+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40884 | |||||||||
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Title | Human VPS29/VPS35L Complex (Locally refined map) | |||||||||
Map data | Locally refined map | |||||||||
Sample |
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Keywords | COMMD / Retriever / Commander / CCC / PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / retromer complex / Golgi to plasma membrane transport / endocytic recycling / retrograde transport, endosome to Golgi / ficolin-1-rich granule membrane / intracellular protein transport / protein transport / late endosome ...retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / retromer complex / Golgi to plasma membrane transport / endocytic recycling / retrograde transport, endosome to Golgi / ficolin-1-rich granule membrane / intracellular protein transport / protein transport / late endosome / early endosome / endosome membrane / endosome / intracellular membrane-bounded organelle / Neutrophil degranulation / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Chen Z / Chen B / Burstein E / Han Y | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structural organization of the retriever-CCC endosomal recycling complex. Authors: Daniel J Boesch / Amika Singla / Yan Han / Daniel A Kramer / Qi Liu / Kohei Suzuki / Puneet Juneja / Xuefeng Zhao / Xin Long / Michael J Medlyn / Daniel D Billadeau / Zhe Chen / Baoyu Chen / Ezra Burstein / Abstract: The recycling of membrane proteins from endosomes to the cell surface is vital for cell signaling and survival. Retriever, a trimeric complex of vacuolar protein-sorting-associated protein (VPS)35L, ...The recycling of membrane proteins from endosomes to the cell surface is vital for cell signaling and survival. Retriever, a trimeric complex of vacuolar protein-sorting-associated protein (VPS)35L, VPS26C and VPS29, together with the CCC complex comprising coiled-coil domain-containing (CCDC)22, CCDC93 and copper metabolism domain-containing (COMMD) proteins, plays a crucial role in this process. The precise mechanisms underlying retriever assembly and its interaction with CCC have remained elusive. Here, we present a high-resolution structure of retriever in humans determined using cryogenic electron microscopy. The structure reveals a unique assembly mechanism, distinguishing it from its remotely related paralog retromer. By combining AlphaFold predictions and biochemical, cellular and proteomic analyses, we further elucidate the structural organization of the entire retriever-CCC complex across evolution and uncover how cancer-associated mutations in humans disrupt complex formation and impair membrane protein homeostasis. These findings provide a fundamental framework for understanding the biological and pathological implications associated with retriever-CCC-mediated endosomal recycling. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40884.map.gz | 91.1 MB | EMDB map data format | |
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Header (meta data) | emd-40884-v30.xml emd-40884.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40884_fsc.xml | 10.4 KB | Display | FSC data file |
Images | emd_40884.png | 117.7 KB | ||
Masks | emd_40884_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-40884.cif.gz | 7.1 KB | ||
Others | emd_40884_half_map_1.map.gz emd_40884_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40884 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40884 | HTTPS FTP |
-Validation report
Summary document | emd_40884_validation.pdf.gz | 981 KB | Display | EMDB validaton report |
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Full document | emd_40884_full_validation.pdf.gz | 980.6 KB | Display | |
Data in XML | emd_40884_validation.xml.gz | 18 KB | Display | |
Data in CIF | emd_40884_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40884 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40884 | HTTPS FTP |
-Related structure data
Related structure data | 8symMC 8synC 8syoC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40884.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Locally refined map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.0624 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_40884_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half Map 1
File | emd_40884_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_40884_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of full-length VPS29 with VPS35L
Entire | Name: Complex of full-length VPS29 with VPS35L |
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Components |
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-Supramolecule #1: Complex of full-length VPS29 with VPS35L
Supramolecule | Name: Complex of full-length VPS29 with VPS35L / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: VPS35 endosomal protein-sorting factor-like
Macromolecule | Name: VPS35 endosomal protein-sorting factor-like / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 109.700453 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAVFPWHSRN RNYKAEFASC RLEAVPLEFG DYHPLKPITV TESKTKKVNR KGSTSSTSSS SSSSVVDPLS SVLDGTDPLS MFAATADPA ALAAAMDSSR RKRDRDDNSV VGSDFEPWTN KRGEILARYT TTEKLSINLF MGSEKGKAGT ATLAMSEKVR T RLEELDDF ...String: MAVFPWHSRN RNYKAEFASC RLEAVPLEFG DYHPLKPITV TESKTKKVNR KGSTSSTSSS SSSSVVDPLS SVLDGTDPLS MFAATADPA ALAAAMDSSR RKRDRDDNSV VGSDFEPWTN KRGEILARYT TTEKLSINLF MGSEKGKAGT ATLAMSEKVR T RLEELDDF EEGSQKELLN LTQQDYVNRI EELNQSLKDA WASDQKVKAL KIVIQCSKLL SDTSVIQFYP SKFVLITDIL DT FGKLVYE RIFSMCVDSR SVLPDHFSPE NANDTAKETC LNWFFKIASI RELIPRFYVE ASILKCNKFL SKTGISECLP RLT CMIRGI GDPLVSVYAR AYLCRVGMEV APHLKETLNK NFFDFLLTFK QIHGDTVQNQ LVVQGVELPS YLPLYPPAMD WIFQ CISYH APEALLTEMM ERCKKLGNNA LLLNSVMSAF RAEFIATRSM DFIGMIKECD ESGFPKHLLF RSLGLNLALA DPPES DRLQ ILNEAWKVIT KLKNPQDYIN CAEVWVEYTC KHFTKREVNT VLADVIKHMT PDRAFEDSYP QLQLIIKKVI AHFHDF SVL FSVEKFLPFL DMFQKESVRV EVCKCIMDAF IKHQQEPTKD PVILNALLHV CKTMHDSVNA LTLEDEKRML SYLINGF IK MVSFGRDFEQ QLSFYVESRS MFCNLEPVLV QLIHSVNRLA METRKVMKGN HSRKTAAFVR ACVAYCFITI PSLAGIFT R LNLYLHSGQV ALANQCLSQA DAFFKAAISL VPEVPKMINI DGKMRPSESF LLEFLCNFFS TLLIVPDHPE HGVLFLVRE LLNVIQDYTW EDNSDEKIRI YTCVLHLLSA MSQETYLYHI DKVDSNDSLY GGDSKFLAEN NKLCETVMAQ ILEHLKTLAK DEALKRQSS LGLSFFNSIL AHGDLRNNKL NQLSVNLWHL AQRHGCADTR TMVKTLEYIK KQSKQPDMTH LTELALRLPL Q TRT UniProtKB: VPS35 endosomal protein-sorting factor-like |
-Macromolecule #2: Vacuolar protein sorting-associated protein 29
Macromolecule | Name: Vacuolar protein sorting-associated protein 29 / 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: 23.03832 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAGHRLVLVL GDLHIPHRCN SLPAKFKKLL VPGKIQHILC TGNLCTKESY DYLKTLAGDV HIVRGDFDEN LNYPEQKVVT VGQFKIGLI HGHQVIPWGD MASLALLQRQ FDVDILISGH THKFEAFEHE NKFYINPGSA TGAYNALETN IIPSFVLMDI Q ASTVVTYV ...String: MAGHRLVLVL GDLHIPHRCN SLPAKFKKLL VPGKIQHILC TGNLCTKESY DYLKTLAGDV HIVRGDFDEN LNYPEQKVVT VGQFKIGLI HGHQVIPWGD MASLALLQRQ FDVDILISGH THKFEAFEHE NKFYINPGSA TGAYNALETN IIPSFVLMDI Q ASTVVTYV YQLIGDDVKV ERIEYKKPEN LYFQGGGSGG SHHHHHH UniProtKB: Vacuolar protein sorting-associated protein 29 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.25 mg/mL | ||||||||||||||||||
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Buffer | pH: 7 Component:
Details: 10 mM HEPES (pH 7.0), 150 mM NaCl, 2 mM MgCl2, 2 mM DTT, and 5% (v/v) glycerol | ||||||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV |
Software | Name: SerialEM |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3594 / Average exposure time: 5.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Software | Name: Coot |
Refinement | Space: REAL / Overall B value: 107.9 |
Output model | PDB-8sym: |