[English] 日本語
Yorodumi
- EMDB-54213: human Fuzzy-Inturned -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54213
Titlehuman Fuzzy-Inturned
Map data
Sample
  • Complex: human Rab23 GEF Fuzzy-Inturned
    • Protein or peptide: Protein fuzzy homolog
    • Protein or peptide: Protein inturned
Keywordslongin domain / GEF / nucleotide exchange / endosome / autophagosome / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


negative regulation of neural crest formation / negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation / tongue morphogenesis / embryonic body morphogenesis / protein localization to organelle / intraciliary transport / spinal cord dorsal/ventral patterning / establishment of planar polarity / regulation of cilium assembly / ciliary transition zone ...negative regulation of neural crest formation / negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation / tongue morphogenesis / embryonic body morphogenesis / protein localization to organelle / intraciliary transport / spinal cord dorsal/ventral patterning / establishment of planar polarity / regulation of cilium assembly / ciliary transition zone / motile cilium assembly / embryonic skeletal system morphogenesis / negative regulation of cell division / positive regulation of cilium assembly / non-motile cilium assembly / regulation of smoothened signaling pathway / positive regulation of smoothened signaling pathway / limb development / neural tube development / motile cilium / embryonic digit morphogenesis / hair follicle morphogenesis / smoothened signaling pathway / roof of mouth development / cilium assembly / regulation of ossification / hair follicle development / negative regulation of keratinocyte proliferation / Hedgehog 'off' state / keratinocyte differentiation / vesicle-mediated transport / centriole / phosphatidylinositol binding / negative regulation of cell migration / neural tube closure / negative regulation of canonical Wnt signaling pathway / nervous system development / protein transport / cytoskeleton / ciliary basal body / cilium / negative regulation of cell population proliferation / cell division / intracellular membrane-bounded organelle / cell surface / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Fuzzy protein / Protein inturned / 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 ...Fuzzy protein / Protein inturned / 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 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Protein fuzzy homolog / Protein inturned
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWilmes S / Schaefer J / Januliene D / Moeller A / Kuemmel D
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1557-P10 Germany
German Research Foundation (DFG)SFB1557-P11 Germany
CitationJournal: To Be Published
Title: Mechanistic Adaptation of the Metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned
Authors: Wilmes S / Toenjes J / Drechsler M / Ruf A / Schaefer J / Luerick A / Januliene D / Apelt S / Di Iorio D / Wegner SV / Loose M / Moeller A / Paululat A / Kuemmel D
History
DepositionJun 30, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_54213.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.)
0.68 Å/pix.
x 384 pix.
= 261.12 Å
0.68 Å/pix.
x 384 pix.
= 261.12 Å
0.68 Å/pix.
x 384 pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density
Contour LevelBy AUTHOR: 0.0654
Minimum - Maximum-0.11266689 - 0.2367901
Average (Standard dev.)0.00021009764 (±0.005913365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_54213_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_54213_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire : human Rab23 GEF Fuzzy-Inturned

EntireName: human Rab23 GEF Fuzzy-Inturned
Components
  • Complex: human Rab23 GEF Fuzzy-Inturned
    • Protein or peptide: Protein fuzzy homolog
    • Protein or peptide: Protein inturned

-
Supramolecule #1: human Rab23 GEF Fuzzy-Inturned

SupramoleculeName: human Rab23 GEF Fuzzy-Inturned / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Protein fuzzy homolog

MacromoleculeName: Protein fuzzy homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.689883 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: VGEEGTGGTV HLLCLAASSG VPLFCRSSRG GAPARQQLPF SVIGSLNGVH MFGQNLEVQL SSARTENTTV VWKSFHDSIT LIVLSSEVG ISELRLERLL QMVFGAMVLL VGLEELTNIR NVERLKKDLR ASYCLIDSFL GDSELIGDLT QCVDCVIPPE G SLLQEALS ...String:
VGEEGTGGTV HLLCLAASSG VPLFCRSSRG GAPARQQLPF SVIGSLNGVH MFGQNLEVQL SSARTENTTV VWKSFHDSIT LIVLSSEVG ISELRLERLL QMVFGAMVLL VGLEELTNIR NVERLKKDLR ASYCLIDSFL GDSELIGDLT QCVDCVIPPE G SLLQEALS GFAEAAGTTF VSLVVSGRVV AATEGWWRLG TPEAVLLPWL VGSLPPQTAR DYPVYLPHGS PTVPHRLLTL TL LPSLELC LLCGPSPPLS QLYPQLLERW WQPLLDPLRA CLPLGPRALP SGFPLHTDIL GLLLLHLELK RCLFTVEPLG DKE PSPEQR RRLLRNFYTL VTSTHFPPEP GPPEKTEDEV YQAQLPRACY LVLGTEEPGT GVRLVALQLG LRRLLLLLSP QSPT HGLRS LATHTLHALT PLL

UniProtKB: Protein fuzzy homolog

-
Macromolecule #2: Protein inturned

MacromoleculeName: Protein inturned / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 107.526023 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKG VPRIPMASVA SCDSRPSSDE LPGDPSSQEE DEDYDFEDRV SDSGSYSSAS SDYDDLEPEW LDSVQKNGEL FYLELSEDE EESLLPETPT VNHVRFSENE IIIEDDYKER KKYEPKLKQF TKILRRKRLL PKRCNKKNSN DNGPVSILKH Q SNQKTGVI ...String:
MDYKDDDDKG VPRIPMASVA SCDSRPSSDE LPGDPSSQEE DEDYDFEDRV SDSGSYSSAS SDYDDLEPEW LDSVQKNGEL FYLELSEDE EESLLPETPT VNHVRFSENE IIIEDDYKER KKYEPKLKQF TKILRRKRLL PKRCNKKNSN DNGPVSILKH Q SNQKTGVI VQQRYKDVNV YVNPKKLTVI KAKEQLKLLE VLVGIIHQTK WSWRRTGKQG DGERLVVHGL LPGGSAMKSG QV LIGDVLV AVNDVDVTTE NIERVLSCIP GPMQVKLTFE NAYDVKRETS HPRQKKTQSN TSDLVKLLWG EEVEGIQQSG LNT PHIIMY LTLQLDSETS KEEQEILYHY PMSEASQKLK SVRGIFLTLC DMLENVTGTQ VTSSSLLLNG KQIHVAYWKE SDKL LLIGL PAEEVPLPRL RNMIENVIQT LKFMYGSLDS AFCQIENVPR LDHFFNLFFQ RALQPAKLHS SASPSAQQYD ASSAV LLDN LPGVRWLTLP LEIKMELDMA LSDLEAADFA ELSEDYYDMR RLYTILGSSL FYKGYLICSH LPKDDLIDIA VYCRHY CLL PLAAKQRIGQ LIIWREVFPQ HHLRPLADSS TEVFPEPEGR YFLLVVGLKH YMLCVLLEAG GCASKAIGSP GPDCVYV DQ VKTTLHQLDG VDSRIDERLA SSPVPCLSCA DWFLTGSREK TDSLTTSPIL SRLQGTSKVA TSPTCRRTLF GDYSLKTR K PSPSCSSGGS DNGCEGGEDD GFSPHTTPDA VRKQRESQGS DGLEESGTLL KVTKKKSTLP NPFHLGNLKK DLPEKELEI YNTVKLTSGP ENTLFHYVAL ETVQGIFITP TLEEVAQLSG SIHPQLIKNF HQCCLSIRAV FQQTLVEEKK KGLNSGDHSD SAKSVSSLN PVKEHGVLFE CSPGNWTDQK KAPPVMAYWV VGRLFLHPKP QELYVCFHDS VTEIAIEIAF KLFFGLTL

UniProtKB: Protein inturned

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.3
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 37728
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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