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- EMDB-0126: Cryo-EM structure of the consensus hub of the clathrin coat complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0126
TitleCryo-EM structure of the consensus hub of the 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
Keywordsclathrin / coat protein / endocytosis / trafficking / TRANSPORT PROTEIN
Function / homology
Function and homology information


clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / clathrin coat of coated pit / clathrin-coated vesicle / vesicle-mediated transport / intracellular protein transport / disordered domain specific binding / nucleolus / structural molecule activity ...clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / clathrin coat of coated pit / clathrin-coated vesicle / vesicle-mediated transport / intracellular protein transport / disordered domain specific binding / nucleolus / structural molecule activity / nucleoplasm / cytosol
Similarity search - Function
Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat ...Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Clathrin heavy chain / Nucleolar protein 16
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.69 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 15, 2023-
Current statusNov 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.195
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.195
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6sct
  • Surface level: 0.195
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0126.png

Downloads & links

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Map

FileDownload / File: emd_0126.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.705 Å
Density
Contour LevelBy AUTHOR: 0.195 / Movie #1: 0.195
Minimum - Maximum-0.15714751 - 0.37421277
Average (Standard dev.)0.0020740747 (±0.016248556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 436.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7051.7051.705
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z436.480436.480436.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1570.3740.002

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Supplemental data

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Mask #1

Fileemd_0126_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional map used during model building at ad-hoc...

Fileemd_0126_additional_1.map
AnnotationAdditional map used during model building at ad-hoc sharpened b-factor of -250.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Post processed map from resolution measurement.

Fileemd_0126_additional_2.map
AnnotationPost processed map from resolution measurement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Soft spherical masked (diameter 320A) applied to remove...

Fileemd_0126_half_map_1.map
AnnotationSoft spherical masked (diameter 320A) applied to remove artifactual density prior to resolution measurement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Soft spherical masked (diameter 320A) applied to remove...

Fileemd_0126_half_map_2.map
AnnotationSoft spherical masked (diameter 320A) applied to remove artifactual density prior to resolution measurement.
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: 540 KDa

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Macromolecule #1: clathrin heavy chain

MacromoleculeName: clathrin heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (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

UniProtKB: Clathrin heavy chain

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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: Sus scrofa (pig) / Organ: BRAIN
SequenceString: 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

UniProtKB: Nucleolar protein 16

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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: Sus scrofa (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
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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.4000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 12785
Startup modelType of model: OTHER
Details: Initial model and angles come from localised reconstruction of the hub (Ilca 2015)
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)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1)
Details: All hub substructures from all coat architectures combined and refined a consensus hub structure
Number images used: 313406
FSC plot (resolution estimation)

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Atomic model buiding 1

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

PDB-6sct:
Cryo-EM structure of the consensus triskelion hub of the clathrin coat complex

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