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- EMDB-62697: Cryo-EM structure of the human MON1A/CCZ1/C18orf8 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62697
TitleCryo-EM structure of the human MON1A/CCZ1/C18orf8 complex
Map data
Sample
  • Complex: MCCR complex
    • Protein or peptide: Vacuolar fusion protein MON1 homolog A
    • Protein or peptide: Vacuolar fusion protein CCZ1 homolog B
    • Protein or peptide: Regulator of MON1-CCZ1 complex
    • Protein or peptide: Ras-related protein Rab-7a
KeywordsMON1A / CCZ1 / C18orf8 / Rab7A / autophagy / SIGNALING PROTEIN
Function / homology
Function and homology information


Mon1-Ccz1 complex / synaptic vesicle recycling via endosome / positive regulation of viral process / lipophagy / phagosome acidification / protein to membrane docking / epidermal growth factor catabolic process / alveolar lamellar body / negative regulation of intralumenal vesicle formation / negative regulation of exosomal secretion ...Mon1-Ccz1 complex / synaptic vesicle recycling via endosome / positive regulation of viral process / lipophagy / phagosome acidification / protein to membrane docking / epidermal growth factor catabolic process / alveolar lamellar body / negative regulation of intralumenal vesicle formation / negative regulation of exosomal secretion / phagosome-lysosome fusion / Suppression of autophagy / establishment of vesicle localization / presynaptic endosome / phagosome maturation / retromer complex binding / neurotransmitter receptor transport, postsynaptic endosome to lysosome / endosome to plasma membrane protein transport / phagophore assembly site membrane / protein targeting to vacuole / RAB geranylgeranylation / protein targeting to lysosome / positive regulation of exosomal secretion / melanosome membrane / early endosome to late endosome transport / RAB GEFs exchange GTP for GDP on RABs / RHOD GTPase cycle / RHOF GTPase cycle / retrograde transport, endosome to Golgi / TBC/RABGAPs / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / viral release from host cell / CDC42 GTPase cycle / autophagosome membrane / RHOH GTPase cycle / protein secretion / autophagosome assembly / RHOG GTPase cycle / RAC2 GTPase cycle / intracellular transport / RAC3 GTPase cycle / bone resorption / lipid catabolic process / phagocytic vesicle / vesicle-mediated transport / lipid droplet / Prevention of phagosomal-lysosomal fusion / MHC class II antigen presentation / RAC1 GTPase cycle / secretory granule membrane / small monomeric GTPase / guanyl-nucleotide exchange factor activity / regulation of autophagy / response to bacterium / mitochondrial membrane / small GTPase binding / autophagy / synaptic vesicle membrane / endocytosis / phagocytic vesicle membrane / positive regulation of protein catabolic process / GDP binding / late endosome membrane / protein transport / late endosome / G protein activity / lysosome / endosome membrane / lysosomal membrane / intracellular membrane-bounded organelle / GTPase activity / Neutrophil degranulation / GTP binding / glutamatergic synapse / Golgi apparatus / mitochondrion / extracellular exosome / plasma membrane / 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 / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ras-related protein Rab-7a / Vacuolar fusion protein CCZ1 homolog B / Vacuolar fusion protein MON1 homolog A / Regulator of MON1-CCZ1 complex
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsTang Y / Han Y / Zhang Y / Pan L
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022ZD0207400 China
National Natural Science Foundation of China (NSFC)92253301 China
National Natural Science Foundation of China (NSFC)32071219 China
CitationJournal: Protein Cell / Year: 2025
Title: Mechanistic insights into the GEF activity of the human MON1A/CCZ1/C18orf8 complex.
Authors: Yubin Tang / Yaoyao Han / Zhenpeng Guo / Ying Li / Xinyu Gong / Yuchao Zhang / Haobo Liu / Xindi Zhou / Daichao Xu / Yixiao Zhang / Lifeng Pan /
History
DepositionDec 12, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62697.png

Downloads & links

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Map

FileDownload / File: emd_62697.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 316.5 Å		1.06 Å/pix.
x 300 pix.
= 316.5 Å		1.06 Å/pix.
x 300 pix.
= 316.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.459
Minimum - Maximum-3.2035809 - 4.503314
Average (Standard dev.)0.0007909163 (±0.07052953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 316.49997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62697_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_62697_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 : MCCR complex

EntireName: MCCR complex
Components
  • Complex: MCCR complex
    • Protein or peptide: Vacuolar fusion protein MON1 homolog A
    • Protein or peptide: Vacuolar fusion protein CCZ1 homolog B
    • Protein or peptide: Regulator of MON1-CCZ1 complex
    • Protein or peptide: Ras-related protein Rab-7a

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Supramolecule #1: MCCR complex

SupramoleculeName: MCCR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Vacuolar fusion protein MON1 homolog A

MacromoleculeName: Vacuolar fusion protein MON1 homolog A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.562395 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GTTEGDEEDA TEAWRLHQKH VFVLSEAGKP VYSRYGSEEA LSSTMGVMVA LVSFLEADKN AIRSIHADGY KVVFVRRSPL VLVAVARTR QSAQELAQEL LYIYYQILSL LTGAQLSHIF QQKQNYDLRR LLSGSERITD NLLQLMARDP SFLMGAARCL P LAAAVRDT ...String:
GTTEGDEEDA TEAWRLHQKH VFVLSEAGKP VYSRYGSEEA LSSTMGVMVA LVSFLEADKN AIRSIHADGY KVVFVRRSPL VLVAVARTR QSAQELAQEL LYIYYQILSL LTGAQLSHIF QQKQNYDLRR LLSGSERITD NLLQLMARDP SFLMGAARCL P LAAAVRDT VSASLQQARA RSLVFSILLA RNQLVALVRR KDQFLHPIDL HLLFNLISSS SSFREGEAWT PVCLPKFNAA GF FHAHISY LEPDTDLCLL LVSTDREDFF AVSDCRRRFQ ERLRKRGAHL ALREALRTPY YSVAQVGIPD LRHFLYKSKS SGL FTSPEI EAPYTSEEEQ ERLLGLYQYL HSRAHNASRP LKTIYYTGPN ENLLAWVTGA FELYMCYSPL GTKASAVSAI HKLM RWIRK EEDRLFILTP LTY

UniProtKB: Vacuolar fusion protein MON1 homolog A

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Macromolecule #2: Vacuolar fusion protein CCZ1 homolog B

MacromoleculeName: Vacuolar fusion protein CCZ1 homolog B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.935016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAAAGAGS GPWAAQEKQF PPALLSFFIY NPRFGPREGQ EENKILFYHP NEVEKNEKIR NVGLCEAIVQ FTRTFSPSKP AKSLHTQKN RQFFNEPEEN FWMVMVVRNP IIEKQSKDGK PVIEYQEEEL LDKVYSSVLR QCYSMYKLFN GTFLKAMEDG G VKLLKERL ...String:
MAAAAAGAGS GPWAAQEKQF PPALLSFFIY NPRFGPREGQ EENKILFYHP NEVEKNEKIR NVGLCEAIVQ FTRTFSPSKP AKSLHTQKN RQFFNEPEEN FWMVMVVRNP IIEKQSKDGK PVIEYQEEEL LDKVYSSVLR QCYSMYKLFN GTFLKAMEDG G VKLLKERL EKFFHRYLQT LHLQSCDLLD IFGGISFFPL DKMTYLKIQS FINRMEESLN IVKYTAFLYN DQLIWSGLEQ DD MRILYKY LTTSLFPRHI EPELAGRDSP IRAEMPGNLQ HYGRFLTGPL NLNDPDAKCR FPKIFVNTDD TYEELHLIVY KAM SAAVCF MIDASVHPTL DFCRRLDSIV GPQLTVLASD ICEQFNINKR MSGSEKEPQF KFIYFNHMNL AEKSTVHMRK TPSV SLTSV HPDLMKILGD INSDFTRVDE DEEIIVKAMS DYWVVGKKSD RRELYVILNQ KNANLIEVNE EVKKLCATQF NNIFF LD

UniProtKB: Vacuolar fusion protein CCZ1 homolog B

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Macromolecule #3: Regulator of MON1-CCZ1 complex

MacromoleculeName: Regulator of MON1-CCZ1 complex / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.068445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGEEDYYLEL CERPVQFEKA NPVNCVFFDE ANKQVFAVRS GGATGVVVKG PDDRNPISFR MDDKGEVKCI KFSLENKILA VQRTSKTVD FCNFIPDNSQ LEYTQECKTK NANILGFCWT SSTEIVFITD QGIEFYQVLP EKRSLKLLKS HNLNVNWYMY C PESAVILL ...String:
MGEEDYYLEL CERPVQFEKA NPVNCVFFDE ANKQVFAVRS GGATGVVVKG PDDRNPISFR MDDKGEVKCI KFSLENKILA VQRTSKTVD FCNFIPDNSQ LEYTQECKTK NANILGFCWT SSTEIVFITD QGIEFYQVLP EKRSLKLLKS HNLNVNWYMY C PESAVILL STTVLENVLQ PFHFRAGTMS KLPKFEIELP AAPKSTKPSL SERDIAMATI YGQLYVLFLR HHSRTSNSTG AE VVLYHLP REGACKKMHI LKLNRTGKFA LNVVDNLVVV HHQDTETSVI FDIKLRGEFD GSVTFHHPVL PARSIQPYQI PIT GPAAVT SQSPVPCKLY SSSWIVFQPD IIISASQGYL WNLQVKLEPI VNLLPDKGRL MDFLLQRKEC KMVILSVCSQ MLSE SDRAS LPVIATVFDK LNHEYKKYLD AEQSYAMAVE AGQSRSSPLL KRPVRTQAVL DQSDVYTHVL SAFVEKKEMP HKFVI AVLM EYIRSLNQFQ IAVQHYLHEL VIKTLVQHNL FYMLHQFLQY HVLSDSKPLA CLLLSLESFY PPAHQLSLDM LKRLST AND EIVEVLLSKH QVLAALRFIR GIGGHDNISA RKFLDAAKQT EDNMLFYTIF RFFEQRNQRL RGSPNFTPGE HCEEHVA FF KQIFGDQALM RPTTF

UniProtKB: Regulator of MON1-CCZ1 complex

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Macromolecule #4: Ras-related protein Rab-7a

MacromoleculeName: Ras-related protein Rab-7a / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.529719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTSRKKVLLK VIILGDSGVG KNSLMNQYVN KKFSNQYKAT IGADFLTKEV MVDDRLVTMQ IWDTAGQERF QSLGVAFYRG ADCCVLVFD VTAPNTFKTL DSWRDEFLIQ ASPRDPENFP FVVLGNKIDL ENRQVATKRA QAWCYSKNNI PYFETSAKEA I NVEQAFQT ...String:
MTSRKKVLLK VIILGDSGVG KNSLMNQYVN KKFSNQYKAT IGADFLTKEV MVDDRLVTMQ IWDTAGQERF QSLGVAFYRG ADCCVLVFD VTAPNTFKTL DSWRDEFLIQ ASPRDPENFP FVVLGNKIDL ENRQVATKRA QAWCYSKNNI PYFETSAKEA I NVEQAFQT IARNALKQET EVELYNEFPE PIKLDKNDRA KASAESCSC

UniProtKB: Ras-related protein Rab-7a

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77193
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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