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- EMDB-23698: Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Parti... -

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Basic information

Entry
Database: EMDB / ID: EMD-23698
TitleHuman Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Particle Cryo-EM
Map dataHuman septin hexameric complex SEPT2G-SEPT6-SEPT7.
Sample
  • Complex: Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7
    • Protein or peptide: Septin-2
    • Protein or peptide: Septin-6
    • Protein or peptide: Septin-7
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


septin collar / regulation of embryonic cell shape / sperm annulus / septin complex / positive regulation of non-motile cilium assembly / photoreceptor connecting cilium / septin ring / cytoskeleton-dependent cytokinesis / regulation of exocytosis / non-motile cilium ...septin collar / regulation of embryonic cell shape / sperm annulus / septin complex / positive regulation of non-motile cilium assembly / photoreceptor connecting cilium / septin ring / cytoskeleton-dependent cytokinesis / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway / cell division site / intercellular bridge / axoneme / cleavage furrow / mitotic cytokinesis / cilium assembly / axon terminus / stress fiber / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / kinetochore / spindle / microtubule cytoskeleton / synaptic vesicle / actin cytoskeleton / midbody / spermatogenesis / cell differentiation / molecular adaptor activity / cadherin binding / GTPase activity / GTP binding / structural molecule activity / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Septin 2 / Septin 7 / Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Septin-6 / Septin-2 / Septin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMendonca DC / Pereira HM / van Heel M / Portugal RV / Garratt RC
Funding support Brazil, 3 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/15546-1 Brazil
Sao Paulo Research Foundation (FAPESP)2017/15340-2 Brazil
Sao Paulo Research Foundation (FAPESP)2018/20209-5 Brazil
CitationJournal: J Mol Biol / Year: 2021
Title: An atomic model for the human septin hexamer by cryo-EM.
Authors: Deborah C Mendonça / Samuel L Guimarães / Humberto D'Muniz Pereira / Andressa A Pinto / Marcelo A de Farias / Andre S de Godoy / Ana P U Araujo / Marin van Heel / Rodrigo V Portugal / Richard C Garratt /
Abstract: In order to form functional filaments, human septins must assemble into hetero-oligomeric rod-like particles which polymerize end-to-end. The rules governing the assembly of these particles and the ...In order to form functional filaments, human septins must assemble into hetero-oligomeric rod-like particles which polymerize end-to-end. The rules governing the assembly of these particles and the subsequent filaments are incompletely understood. Although crystallographic approaches have been successful in studying the separate components of the system, there has been difficulty in obtaining high resolution structures of the full particle. Here we report a first cryo-EM structure for a hexameric rod composed of human septins 2, 6 and 7 with a global resolution of ~3.6 Å and a local resolution of between ~3.0 Å and ~5.0 Å. By fitting the previously determined high-resolution crystal structures of the component subunits into the cryo-EM map, we are able to provide an essentially complete model for the particle. This exposes SEPT2 NC-interfaces at the termini of the hexamer and leaves internal cavities between the SEPT6-SEPT7 pairs. The floor of the cavity is formed by the two α helices including their polybasic regions. These are locked into place between the two subunits by interactions made with the α and α helices of the neighbouring monomer together with its polyacidic region. The cavity may serve to provide space allowing the subunits to move with respect to one another. The elongated particle shows a tendency to bend at its centre where two copies of SEPT7 form a homodimeric G-interface. Such bending is almost certainly related to the ability of septin filaments to recognize and even induce membrane curvature.
History
DepositionMar 25, 2021-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.76
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.76
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7m6j
  • Surface level: 0.76
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23698.png

Downloads & links

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Map

FileDownload / File: emd_23698.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman septin hexameric complex SEPT2G-SEPT6-SEPT7.
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.76 / Movie #1: 0.76
Minimum - Maximum-1.9951682 - 5.2883015
Average (Standard dev.)-0.00026589687 (±0.07067203)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 430.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z430.000430.000430.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-1.9955.288-0.000

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Supplemental data

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Half map: Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Particle...

Fileemd_23698_half_map_1.map
AnnotationHuman Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Particle Cryo-EM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Particle...

Fileemd_23698_half_map_2.map
AnnotationHuman Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Particle Cryo-EM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7

EntireName: Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7
Components
  • Complex: Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7
    • Protein or peptide: Septin-2
    • Protein or peptide: Septin-6
    • Protein or peptide: Septin-7
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7

SupramoleculeName: Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Septin-2

MacromoleculeName: Septin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.748352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGFEFTLMVV GESGLGKSTL INSLFLTDLY PERVIPGAAE KIERTVQIEA STVEIEERGV KLRLTVVDTP GYGDAINCRD CFKTIISYI DEQFERYLHD ESGLNRRHII DNRVHCCFYF ISPFGHGLKP LDVAFMKAIH NKVNIVPVIA KADTLTLKER E RLKKRILD ...String:
MGFEFTLMVV GESGLGKSTL INSLFLTDLY PERVIPGAAE KIERTVQIEA STVEIEERGV KLRLTVVDTP GYGDAINCRD CFKTIISYI DEQFERYLHD ESGLNRRHII DNRVHCCFYF ISPFGHGLKP LDVAFMKAIH NKVNIVPVIA KADTLTLKER E RLKKRILD EIEEHNIKIY HLPDAESDED EDFKEQTRLL KASIPFSVVG SNQLIEAKGK KVRGRLYPWG VVEVENPEHN DF LKLRTML ITHMQDLQEV TQDLHYENFR SERLKRGG

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Macromolecule #2: Septin-6

MacromoleculeName: Septin-6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.948723 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAATDIARQV GEGCRTVPLA GHVGFDSLPD QLVNKSVSQG FCFNILCVGE TGLGKSTLMD TLFNTKFEGE PATHTQPGVQ LQSNTYDLQ ESNVRLKLTI VSTVGFGDQI NKEDSYKPIV EFIDAQFEAY LQEELKIRRV LHTYHDSRIH VCLYFIAPTG H SLKSLDLV ...String:
MAATDIARQV GEGCRTVPLA GHVGFDSLPD QLVNKSVSQG FCFNILCVGE TGLGKSTLMD TLFNTKFEGE PATHTQPGVQ LQSNTYDLQ ESNVRLKLTI VSTVGFGDQI NKEDSYKPIV EFIDAQFEAY LQEELKIRRV LHTYHDSRIH VCLYFIAPTG H SLKSLDLV TMKKLDSKVN IIPIIAKADA ISKSELTKFK IKITSELVSN GVQIYQFPTD DESVAEINGT MNAHLPFAVI GS TEELKIG NKMMRARQYP WGTVQVENEA HCDFVKLREM LIRVNMEDLR EQTHTRHYEL YRRCKLEEMG FKDTDPDSKP FSL QETYEA KRNEFLGELQ KKEEEMRQMF VQRVKEKEAE LKEAEKELHE KFDRLKKLHQ DEKKKLEDKK KSLDDEVNAF KQRK TAAEL LQSQGSQAGG SQTLKRDKEK KN

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Macromolecule #3: Septin-7

MacromoleculeName: Septin-7 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.456645 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPMVAQQK NLEGYVGFAN LPNQVYRKSV KRGFEFTLMV VGESGLGKST LINSLFLTDL YSPEYPGPSH RIKKTVQVE QSKVLIKEGG VQLLLTIVDT PGFGDAVDNS NCWQPVIDYI DSKFEDYLNA ESRVNRRQMP DNRVQCCLYF I APSGHGLK ...String:
MGSSHHHHHH SQDPMVAQQK NLEGYVGFAN LPNQVYRKSV KRGFEFTLMV VGESGLGKST LINSLFLTDL YSPEYPGPSH RIKKTVQVE QSKVLIKEGG VQLLLTIVDT PGFGDAVDNS NCWQPVIDYI DSKFEDYLNA ESRVNRRQMP DNRVQCCLYF I APSGHGLK PLDIEFMKRL HEKVNIIPLI AKADTLTPEE CQQFKKQIMK EIQEHKIKIY EFPETDDEEE NKLVKKIKDR LP LAVVGSN TIIEVNGKRV RGRQYPWGVA EVENGEHCDF TILRNMLIRT HMQDLKDVTN NVHYENYRSR KLAAVTYNGV DNN KNKGQL TKSPLAQMEE ERREHVAKMK KMEMEMEQVF EMKVKEKVQK LKDSEAELQR RHEQMKKNLE AQHKELEEKR RQFE DEKAN WEAQQRILEQ QNSSRTLEKN KKKGKIF

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Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Number images used: 108262
FSC plot (resolution estimation)

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