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- EMDB-0115: Cryo-EM structure of the 32 triskelia sweet potato clathrin coat ... -

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Basic information

Entry
Database: EMDB / ID: EMD-0115
TitleCryo-EM structure of the 32 triskelia sweet potato clathrin coat complex
Map data
Sample
  • Complex: Assembly of clathrin heavy and light chain into coat complexes
    • Protein or peptide: clathrin heavy chain
    • Protein or peptide: clathrin light chain b
    • Protein or peptide: clathrin light chain a
Biological speciesSus scrofa (pig) / pig (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 23.68 Å
AuthorsMorris KL / Smith CJ
CitationJournal: Nat Struct Mol Biol / Year: 2019
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
DepositionJul 10, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseOct 2, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0115.png

Downloads & links

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Map

FileDownload / File: emd_0115.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.71 Å/pix.
x 500 pix.
= 852.5 Å		1.71 Å/pix.
x 500 pix.
= 852.5 Å		1.71 Å/pix.
x 500 pix.
= 852.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.705 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.01592654 - 0.093167126
Average (Standard dev.)0.0023774893 (±0.010011614)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 852.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7051.7051.705
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z852.500852.500852.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0160.0930.002

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Supplemental data

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Mask #1

Fileemd_0115_msk_1.map
Projections & Slices
AxesZYX

Projections

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Histogram (log scale)

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Additional map: Whole cage autorefine and map used for mask creation.

Fileemd_0115_additional.map
AnnotationWhole cage autorefine and map used for mask creation.
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Whole cage autorefine and map used for mask creation.

Fileemd_0115_additional_1.map
AnnotationWhole cage autorefine and map used for mask creation.
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Phase flipped whole cage half map.

Fileemd_0115_half_map_1.map
AnnotationPhase flipped whole cage half map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Phase flipped whole cage half map.

Fileemd_0115_half_map_2.map
AnnotationPhase flipped whole cage half map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Assembly of clathrin heavy and light chain into coat complexes

EntireName: Assembly of clathrin heavy and light chain into coat complexes
Components
  • Complex: Assembly of clathrin heavy and light chain into coat complexes
    • Protein or peptide: clathrin heavy chain
    • Protein or peptide: clathrin light chain b
    • Protein or peptide: clathrin light chain a

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Supramolecule #1: Assembly of clathrin heavy and light chain into coat complexes

SupramoleculeName: Assembly of clathrin heavy and light chain into coat complexes
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sus scrofa (pig) / Organ: BRAIN
Molecular weightTheoretical: 20.2 MDa

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Macromolecule #1: clathrin heavy chain

MacromoleculeName: clathrin heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig) / Organ: BRAIN
SequenceString: 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

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Macromolecule #2: clathrin light chain b

MacromoleculeName: clathrin light chain b / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: pig (pig) / Organ: BRAIN
SequenceString: MADDFGFFSS SESGAPEVAE EDPAAAFLAQ QESEIAGIEN DEGFGAPAGS QAALAQPGPA SGAGPEDMGT TVNGDVFQDA NGPADGYAAI AQADRLTQEP ESIRKWREEQ RKRLQELDAA SKVTEQEWRE KAKKDLEEWN QRQSEQVEKN KINNRIADKA FYQQPDADII ...String:
MADDFGFFSS SESGAPEVAE EDPAAAFLAQ QESEIAGIEN DEGFGAPAGS QAALAQPGPA SGAGPEDMGT TVNGDVFQDA NGPADGYAAI AQADRLTQEP ESIRKWREEQ RKRLQELDAA SKVTEQEWRE KAKKDLEEWN QRQSEQVEKN KINNRIADKA FYQQPDADII GYVASEEAFV KESKEETPGT EWEKVAQLCD FNPKSSKQCK DVSRLRSVLM SLKQTPLSR

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Macromolecule #3: clathrin light chain a

MacromoleculeName: clathrin light chain a / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: pig (pig) / Organ: BRAIN
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6.32 mg/mL
BufferpH: 6.4
Component:
ConcentrationFormulaName
100.0 mMC6H13NO4SMES
1.5 mMMgCl2Magnesium chloride
0.2 mMC14H24N2O10EGTA
0.02 w/vNaN3Sodium azide
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
Details: 3 uL applied to a grid at room temperature and humidity. 3 second hand blot and plunge..
DetailsClathrin coat complexes, end point assembly exhibiting architectural heterogeneity

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen 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

Particle selectionNumber selected: 12785
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: OTHER / Details: Map from supervised 3D classification
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 23.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 1761
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Details: Initial model and angles come from localised reconstruction of the hub (Ilca 2015)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient

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