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- EMDB-36143: CryoEM Structure of metazoan Mon1-Ccz1-RMC1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-36143
TitleCryoEM Structure of metazoan Mon1-Ccz1-RMC1 complex
Map data
Sample
  • Complex: CryoEM structure of the metazoan Mon1-Ccz1-RMC1 complex
    • Protein or peptide: MIP05619p
    • Protein or peptide: Caffeine, calcium, zinc sensitivity 1
    • Protein or peptide: Vacuolar fusion protein MON1 homolog
KeywordsRab cascade / Rab GTPase / guanine nucleotide exchange factors / autophagy / Cryo-EM / SIGNALING PROTEIN
Function / homology
Function and homology information


guanyl nucleotide exchange factor inhibitor activity / Mon1-Ccz1 complex / RAB GEFs exchange GTP for GDP on RABs / guanyl-nucleotide exchange factor adaptor activity / protein targeting to vacuole / endosome to lysosome transport via multivesicular body sorting pathway / neuromuscular junction development / synaptic cleft / vesicle-mediated transport / guanyl-nucleotide exchange factor activity ...guanyl nucleotide exchange factor inhibitor activity / Mon1-Ccz1 complex / RAB GEFs exchange GTP for GDP on RABs / guanyl-nucleotide exchange factor adaptor activity / protein targeting to vacuole / endosome to lysosome transport via multivesicular body sorting pathway / neuromuscular junction development / synaptic cleft / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / autophagy / late endosome membrane / regulation of autophagy / intracellular membrane-bounded organelle / lipid binding / cytosol
Similarity search - Function
Regulator of MON1-CCZ1 complex, C-terminal / Regulator of MON1-CCZ1 complex / : / Regulator of MON1-CCZ1 complex, C-terminal / Regulator of MON1-CCZ1 complex, N-terminal / Vacuolar fusion protein Ccz1 / Vacuolar fusion protein Mon1 / CCZ1/INTU, second Longin domain / CCZ1/INTU/HPS4, third Longin domain / Intu longin-like domain 2 ...Regulator of MON1-CCZ1 complex, C-terminal / Regulator of MON1-CCZ1 complex / : / Regulator of MON1-CCZ1 complex, C-terminal / Regulator of MON1-CCZ1 complex, N-terminal / Vacuolar fusion protein Ccz1 / Vacuolar fusion protein Mon1 / CCZ1/INTU, second Longin domain / CCZ1/INTU/HPS4, third Longin domain / Intu longin-like domain 2 / Intu longin-like domain 3 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain / FUZ/MON1/HPS1, second Longin domain / FUZ/MON1/HPS1, first Longin domain / First Longin domain of FUZ, MON1 and HPS1 / Second Longin domain of FUZ, MON1 and HPS1 / Third Longin domain of FUZ, MON1 and HPS1
Similarity search - Domain/homology
Regulator of MON1-CCZ1 complex / Vacuolar fusion protein MON1 homolog / Vacuolar fusion protein CCZ1 homolog
Similarity search - Component
Biological speciesDrosophila (fruit flies)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsJia GW / Yong X / Su ZM / Jia D
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32222040 China
National Natural Science Foundation of China (NSFC)32070049 China
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
CitationJournal: To Be Published
Title: CryoEM Structure of metazoan Mon1-Ccz1-RMC1 complex
Authors: Jia GW / Yong X / Su ZM / Jia D
History
DepositionMay 8, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36143.png

Downloads & links

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Map

FileDownload / File: emd_36143.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 384 pix.
= 326.4 Å		0.85 Å/pix.
x 384 pix.
= 326.4 Å		0.85 Å/pix.
x 384 pix.
= 326.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.156
Minimum - Maximum-0.7431838 - 1.2926095
Average (Standard dev.)0.00032284207 (±0.023989944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 326.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36143_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36143_half_map_2.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 : CryoEM structure of the metazoan Mon1-Ccz1-RMC1 complex

EntireName: CryoEM structure of the metazoan Mon1-Ccz1-RMC1 complex
Components
  • Complex: CryoEM structure of the metazoan Mon1-Ccz1-RMC1 complex
    • Protein or peptide: MIP05619p
    • Protein or peptide: Caffeine, calcium, zinc sensitivity 1
    • Protein or peptide: Vacuolar fusion protein MON1 homolog

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Supramolecule #1: CryoEM structure of the metazoan Mon1-Ccz1-RMC1 complex

SupramoleculeName: CryoEM structure of the metazoan Mon1-Ccz1-RMC1 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila (fruit flies)

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Macromolecule #1: MIP05619p

MacromoleculeName: MIP05619p / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila (fruit flies)
Molecular weightTheoretical: 72.058391 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDNSNGIHYI ELTPNPIRFD AVSQLTNVFF DDSNKQIFAV RSGGATGVVV KGPGSPDDVV ISFCMSDRGG AIRSIKFSPD NQILAVQRK ENSVEFICFQ GDQPLLQDII THQVKTLIHG FVWVHNREVA LISNTGVEVY TVVPEKRQVR SVKSLSIGIK W FAWCCDAN ...String:
MDNSNGIHYI ELTPNPIRFD AVSQLTNVFF DDSNKQIFAV RSGGATGVVV KGPGSPDDVV ISFCMSDRGG AIRSIKFSPD NQILAVQRK ENSVEFICFQ GDQPLLQDII THQVKTLIHG FVWVHNREVA LISNTGVEVY TVVPEKRQVR SVKSLSIGIK W FAWCCDAN VALLCTSEGN SLIPVLVKQK VITKLPKVDL GNPSRDVQES KVTLGQVYGV LAVLILQSNS TTGLMEVEVH LL NGPGLAP RKCHVLRLSL LGRFAINTVD NLIVVHHQAS GTSLLFDISL PGEVINEITY HTPITPGRSI KPFGLKLPSL SPD GQILQC ELYSTHWVLF QPNIVIDAKL GCMWFLNLCI EPLCQLISDR IRLTEFLLQR SNGKQMLLKV IGQLVDDQYK GTLL PVLET IFSRINKIYA SWVQLELQNQ TAQPSNVKTT TLKQSTPPIV LIEQLDMVQI FQRIARRPYT ESILMLYLQS LNKFN IAAQ EELSKMIISE LISNRSFDTL RRLVSYSMLL ESKSVACFLL SHSNVDTAIS QVAIDMLGRI EAHEIIIEVM LGQGKV IDA LRLAKNSMGL EKVPARKFLE AAHKTKDDLI FHSVYRFFQM RNLKLYETLS FPKAEQCTEF IQHYNNTFPA DNPTRQP VS

UniProtKB: Regulator of MON1-CCZ1 complex

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Macromolecule #2: Caffeine, calcium, zinc sensitivity 1

MacromoleculeName: Caffeine, calcium, zinc sensitivity 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila (fruit flies)
Molecular weightTheoretical: 55.589875 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAKLLQRVEI TLRSFYIFNS TFGQVEGEEH KKVLFYHPND IELNTKIKDV GLSEAIIRFT GTFTSEDDCQ ALHTQKTTQL FYQPEPGYW LVLVLNVPKE VRLKEGVEVA DYRGAEISDR IYRAILRQCY QMFRFQNGCF SSCGSEEPNP DKRRELLCQK L LQFYDQHL ...String:
MAKLLQRVEI TLRSFYIFNS TFGQVEGEEH KKVLFYHPND IELNTKIKDV GLSEAIIRFT GTFTSEDDCQ ALHTQKTTQL FYQPEPGYW LVLVLNVPKE VRLKEGVEVA DYRGAEISDR IYRAILRQCY QMFRFQNGCF SSCGSEEPNP DKRRELLCQK L LQFYDQHL TNLRDPAQCD IIDMLHSIQY LPLDKTLFLR AQNFGTLCET FPDIKESIML YQEQVLCGGK LSPEDLHCVH SY VVQHVLK VEASSSTIAV SPSLKRSISE CQVGGFVRSR QKVAGDEHDA VNEEDHPMKV YVTLDKEAKP YYLLIYRALH ITL CLFLNA DQVAPKQDLY DDLHAYMAPQ LTSLARDISS ELTKEAVGAA GQDNSSGNSE TAPKYLFINE QSLQHHTNFQ RHLP QGLPR NVLSIIADLA NGSGKAEMES APAEEVQVKT TNDYWIVKRR CNYRQYYVIL CNSKATLLDV TQEARRIFEQ ELTDD VFFD K

UniProtKB: Vacuolar fusion protein CCZ1 homolog

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Macromolecule #3: Vacuolar fusion protein MON1 homolog

MacromoleculeName: Vacuolar fusion protein MON1 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila (fruit flies)
Molecular weightTheoretical: 62.338719 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHHHHH ENLYFQGGGS MEVEQTSVRS DTNSTCEYLD AEGDPESPNL YQEADPDQEA EQQNHSIISE LRDGLGTMRD NSALSPEPG QENKGLAASV ESLALSTSTS AKTEDSIGGG LEEEYDYQHD SLWQGQKKHI FILSEAGKPI FSLHGNEDKL A TLFGVIQA ...String:
HHHHHHHHHH ENLYFQGGGS MEVEQTSVRS DTNSTCEYLD AEGDPESPNL YQEADPDQEA EQQNHSIISE LRDGLGTMRD NSALSPEPG QENKGLAASV ESLALSTSTS AKTEDSIGGG LEEEYDYQHD SLWQGQKKHI FILSEAGKPI FSLHGNEDKL A TLFGVIQA LVSFVQMGQD AITSIHAGGI KFAFMQRSSL ILVAASRSNM SVQQLQLQLG DVYNQILSIL TYSHMTKIFE RR KNFDLRR LLSGSERLFY NLLANDSSSA KVSNNIFTFL TNSIRVFPLP TTIRSQITSA IQSNCSKIKN LVFAVLIANN KLI ALVRMK KYSIHPADLR LIFNLVECSE SFKSSENWSP ICLPKFDMNG YLHAHVSYLA DDCQACLLLL SVDRDAFFTL AEAK AKITE KLRKSHCLEA INEELQQPFN AKLYQQVVGI PELRHFLYKP KSTAQLLCPM LRHPYKSLTE LERLEAIYCD LLHRI HNSS RPLKLIYEMK EREVVLAWAT GTYELYAIFE PVVDKATVIK YVDKLIKWIE KEYDVYFIRN HATF

UniProtKB: Vacuolar fusion protein MON1 homolog

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 63.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111235
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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