[English] 日本語
Yorodumi
- EMDB-50026: CryoEM structure of human MICAL1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50026
TitleCryoEM structure of human MICAL1
Map datahMICAL map
Sample
  • Complex: MICAL1 with the FAD cofactor
    • Protein or peptide: [F-actin]-monooxygenase MICAL1
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: ZINC ION
KeywordsMICAL / actin / actin depolymerization / axon guidance plexin / Rab / SIGNALING PROTEIN
Function / homology
Function and homology information


hippocampal mossy fiber expansion / : / F-actin monooxygenase / F-actin monooxygenase activity / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / regulation of regulated secretory pathway / NAD(P)H oxidase H2O2-forming activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / actin filament depolymerization ...hippocampal mossy fiber expansion / : / F-actin monooxygenase / F-actin monooxygenase activity / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / regulation of regulated secretory pathway / NAD(P)H oxidase H2O2-forming activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / actin filament depolymerization / intermediate filament / actin filament bundle assembly / intercellular bridge / cytoskeleton organization / FAD binding / actin filament / monooxygenase activity / small GTPase binding / SH3 domain binding / actin filament binding / actin cytoskeleton / actin binding / Factors involved in megakaryocyte development and platelet production / midbody / endosome membrane / ciliary basal body / cilium / negative regulation of apoptotic process / protein kinase binding / signal transduction / nucleoplasm / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. ...bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / FAD-binding domain / FAD binding domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
[F-actin]-monooxygenase MICAL1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSchrofel A / Pinkas D / Novacek J / Rozbesky D
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Czech Science Foundation21-27204M Czech Republic
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis of MICAL autoinhibition.
Authors: Matej Horvath / Adam Schrofel / Karolina Kowalska / Jan Sabo / Jonas Vlasak / Farahdokht Nourisanami / Margarita Sobol / Daniel Pinkas / Krystof Knapp / Nicola Koupilova / Jiri Novacek / ...Authors: Matej Horvath / Adam Schrofel / Karolina Kowalska / Jan Sabo / Jonas Vlasak / Farahdokht Nourisanami / Margarita Sobol / Daniel Pinkas / Krystof Knapp / Nicola Koupilova / Jiri Novacek / Vaclav Veverka / Zdenek Lansky / Daniel Rozbesky
Abstract: MICAL proteins play a crucial role in cellular dynamics by binding and disassembling actin filaments, impacting processes like axon guidance, cytokinesis, and cell morphology. Their cellular activity ...MICAL proteins play a crucial role in cellular dynamics by binding and disassembling actin filaments, impacting processes like axon guidance, cytokinesis, and cell morphology. Their cellular activity is tightly controlled, as dysregulation can lead to detrimental effects on cellular morphology. Although previous studies have suggested that MICALs are autoinhibited, and require Rab proteins to become active, the detailed molecular mechanisms remained unclear. Here, we report the cryo-EM structure of human MICAL1 at a nominal resolution of 3.1 Å. Structural analyses, alongside biochemical and functional studies, show that MICAL1 autoinhibition is mediated by an intramolecular interaction between its N-terminal catalytic and C-terminal coiled-coil domains, blocking F-actin interaction. Moreover, we demonstrate that allosteric changes in the coiled-coil domain and the binding of the tripartite assembly of CH-L2α1-LIM domains to the coiled-coil domain are crucial for MICAL activation and autoinhibition. These mechanisms appear to be evolutionarily conserved, suggesting a potential universality across the MICAL family.
History
DepositionApr 5, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50026.png

Downloads & links

-
Map

FileDownload / File: emd_50026.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationhMICAL map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.83 Å/pix.
x 320 pix.
= 266.88 Å		0.83 Å/pix.
x 320 pix.
= 266.88 Å		0.83 Å/pix.
x 320 pix.
= 266.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.028473213 - 0.05797473
Average (Standard dev.)0.000014005907 (±0.0008337173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: hMICAL map

Fileemd_50026_half_map_1.map
AnnotationhMICAL map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_50026_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MICAL1 with the FAD cofactor

EntireName: MICAL1 with the FAD cofactor
Components
  • Complex: MICAL1 with the FAD cofactor
    • Protein or peptide: [F-actin]-monooxygenase MICAL1
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: ZINC ION

-
Supramolecule #1: MICAL1 with the FAD cofactor

SupramoleculeName: MICAL1 with the FAD cofactor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: [F-actin]-monooxygenase MICAL1

MacromoleculeName: [F-actin]-monooxygenase MICAL1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: F-actin monooxygenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.014734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASPTSTNPA HAHFESFLQA QLCQDVLSSF QELCGALGLE PGGGLPQYHK IKDQLNYWSA KSLWTKLDKR AGQPVYQQGR ACTSTKCLV VGAGPCGLRV AVELALLGAR VVLVEKRTKF SRHNVLHLWP FTIHDLRALG AKKFYGRFCT GTLDHISIRQ L QLLLLKVA ...String:
MASPTSTNPA HAHFESFLQA QLCQDVLSSF QELCGALGLE PGGGLPQYHK IKDQLNYWSA KSLWTKLDKR AGQPVYQQGR ACTSTKCLV VGAGPCGLRV AVELALLGAR VVLVEKRTKF SRHNVLHLWP FTIHDLRALG AKKFYGRFCT GTLDHISIRQ L QLLLLKVA LLLGVEIHWG VTFTGLQPPP RKGSGWRAQL QPNPPAQLAN YEFDVLISAA GGKFVPEGFK VREMRGKLAI GI TANFVNG RTVEETQVPE ISGVARIYNQ SFFQSLLKAT GIDLENIVYY KDDTHYFVMT AKKQCLLRLG VLRQDWPDTN RLL GSANVV PEALQRFTRA AADFATHGKL GKLEFAQDAH GQPDVSAFDF TSMMRAESSA RVQEKHGARL LLGLVGDCLV EPFW PLGTG VARGFLAAFD AAWMVKRWAE GAESLEVLAE RESLYQLLSQ TSPENMHRNV AQYGLDPATR YPNLNLRAVT PNQVR DLYD VLAKEPVQRN NDKTDTGMPA TGSAGTQEEL LRWCQEQTAG YPGVHVSDLS SSWADGLALC ALVYRLQPGL LEPSEL QGL GALEATAWAL KVAENELGIT PVVSAQAVVA GSDPLGLIAY LSHFHSAFKS MAHSPGPVSQ ASPGTSSAVL FLSKLQR TL QRSRAKENAE DAGGKKLRLE MEAETPSTEV PPDPEPGVPL TPPSQHQEAG AGDLCALCGE HLYVLERLCV NGHFFHRS C FRCHTCEATL WPGGYEQHPG DGHFYCLQHL PQTDHKAEGS DRGPESPELP TPSENSMPPG LSTPTASQEG AGPVPDPSQ PTRRQIRLSS PERQRLSSLN LTPDPEMEPP PKPPRSCSAL ARHALESSFV GWGLPVQSPQ ALVAMEKEEK ESPFSSEEEE EDVPLDSDV EQALQTFAKT SGTMNNYPTW RRTLLRRAKE EEMKRFCKAQ TIQRRLNEIE AALRELEAEG VKLELALRRQ S SSPEQQKK LWVGQLLQLV DKKNSLVAEE AELMITVQEL NLEEKQWQLD QELRGYMNRE ENLKTAADRQ AEDQVLRKLV DL VNQRDAL IRFQEERRLS ELALGTGAQG

UniProtKB: [F-actin]-monooxygenase MICAL1

-
Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
0.015 MTris
0.15 Msodium chlorideNaCl
0.002 MDTT
0.003 MCHAPSO
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 59961 / Average exposure time: 2.7 sec. / Average electron dose: 21.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 59981 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 6256757
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2bry

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 84863
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4.1)

-
Atomic model buiding 1

Initial model
PDB IDChain

2bry

chain_id: A, source_name: PDB, initial_model_type: experimental model

4txi

source_name: PDB, initial_model_type: experimental model

5le0

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 77.02
Output model

PDB-9ewy:
CryoEM structure of human MICAL1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more