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- EMDB-0121: Cryo-EM structure of the hub of the 28 triskelia mini clathrin co... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0121 | |||||||||
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Title | Cryo-EM structure of the hub of the 28 triskelia mini clathrin coat complex | |||||||||
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Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.08 Å | |||||||||
![]() | Morris KL / Smith CJ | |||||||||
![]() | ![]() Title: Cryo-EM of multiple cage architectures reveals a universal mode of clathrin self-assembly. Authors: Kyle L Morris / Joseph R Jones / Mary Halebian / Shenping Wu / Michael Baker / Jean-Paul Armache / Amaurys Avila Ibarra / Richard B Sessions / Alexander D Cameron / Yifan Cheng / Corinne J Smith / ![]() ![]() Abstract: Clathrin forms diverse lattice and cage structures that change size and shape rapidly in response to the needs of eukaryotic cells during clathrin-mediated endocytosis and intracellular trafficking. ...Clathrin forms diverse lattice and cage structures that change size and shape rapidly in response to the needs of eukaryotic cells during clathrin-mediated endocytosis and intracellular trafficking. We present the cryo-EM structure and molecular model of assembled porcine clathrin, providing insights into interactions that stabilize key elements of the clathrin lattice, namely, between adjacent heavy chains, at the light chain-heavy chain interface and within the trimerization domain. Furthermore, we report cryo-EM maps for five different clathrin cage architectures. Fitting structural models to three of these maps shows that their assembly requires only a limited range of triskelion leg conformations, yet inherent flexibility is required to maintain contacts. Analysis of the protein-protein interfaces shows remarkable conservation of contact sites despite architectural variation. These data reveal a universal mode of clathrin assembly that allows variable cage architecture and adaptation of coated vesicle size and shape during clathrin-mediated vesicular trafficking or endocytosis. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 10.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.8 KB 20.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 115 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Others | ![]() ![]() | 14.9 MB 14.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0114C ![]() 0115C ![]() 0116C ![]() 0118C ![]() 0120C ![]() 0122C ![]() 0123C ![]() 0124C ![]() 0125C ![]() 0126C ![]() 6sctC C: citing same article ( |
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EM raw data | ![]() Data size: 88.4 Data #1: Hub subparticles of the 28 mini coat [picked particles - multiframe - unprocessed] Data #2: Hub subparticles of the 32 sweet potato [picked particles - multiframe - unprocessed] Data #3: Hub subparticles of the 36 D6 barrel [picked particles - multiframe - unprocessed] Data #4: Hub subparticles of the 36 tennis ball [picked particles - multiframe - unprocessed] Data #5: Hub subparticles of the 37 big apple [picked particles - multiframe - unprocessed]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.705 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Soft spherical masked (diameter 320A) applied to remove...
File | emd_0121_half_map_1.map | ||||||||||||
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Annotation | Soft spherical masked (diameter 320A) applied to remove artifactual density prior to resolution measurement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Soft spherical masked (diameter 320A) applied to remove...
File | emd_0121_half_map_2.map | ||||||||||||
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Annotation | Soft spherical masked (diameter 320A) applied to remove artifactual density prior to resolution measurement. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Assembly of clathrin heavy and light chain into coat complexes
Entire | Name: Assembly of clathrin heavy and light chain into coat complexes |
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Components |
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-Supramolecule #1: Assembly of clathrin heavy and light chain into coat complexes
Supramolecule | Name: Assembly of clathrin heavy and light chain into coat complexes type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 540 KDa |
-Macromolecule #1: clathrin heavy chain
Macromolecule | Name: clathrin heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: MAQILPIRFQ EHLQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV VIIDMNDPSN PIRRPISAD SAIMNPASKV IALKAGKTLQ IFNIEMKSKM KAHTMTDDVT FWKWISLNTV A LVTDNAVY HWSMEGESQP VKMFDRHSSL AGCQIINYRT DAKQKWLLLT ...String: MAQILPIRFQ EHLQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV VIIDMNDPSN PIRRPISAD SAIMNPASKV IALKAGKTLQ IFNIEMKSKM KAHTMTDDVT FWKWISLNTV A LVTDNAVY HWSMEGESQP VKMFDRHSSL AGCQIINYRT DAKQKWLLLT GISAQQNRVV GA MQLYSVD RKVSQPIEGH AASFAQFKME GNAEESTLFC FAVRGQAGGK LHIIEVGTPP TGN QPFPKK AVDVFFPPEA QNDFPVAMQI SEKHDVVFLI TKYGYIHLYD LETGTCIYMN RISG ETIFV TAPHEATAGI IGVNRKGQVL SVCVEEENII PYITNVLQNP DLALRMAVRN NLAGA EELF ARKFNALFAQ GNYSEAAKVA ANAPKGILRT PDTIRRFQSV PAQPGQTSPL LQYFGI LLD QGQLNKYESL ELCRPVLQQG RKQLLEKWLK EDKLECSEEL GDLVKSVDPT LALSVYL RA NVPNKVIQCF AETGQVQKIV LYAKKVGYTP DWIFLLRNVM RISPDQGQQF AQMLVQDE E PLADITQIVD VFMEYNLIQQ CTAFLLDALK NNRPSEGPLQ TRLLEMNLMH APQVADAIL GNQMFTHYDR AHIAQLCEKA GLLQRALEHF TDLYDIKRAV VHTHLLNPEW LVNYFGSLSV EDSLECLRA MLSANIRQNL QICVQVASKY HEQLSTQSLI ELFESFKSFE GLFYFLGSIV N FSQDPDVH FKYIQAACKT GQIKEVERIC RESNCYDPER VKNFLKEAKL TDQLPLIIVC DR FDFVHDL VLYLYRNNLQ KYIEIYVQKV NPSRLPVVIG GLLDVDCSED VIKNLILVVR GQF STDELV AEVEKRNRLK LLLPWLEARI HEGCEEPATH NALAKIYIDS NNNPERFLRE NPYY DSRVV GKYCEKRDPH LACVAYERGQ CDLELINVCN ENSLFKSLSR YLVRRKDPEL WGSVL LESN PYRRPLIDQV VQTALSETQD PEEVSVTVKA FMTADLPNEL IELLEKIVLD NSVFSE HRN LQNLLILTAI KADRTRVMEY INRLDNYDAP DIANIAISNE LFEEAFAIFR KFDVNTS AV QVLIEHIGNL DRAYEFAERC NEPAVWSQLA KAQLQKGMVK EAIDSYIKAD DPSSYMEV V QAANTSGNWE ELVKYLQMAR KKARESYVET ELIFALAKTN RLAELEEFIN GPNNAHIQQ VGDRCYDEKM YDAAKLLYNN VSNFGRLAST LVHLGEYQAA VDGARKANST RTWKEVCFAC VDGKEFRLA QMCGLHIVVH ADELEELINY YQDRGYFEEL ITMLEAALGL ERAHMGMFTE L AILYSKFK PQKMREHLEL FWSRVNIPKV LRAAEQAHLW AELVFLYDKY EEYDNAIITM MN HPTDAWK EGQFKDIITK VANVELYYRA IQFYLEFKPL LLNDLLMVLS PRLDHTRAVN YFS KVKQLP LVKPYLRSVQ NHNNKSVNES LNNLFITEED YQALRTSIDA YDNFDNISLA QRLE KHELI EFRRIAAYLF KGNNRWKQSV ELCKKDSLYK DAMQYASESK DTELAEELLQ WFLQE EKRE CFGACLFTCY DLLRPDVVLE TAWRHNIMDF AMPYFIQVMK EYLTKVDKLD ASESLR KEE EQATETQPIV YGQPQLMLTA GPSVAVPPQA PFGYGYTAPP YGQPQPGFGY SM |
-Macromolecule #2: clathrin light chain B
Macromolecule | Name: clathrin light chain B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: MADDFGFFSS SESGAPEVAE EDPAAAFLAQ QESEIAGIEN DEGFGAPAGS QAALAQPGPA SGAGPEDMG TTVNGDVFQD ANGPADGYAA IAQADRLTQE PESIRKWREE QRKRLQELDA A SKVTEQEW REKAKKDLEE WNQRQSEQVE KNKINNRIAD KAFYQQPDAD ...String: MADDFGFFSS SESGAPEVAE EDPAAAFLAQ QESEIAGIEN DEGFGAPAGS QAALAQPGPA SGAGPEDMG TTVNGDVFQD ANGPADGYAA IAQADRLTQE PESIRKWREE QRKRLQELDA A SKVTEQEW REKAKKDLEE WNQRQSEQVE KNKINNRIAD KAFYQQPDAD IIGYVASEEA FV KESKEET PGTEWEKVAQ LCDFNPKSSK QCKDVSRLRS VLMSLKQTPL SR |
-Macromolecule #3: clathrin light chain A
Macromolecule | Name: clathrin light chain A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: MADLDPFGAP AGPSLGNGVA GEEDPAAAFL AQQESEIAGI ENDEAFAILD GGAPGPQPHG EPPGGPDAV DGVMNGEYYQ ESNGPTDSYA AISQVDRLQS EPESIRKWRE EQTERLEALD A NSRKQEAE WKEKAIKELE EWYARQDEQL QKTKANNRVA DEAFYKQPFA ...String: MADLDPFGAP AGPSLGNGVA GEEDPAAAFL AQQESEIAGI ENDEAFAILD GGAPGPQPHG EPPGGPDAV DGVMNGEYYQ ESNGPTDSYA AISQVDRLQS EPESIRKWRE EQTERLEALD A NSRKQEAE WKEKAIKELE EWYARQDEQL QKTKANNRVA DEAFYKQPFA DVIGYVAAEE AF VNDIEES SPGTEWERVA RLCDFNPKSS KQAKDVSRMR SVLISLKQAP LVH |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6.32 mg/mL | |||||||||||||||
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Buffer | pH: 6.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER Details: 3 uL applied to a grid at room temperature and humidity. 3 second hand blot and plunge.. | |||||||||||||||
Details | Clathrin coat complexes, end point assembly exhibiting architectural heterogeneity |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 3.0 sec. / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 82111 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.4 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient |
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