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- EMDB-12273: Cryo-EM structure of the human FERRY complex -

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Basic information

Entry
Database: EMDB / ID: EMD-12273
TitleCryo-EM structure of the human FERRY complex
Map dataCryo-EM structure of the FERRY complex core
Sample
  • Complex: Human FERRY (Five-subunit Early endosome RNA and Ribosome intermediarY) complex
    • Complex: Protein phosphatase 1 regulatory subunit 21
      • Protein or peptide: Protein phosphatase 1 regulatory subunit 21
    • Complex: Quinone oxidoreductase-like protein 1
      • Protein or peptide: Quinone oxidoreductase-like protein 1
    • Complex: Glutamine amidotransferase-like class 1 domain-containing protein 1
      • Protein or peptide: Glutamine amidotransferase-like class 1 domain-containing protein 1
KeywordsHuman FERRY complex / Five-subunit Early endosome RNA and Ribosome intermediarY complex / Intracellular RNA transport / Early Endosome-associated transport of RNA / RNA BINDING PROTEIN
Function / homology
Function and homology information


quinone metabolic process / glyoxalase III activity / NADPH:quinone reductase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / Oxidoreductases / NADP binding / early endosome / extracellular exosome / membrane / cytoplasm / cytosol
Similarity search - Function
Uncharacterised domain KLRAQ/TTKRSYEDQ, N-terminal / Uncharacterised domain KLRAQ/TTKRSYEDQ, C-terminal / Protein phosphatase 1 regulatory subunit 21 / Predicted coiled-coil domain-containing protein / Protein phosphatase 1 regulatory subunit 21, six-helix bundle / Predicted coiled-coil domain-containing protein / Quinone oxidoreductase-like protein 1 / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily ...Uncharacterised domain KLRAQ/TTKRSYEDQ, N-terminal / Uncharacterised domain KLRAQ/TTKRSYEDQ, C-terminal / Protein phosphatase 1 regulatory subunit 21 / Predicted coiled-coil domain-containing protein / Protein phosphatase 1 regulatory subunit 21, six-helix bundle / Predicted coiled-coil domain-containing protein / Quinone oxidoreductase-like protein 1 / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / Class I glutamine amidotransferase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Quinone oxidoreductase-like protein 1 / Protein phosphatase 1 regulatory subunit 21 / Glutamine amidotransferase-like class 1 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsQuentin D / Klink BU / Raunser S
Funding support1 items
OrganizationGrant numberCountry
European Research Council (ERC)615984
CitationJournal: Mol Cell / Year: 2023
Title: Structural basis of mRNA binding by the human FERRY Rab5 effector complex.
Authors: Dennis Quentin / Jan S Schuhmacher / Björn U Klink / Jeni Lauer / Tanvir R Shaikh / Pim J Huis In 't Veld / Luisa M Welp / Henning Urlaub / Marino Zerial / Stefan Raunser /
Abstract: The pentameric FERRY Rab5 effector complex is a molecular link between mRNA and early endosomes in mRNA intracellular distribution. Here, we determine the cryo-EM structure of human FERRY. It reveals ...The pentameric FERRY Rab5 effector complex is a molecular link between mRNA and early endosomes in mRNA intracellular distribution. Here, we determine the cryo-EM structure of human FERRY. It reveals a unique clamp-like architecture that bears no resemblance to any known structure of Rab effectors. A combination of functional and mutational studies reveals that while the Fy-2 C-terminal coiled-coil acts as binding region for Fy-1/3 and Rab5, both coiled-coils and Fy-5 concur to bind mRNA. Mutations causing truncations of Fy-2 in patients with neurological disorders impair Rab5 binding or FERRY complex assembly. Thus, Fy-2 serves as a binding hub connecting all five complex subunits and mediating the binding to mRNA and early endosomes via Rab5. Our study provides mechanistic insights into long-distance mRNA transport and demonstrates that the particular architecture of FERRY is closely linked to a previously undescribed mode of RNA binding, involving coiled-coil domains.
History
DepositionJan 29, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-7nd2
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7nd2
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12273.png

Downloads & links

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Map

FileDownload / File: emd_12273.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the FERRY complex core
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.011 / Movie #1: 0.01
Minimum - Maximum-0.025887525 - 0.04872177
Average (Standard dev.)0.00011392889 (±0.0011070273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 285.12003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z285.120285.120285.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-0.0260.0490.000

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Supplemental data

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Additional map: L-AFTER filtered Cryo-EM density map of the FERRY complex core

Fileemd_12273_additional_1.map
AnnotationL-AFTER filtered Cryo-EM density map of the FERRY complex core
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human FERRY (Five-subunit Early endosome RNA and Ribosome interme...

EntireName: Human FERRY (Five-subunit Early endosome RNA and Ribosome intermediarY) complex
Components
  • Complex: Human FERRY (Five-subunit Early endosome RNA and Ribosome intermediarY) complex
    • Complex: Protein phosphatase 1 regulatory subunit 21
      • Protein or peptide: Protein phosphatase 1 regulatory subunit 21
    • Complex: Quinone oxidoreductase-like protein 1
      • Protein or peptide: Quinone oxidoreductase-like protein 1
    • Complex: Glutamine amidotransferase-like class 1 domain-containing protein 1
      • Protein or peptide: Glutamine amidotransferase-like class 1 domain-containing protein 1

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Supramolecule #1: Human FERRY (Five-subunit Early endosome RNA and Ribosome interme...

SupramoleculeName: Human FERRY (Five-subunit Early endosome RNA and Ribosome intermediarY) complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Protein phosphatase 1 regulatory subunit 21

SupramoleculeName: Protein phosphatase 1 regulatory subunit 21 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Quinone oxidoreductase-like protein 1

SupramoleculeName: Quinone oxidoreductase-like protein 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Glutamine amidotransferase-like class 1 domain-containing protein 1

SupramoleculeName: Glutamine amidotransferase-like class 1 domain-containing protein 1
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein phosphatase 1 regulatory subunit 21

MacromoleculeName: Protein phosphatase 1 regulatory subunit 21 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.782836 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAAMASAEL QGKYQKLAQE YSKLRAQNQV LKKGVVDEQA NSAALKEQLK MKDQSLRKLQ QEMDSLTFRN LQLAKRVELL QDELALSEP RGKKNKKSGE SSSQLSQEQK SVFDEDLQKK IEENERLHIQ FFEADEQHKH VEAELRSRLA TLETEAAQHQ A VVDGLTRK ...String:
MAAAMASAEL QGKYQKLAQE YSKLRAQNQV LKKGVVDEQA NSAALKEQLK MKDQSLRKLQ QEMDSLTFRN LQLAKRVELL QDELALSEP RGKKNKKSGE SSSQLSQEQK SVFDEDLQKK IEENERLHIQ FFEADEQHKH VEAELRSRLA TLETEAAQHQ A VVDGLTRK YMETIEKLQN DKAKLEVKSQ TLEKEAKECR LRTEECQLQL KTLHEDLSGR LEESLSIINE KVPFNDTKYS QY NALNVPL HNRRHQLKMR DIAGQALAFV QDLVTALLNF HTYTEQRIQI FPVDSAIDTI SPLNQKFSQY LHENASYVRP LEE GMLHLF ESITEDTVTV LETTVKLKTF SEHLTSYICF LRKILPYQLK SLEEECESSL CTSALRARNL ELSQDMKKMT AVFE KLQTY IALLALPSTE PDGLLRTNYS SVLTNVGAAL HGFHDVMKDI SKHYSQKAAI EHELPTATQK LITTNDCILS SVVAL TNGA GKIASFFSNN LDYFIASLSY GPKAASGFIS PLSAECMLQY KKKAAAYMKS LRKPLLESVP YEEALANRRI LLSSTE SRE GLAQQVQQSL EKISKLEQEK EHWMLEAQLA KIKLEKENQR IADKLKNTGS AQLVGLAQEN AAVSNTAGQD EATAKAV LE PIQSTSLIGT LTRTSDSEVP DVESREDLIK NHYMARIVEL TSQLQLADSK SVHFYAECRA LSKRLALAEK SKEALTEE M KLASQNISRL QDELTTTKRS YEDQLSMMSD HLCSMNETLS KQREEIDTLK MSSKGNSKKN KSR

UniProtKB: Protein phosphatase 1 regulatory subunit 21

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Macromolecule #2: Quinone oxidoreductase-like protein 1

MacromoleculeName: Quinone oxidoreductase-like protein 1 / type: protein_or_peptide / ID: 2 / Details: N-terminal His-6 tag / Number of copies: 2 / Enantiomer: LEVO / EC number: Oxidoreductases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.661414 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSHHHHHHKG LYFQQSSTDE EITFVFQEKE DLPVTEDNFV KLQVKACALS QINTKLLAEM KMKKDLFPVG REIAGIVLDV GSKVSFFQP DDEVVGILPL DSEDPGLCEV VRVHEHYLVH KPEKVTWTEA AGSIRDGVRA YTALHYLSHL SPGKSVLIMD G ASAFGTIA ...String:
MSHHHHHHKG LYFQQSSTDE EITFVFQEKE DLPVTEDNFV KLQVKACALS QINTKLLAEM KMKKDLFPVG REIAGIVLDV GSKVSFFQP DDEVVGILPL DSEDPGLCEV VRVHEHYLVH KPEKVTWTEA AGSIRDGVRA YTALHYLSHL SPGKSVLIMD G ASAFGTIA IQLAHHRGAK VISTACSLED KQCLERFRPP IARVIDVSNG KVHVAESCLE ETGGLGVDIV LDAGVRLYSK DD EPAVKLQ LLPHKHDIIT LLGVGGHWVT TEENLQLDPP DSHCLFLKGA TLAFLNDEVW NLSNVQQGKY LCILKDVMEK LST GVFRPQ LDEPIPLYEA KVSMEAVQKN QGRKKQVVQF

UniProtKB: Quinone oxidoreductase-like protein 1

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Macromolecule #3: Glutamine amidotransferase-like class 1 domain-containing protein 1

MacromoleculeName: Glutamine amidotransferase-like class 1 domain-containing protein 1
type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.237488 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSHHHHHHAS ERLPNRPACL LVASGAAEGV SAQSFLHCFT MASTAFNLQV ATPGGKAMEF VDVTESNARW VQDFRLKAYA SPAKLESID GARYHALLIP SCPGALTDLA SSGSLARILQ HFHSESKPIC AVGHGVAALC CATNEDRSWV FDSYSLTGPS V CELVRAPG ...String:
MSHHHHHHAS ERLPNRPACL LVASGAAEGV SAQSFLHCFT MASTAFNLQV ATPGGKAMEF VDVTESNARW VQDFRLKAYA SPAKLESID GARYHALLIP SCPGALTDLA SSGSLARILQ HFHSESKPIC AVGHGVAALC CATNEDRSWV FDSYSLTGPS V CELVRAPG FARLPLVVED FVKDSGACFS ASEPDAVHVV LDRHLVTGQN ASSTVPAVQN LLFLCGSRK

UniProtKB: Glutamine amidotransferase-like class 1 domain-containing protein 1

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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

Concentration0.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormula
20.0 mMHEPES
250.0 mMNaCl
20.0 mMKCl
20.0 mMMgCl2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK III / Details: 3s blotting time.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1879 / Average exposure time: 15.0 sec. / Average electron dose: 75.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.8000000000000003 µm / Calibrated defocus min: 1.6 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1800000
Startup modelType of model: OTHER
Details: Ab initio 3D structure obtained with RVIPER of the SPHIRE software package
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 18300
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE
Final 3D classificationSoftware - Name: SPHIRE / Details: ISAC classification in SPHIRE

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Atomic model buiding 1

DetailsTo build the model for the (CRYZL1)2(PPP1r21)2(GATD1)4 core of the FERRY complex, the obtained crystal structures of CRYZL1 and GATD1 were initially fitted into the corresponding density using the rigid body fitting tool in Chimera. trRosetta, a de novo protein structure prediction algorithm that is based on direct energy minimization with restrained Rosetta, was used to obtain initial models for PPP1r21. The predicted model for the 6-helix bundle domain, containing residues 246 to 498, that matched our experimental density best was subsequently fitted similar as CRYZL1 and GATD1 using rigid body fit. Manual model building for the regions N- and C-terminal 6-helix bundle, which comprise residues 218 to 245 and 499 to 552, respectively, was further guided by secondary structure predictions of individual trRosetta runs for these regions, that include the vertical helix as well as the beginning of the two terminal coiled-coils of PPP1r21. With the resulting combined model, containing residues 2 to 349, 218 to 552 and 8 to 217 of CRYZL1, PPP1r21 and GATD1, respectively, a restrained refinement in PHENIX was performed. In the next step, the model was further refined using a combination of manual building in COOT and real-space refinement in PHENIX.
Output model

PDB-7nd2:
Cryo-EM structure of the human FERRY complex

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