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- EMDB-27818: Symmetry expansion of dimeric LRRK1 -

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Basic information

Entry
Database: EMDB / ID: EMD-27818
TitleSymmetry expansion of dimeric LRRK1
Map data
Sample
  • Complex: Symmetry expansion of dimeric LRRK1
    • Protein or peptide: Leucine-rich repeat serine/threonine-protein kinase 1
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
Keywordsdimer / TRANSFERASE
Function / homology
Function and homology information


negative regulation of peptidyl-tyrosine phosphorylation / osteoclast development / positive regulation of intracellular signal transduction / bone resorption / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity ...negative regulation of peptidyl-tyrosine phosphorylation / osteoclast development / positive regulation of intracellular signal transduction / bone resorption / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / GTP binding / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
: / C-terminal of Roc (COR) domain / C-terminal of Roc, COR, domain / Ras of Complex, Roc, domain of DAPkinase / Roc domain profile. / Roc domain / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...: / C-terminal of Roc (COR) domain / C-terminal of Roc, COR, domain / Ras of Complex, Roc, domain of DAPkinase / Roc domain profile. / Roc domain / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Leucine-rich repeat domain superfamily / Ankyrin repeat-containing domain superfamily / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Leucine-rich repeat serine/threonine-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsReimer JM / Lin YX / Leschziner AE
Funding support United States, 4 items
OrganizationGrant numberCountry
Damon Runyon Cancer Research FoundationDRG-2370-19 United States
Michael J. Fox Foundation18321 United States
Other privateASAP-000519
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM107214 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structure of LRRK1 and mechanisms of autoinhibition and activation.
Authors: Janice M Reimer / Andrea M Dickey / Yu Xuan Lin / Robert G Abrisch / Sebastian Mathea / Deep Chatterjee / Elizabeth J Fay / Stefan Knapp / Matthew D Daugherty / Samara L Reck-Peterson / Andres E Leschziner /
Abstract: Leucine Rich Repeat Kinase 1 and 2 (LRRK1 and LRRK2) are homologs in the ROCO family of proteins in humans. Despite their shared domain architecture and involvement in intracellular trafficking, ...Leucine Rich Repeat Kinase 1 and 2 (LRRK1 and LRRK2) are homologs in the ROCO family of proteins in humans. Despite their shared domain architecture and involvement in intracellular trafficking, their disease associations are strikingly different: LRRK2 is involved in familial Parkinson's disease while LRRK1 is linked to bone diseases. Furthermore, Parkinson's disease-linked mutations in LRRK2 are typically autosomal dominant gain-of-function while those in LRRK1 are autosomal recessive loss-of-function. Here, to understand these differences, we solved cryo-EM structures of LRRK1 in its monomeric and dimeric forms. Both differ from the corresponding LRRK2 structures. Unlike LRRK2, which is sterically autoinhibited as a monomer, LRRK1 is sterically autoinhibited in a dimer-dependent manner. LRRK1 has an additional level of autoinhibition that prevents activation of the kinase and is absent in LRRK2. Finally, we place the structural signatures of LRRK1 and LRRK2 in the context of the evolution of the LRRK family of proteins.
History
DepositionAug 8, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27818.png

Downloads & links

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Map

FileDownload / File: emd_27818.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 288 pix.
= 334.08 Å		1.16 Å/pix.
x 288 pix.
= 334.08 Å		1.16 Å/pix.
x 288 pix.
= 334.08 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.195
Minimum - Maximum-0.49688596 - 0.90911794
Average (Standard dev.)0.001018711 (±0.022935977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 334.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27818_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27818_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Symmetry expansion of dimeric LRRK1

EntireName: Symmetry expansion of dimeric LRRK1
Components
  • Complex: Symmetry expansion of dimeric LRRK1
    • Protein or peptide: Leucine-rich repeat serine/threonine-protein kinase 1
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Symmetry expansion of dimeric LRRK1

SupramoleculeName: Symmetry expansion of dimeric LRRK1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Leucine-rich repeat serine/threonine-protein kinase 1

MacromoleculeName: Leucine-rich repeat serine/threonine-protein kinase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 225.739219 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SMAGMSQRPP SMYWCVGPEE SAVCPERAME TLNGAGDTGG KPSTRGGDPA ARSRRTEGIR AAYRRGDRGG ARDLLEEACD QCASQLEKG QLLSIPAAYG DLEMVRYLLS KRLVELPTEP TDDNPAVVAA YFGHTAVVQE LLESLPGPCS PQRLLNWMLA L ACQRGHLG ...String:
SMAGMSQRPP SMYWCVGPEE SAVCPERAME TLNGAGDTGG KPSTRGGDPA ARSRRTEGIR AAYRRGDRGG ARDLLEEACD QCASQLEKG QLLSIPAAYG DLEMVRYLLS KRLVELPTEP TDDNPAVVAA YFGHTAVVQE LLESLPGPCS PQRLLNWMLA L ACQRGHLG VVKLLVLTHG ADPESYAVRK NEFPVIVRLP LYAAIKSGNE DIAIFLLRHG AYFCSYILLD SPDPSKHLLR KY FIEASPL PSSYPGKTAL RVKWSHLRLP WVDLDWLIDI SCQITELDLS ANCLATLPSV IPWGLINLRK LNLSDNHLGE LPG VQSSDE IICSRLLEID ISSNKLSHLP PGFLHLSKLQ KLTASKNCLE KLFEEENATN WIGLRKLQEL DISDNKLTEL PALF LHSFK SLNSLNVSRN NLKVFPDPWA CPLKCCKASR NALECLPDKM AVFWKNHLKD VDFSENALKE VPLGLFQLDA LMFLR LQGN QLAALPPQEK WTCRQLKTLD LSRNQLGKNE DGLKTKRIAF FTTRGRQRSG TEAASVLEFP AFLSESLEVL CLNDNH LDT VPPSVCLLKS LSELYLGNNP GLRELPPELG QLGNLWQLDT EDLTISNVPA EIQKEGPKAM LSYLRAQLRK AEKCKLM KM IIVGPPRQGK STLLEILQTG RAPQVVHGEA TIRTTKWELQ RPAGSRAKVE SVEFNVWDIG GPASMATVNQ CFFTDKAL Y VVVWNLALGE EAVANLQFWL LNIEAKAPNA VVLVVGTHLD LIEAKFRVER IATLRAYVLA LCRSPSGSRA TGFPDITFK HLHEISCKSL EGQEGLRQLI FHVTCSMKDV GSTIGCQRLA GRLIPRSYLS LQEAVLAEQQ RRSRDDDVQY LTDRQLEQLV EQTPDNDIK DYEDLQSAIS FLIETGTLLH FPDTSHGLRN LYFLDPIWLS ECLQRIFNIK GSRSVAKNGV IRAEDLRMLL V GTGFTQQT EEQYFQFLAK FEIALPVAND SYLLPHLLPS KPGLDTHGMR HPTANTIQRV FKMSFVPVGF WQRFIARMLI SL AEMDLQL FENKKNTKSR NRKVTIYSFT GNQRNRCSTF RVKRNQTIYW QEGLLVTFDG GYLSVESSDV NWKKKKSGGM KIV CQSEVR DFSAMAFITD HVNSLIDQWF PALTATESDG TPLMEQYVPC PVCETAWAQH TDPSEKSEDV QYFDMEDCVL TAIE RDFIS CPRHPDLPVP LQELVPELFM TDFPARLFLE NSKLEHSEDE GSVLGQGGSG TVIYRARYQG QPVAVKRFHI KKFKN FANV PADTMLRHLR ATDAMKNFSE FRQEASMLHA LQHPCIVALI GISIHPLCFA LELAPLSSLN TVLSENARDS SFIPLG HML TQKIAYQIAS GLAYLHKKNI IFCDLKSDNI LVWSLDVKEH INIKLSDYGI SRQSFHEGAL GVEGTPGYQA PEIRPRI VY DEKVDMFSYG MVLYELLSGQ RPALGHHQLQ IAKKLSKGIR PVLGQPEEVQ FRRLQALMME CWDTKPEKRP LALSVVSQ M KDPTFATFMY ELCCGKQTAF FSSQGQEYTV VFWDGKEESR NYTVVNTEKG LMEVQRMCCP GMKVSCQLQV QRSLWTATE DQKIYIYTLK GMCPLNTPQQ ALDTPAVVTC FLAVPVIKKN SYLVLAGLAD GLVAVFPVVR GTPKDSCSYL CSHTANRSKF SIADEDARQ NPYPVKAMEV VNSGSEVWYS NGPGLLVIDC ASLEICRRLE PYMAPSMVTS VVCSSEGRGE EVVWCLDDKA N SLVMYHST TYQLCARYFC GVPSPLRDMF PVRPLDTEPP AASHTANPKV PEGDSIADVS IMYSEELGTQ ILIHQESLTD YC SMSSYSS SPPRQAARSP SSLPSSPASS SSVPFSTDCE DSDMLHTPGA ASDRSEHDLT PMDGETFSQH LQAVKILAVR DLI WVPRRG GDVIVIGLEK DSGAQRGRVI AVLKARELTP HGVLVDAAVV AKDTVVCTFE NENTEWCLAV WRGWGAREFD IFYQ SYEEL GRLEACTRKR R

UniProtKB: Leucine-rich repeat serine/threonine-protein kinase 1

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Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.124 µm / Nominal defocus min: 1.2630000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 117826
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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