466 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 904481 / Details: Semi-auto-picked by RELION1.4.
Startup modelType of model: RANDOM CONICAL TILT / Random conical tilt - Number images: 30 / Random conical tilt - Tilt angle: 50 degrees
Details: 4516 tilt-pair particles were picked by EMAN2 subroutine e2RCTboxer.py in an interactive RCT-boxing mode. A low-resolution 3D map was generated by SPIDER.
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 4 / Avg.num./class: 100000 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 343342
DetailsThe selected image stacks were motion corrected by Motioncor2 software and distortion magnification corrected by script.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2b1e


Chain - Chain ID: A / Chain - Residue range: 67-623 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsExo70 (a.a.67-623) was first fit into the map with Situs as a rigid body. Then it was split as Exo70 (a.a.67-344) and Exo70 (a.a.345-623), and fit into the same position with Chimera.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5yfp:
Cryo-EM Structure of the Exocyst Complex

+
Atomic model buiding 2

Initial modelPDB ID:

2d2s


Chain - Chain ID: A / Chain - Residue range: 525-753 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsWell fit by one step Situs fitting.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5yfp:
Cryo-EM Structure of the Exocyst Complex

+
Atomic model buiding 3

Initial modelPDB ID:

2fji


Chain - Chain ID: A / Chain - Residue range: 411-805 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe fitting position of this chain was determined by cross-link mass spectrum.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5yfp:
Cryo-EM Structure of the Exocyst Complex

+
Atomic model buiding 4

Initial modelPDB ID:

5h11


Chain - Chain ID: A / Chain - Residue range: 195-708 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe yeast Sec10 (a.a.234-867) model was first obtained with Swiss-Model prediction based on this zebrafish originated initial model, and then fit into the map. Local adjustment was made with Coot. Final refinement was proceeded with Phenix real-space refinement.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5yfp:
Cryo-EM Structure of the Exocyst Complex

+
Atomic model buiding 5

Initial modelPDB ID:

1zc4


Chain - Chain ID: B / Chain - Residue range: 171-283 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe yeast Exo84 (a.a.346-470) model was first obtained with PHYRE2 prediction based on this rat originated initial model, and then fit into the map. Final refinement was proceeded with Phenix real-space refinement.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5yfp:
Cryo-EM Structure of the Exocyst Complex

+
Atomic model buiding 6

Initial modelPDB ID:

2a2f


Chain - Chain ID: X / Chain - Residue range: 383-699 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe yeast Sec15 (a.a.482-896) model was first obtained with PHYRE2 prediction based on this Drosophila originated initial model, and then fit into the map. Local adjustment was made with Coot. Final refinement was proceeded with Phenix real-space refinement.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5yfp:
Cryo-EM Structure of the Exocyst Complex

+
Atomic model buiding 7

DetailsAll remaining models were manually built as backbone tracing Poly-Alanine, yet the present residues are shown as original. The backbone trace was guided by the EM map connectivity, secondary structure prediction and cross-link mass spectrum. The model was validated with different sets of cross-link mass spectrum data to confirmed the correctness.
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-5yfp:
Cryo-EM Structure of the Exocyst Complex

+
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