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Yorodumi- EMDB-17339: Structure of the human Commander complex coiled coils, DENND10 an... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17339 | |||||||||||||||
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Title | Structure of the human Commander complex coiled coils, DENND10 and partial Retriever subcomplex | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Coiled-coil / DENND domain / alpha solenoid / calponin homology / UNKNOWN FUNCTION | |||||||||||||||
Function / homology | Function and homology information retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / cytoplasmic sequestering of NF-kappaB / endosome transport via multivesicular body sorting pathway / retromer complex / Golgi to plasma membrane transport / positive regulation of ubiquitin-dependent protein catabolic process / endocytic recycling / retrograde transport, endosome to Golgi / regulation of early endosome to late endosome transport ...retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / cytoplasmic sequestering of NF-kappaB / endosome transport via multivesicular body sorting pathway / retromer complex / Golgi to plasma membrane transport / positive regulation of ubiquitin-dependent protein catabolic process / endocytic recycling / retrograde transport, endosome to Golgi / regulation of early endosome to late endosome transport / cullin family protein binding / ficolin-1-rich granule membrane / intracellular copper ion homeostasis / negative regulation of canonical NF-kappaB signal transduction / guanyl-nucleotide exchange factor activity / intracellular protein transport / small GTPase binding / protein transport / late endosome / Neddylation / positive regulation of canonical NF-kappaB signal transduction / early endosome / endosome membrane / endosome / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / nucleoplasm / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||||||||
Authors | Kumpula EP / Laulumaa S / Huiskonen JT | |||||||||||||||
Funding support | Finland, 4 items
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Citation | Journal: Protein Sci / Year: 2018 Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin / Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17339.map.gz | 630.5 MB | EMDB map data format | |
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Header (meta data) | emd-17339-v30.xml emd-17339.xml | 25.4 KB 25.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17339_fsc.xml | 18.8 KB | Display | FSC data file |
Images | emd_17339.png | 40.1 KB | ||
Masks | emd_17339_msk_1.map | 669.9 MB | Mask map | |
Filedesc metadata | emd-17339.cif.gz | 8.2 KB | ||
Others | emd_17339_half_map_1.map.gz emd_17339_half_map_2.map.gz | 622.5 MB 622.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17339 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17339 | HTTPS FTP |
-Related structure data
Related structure data | 8p0vMC 8p0wC 8p0xC M: atomic model generated by this map C: citing same article (ref.) |
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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_17339.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8464 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17339_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17339_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17339_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human Commander Complex coiled coil region, partial Retriever sub...
Entire | Name: Human Commander Complex coiled coil region, partial Retriever subcomplex |
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Components |
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-Supramolecule #1: Human Commander Complex coiled coil region, partial Retriever sub...
Supramolecule | Name: Human Commander Complex coiled coil region, partial Retriever subcomplex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 560 KDa |
-Macromolecule #1: Coiled-coil domain-containing protein 93
Macromolecule | Name: Coiled-coil domain-containing protein 93 / 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: 73.319734 KDa |
Sequence | String: MGLPRGPEGQ GLPEVETRED EEQNVKLTEI LELLVAAGYF RARIKGLSPF DKVVGGMTWC ITTCNFDVDV DLLFQENSTI GQKIALSEK IVSVLPRMKC PHQLEPHQIQ GMDFIHIFPV VQWLVKRAIE TKEEMGDYIR SYSVSQFQKT YSLPEDDDFI K RKEKAIKT ...String: MGLPRGPEGQ GLPEVETRED EEQNVKLTEI LELLVAAGYF RARIKGLSPF DKVVGGMTWC ITTCNFDVDV DLLFQENSTI GQKIALSEK IVSVLPRMKC PHQLEPHQIQ GMDFIHIFPV VQWLVKRAIE TKEEMGDYIR SYSVSQFQKT YSLPEDDDFI K RKEKAIKT VVDLSEVYKP RRKYKRHQGA EELLDEESRI HATLLEYGRR YGFSRQSKME KAEDKKTALP AGLSATEKAD AH EEDELRA AEEQRIQSLM TKMTAMANEE SRLTASSVGQ IVGLCSAEIK QIVSEYAEKQ SELSAEESPE KLGTSQLHRR KVI SLNKQI AQKTKHLEEL RASHTSLQAR YNEAKKTLTE LKTYSEKLDK EQAALEKIES KADPSILQNL RALVAMNENL KSQE QEFKA HCREEMTRLQ QEIENLKAER APRGDEKTLS SGEPPGTLTS AMTHDEDLDR RYNMEKEKLY KIRLLQARRN REIAI LHRK IDEVPSRAEL IQYQKRFIEL YRQISAVHKE TKQFFTLYNT LDDKKVYLEK EISLLNSIHE NFSQAMASPA ARDQFL RQM EQIVEGIKQS RMKMEKKKQE NKMRRDQLND QYLELLEKQR LYFKTVKEFK EEGRKNEMLL SKVKAKAS UniProtKB: Coiled-coil domain-containing protein 93 |
-Macromolecule #2: Coiled-coil domain-containing protein 22
Macromolecule | Name: Coiled-coil domain-containing protein 22 / 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: 70.856555 KDa |
Sequence | String: MEEADRILIH SLRQAGTAVP PDVQTLRAFT TELVVEAVVR CLRVINPAVG SGLSPLLPLA MSARFRLAMS LAQACMDLGY PLELGYQNF LYPSEPDLRD LLLFLAERLP TDASEDADQP AGDSAILLRA IGSQIRDQLA LPWVPPHLRT PKLQHLQGSA L QKPFHASR ...String: MEEADRILIH SLRQAGTAVP PDVQTLRAFT TELVVEAVVR CLRVINPAVG SGLSPLLPLA MSARFRLAMS LAQACMDLGY PLELGYQNF LYPSEPDLRD LLLFLAERLP TDASEDADQP AGDSAILLRA IGSQIRDQLA LPWVPPHLRT PKLQHLQGSA L QKPFHASR LVVPELSSRG EPREFQASPL LLPVPTQVPQ PVGRVASLLE HHALQLCQQT GRDRPGDEDW VHRTSRLPPQ ED TRAQRQR LQKQLTEHLR QSWGLLGAPI QARDLGELLQ AWGAGAKTGA PKGSRFTHSE KFTFHLEPQA QATQVSDVPA TSR RPEQVT WAAQEQELES LREQLEGVNR SIEEVEADMK TLGVSFVQAE SECRHSKLST AEREQALRLK SRAVELLPDG TANL AKLQL VVENSAQRVI HLAGQWEKHR VPLLAEYRHL RKLQDCRELE SSRRLAEIQE LHQSVRAAAE EARRKEEVYK QLMSE LETL PRDVSRLAYT QRILEIVGNI RKQKEEITKI LSDTKELQKE INSLSGKLDR TFAVTDELVF KDAKKDDAVR KAYKYL AAL HENCSQLIQT IEDTGTIMRE VRDLEEQIET ELGKKTLSNL EKIREDYRAL RQENAGLLGR VREA UniProtKB: Coiled-coil domain-containing protein 22 |
-Macromolecule #3: DENN domain-containing protein 10
Macromolecule | Name: DENN domain-containing protein 10 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 40.562992 KDa |
Sequence | String: MAAAEVADTQ LMLGVGLIEK DTNGEVLWVW CYPSTTATLR NLLLRKCCLT DENKLLHPFV FGQYRRTWFY ITTIEVPDSS ILKKVTHFS IVLTAKDFNP EKYAAFTRIL CRMYLKHGSP VKMMESYIAV LTKGICQSEE NGSFLSKDFD ARKAYLAGSI K DIVSQFGM ...String: MAAAEVADTQ LMLGVGLIEK DTNGEVLWVW CYPSTTATLR NLLLRKCCLT DENKLLHPFV FGQYRRTWFY ITTIEVPDSS ILKKVTHFS IVLTAKDFNP EKYAAFTRIL CRMYLKHGSP VKMMESYIAV LTKGICQSEE NGSFLSKDFD ARKAYLAGSI K DIVSQFGM ETVILHTALM LKKRIVVYHP KIEAVQEFTR TLPALVWHRQ DWTILHSYVH LNADELEALQ MCTGYVAGFV DL EVSNRPD LYDVFVNLAE SEITIAPLAK EAMAMGKLHK EMGQLIVQSA EDPEKSESHV IQDIALKTRE IFTNLAPFSE VSA DGEKRV LNLEALKQKR FPPATENFLY HLAAAEQMLK I UniProtKB: DENN domain-containing protein 10 |
-Macromolecule #4: Vacuolar protein sorting-associated protein 29
Macromolecule | Name: Vacuolar protein sorting-associated protein 29 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 20.531705 KDa |
Sequence | String: MLVLVLGDLH IPHRCNSLPA KFKKLLVPGK IQHILCTGNL CTKESYDYLK TLAGDVHIVR GDFDENLNYP EQKVVTVGQF KIGLIHGHQ VIPWGDMASL ALLQRQFDVD ILISGHTHKF EAFEHENKFY INPGSATGAY NALETNIIPS FVLMDIQAST V VTYVYQLI GDDVKVERIE YKKP UniProtKB: Vacuolar protein sorting-associated protein 29 |
-Macromolecule #5: VPS35 endosomal protein-sorting factor-like
Macromolecule | Name: VPS35 endosomal protein-sorting factor-like / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 109.700453 KDa |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.107 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 55769 / Average electron dose: 59.0 e/Å2 Details: Two datasets were collected from identical grids prepared in the same session. Dataset 1: 20675 movies 50 frames / movie 59 e-/A2 total dose Dataset 2: 35084 movies 45 frames / movie 56 e-/A2 total dose |
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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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-8p0v: |