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- EMDB-8315: Structure of the STRA6 receptor for retinol uptake in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-8315
TitleStructure of the STRA6 receptor for retinol uptake in complex with calmodulin
Map dataReconstruction of STRA6/CaM complex
Sample
  • Complex: Complex of zebrafish (D. rerio) STRA6 with copurified calmodulin reconstituted in amphipol A8-35
    • Protein or peptide: Calmodulin
    • Protein or peptide: STRA6Vitamin A receptor
  • Ligand: CALCIUM IONCalcium
  • Ligand: CHOLESTEROL
KeywordsVitamin A / retinol / STRA6 / membrane / MEMBRANE PROTEIN-CALCIUM BINDING PROTEIN complex
Function / homology
Function and homology information


vitamin A import into cell / The canonical retinoid cycle in rods (twilight vision) / retinol transport / retinol transmembrane transporter activity / chordate embryonic development / retinal binding / retinol binding / plasma membrane => GO:0005886 / calcium-mediated signaling / signaling receptor activity ...vitamin A import into cell / The canonical retinoid cycle in rods (twilight vision) / retinol transport / retinol transmembrane transporter activity / chordate embryonic development / retinal binding / retinol binding / plasma membrane => GO:0005886 / calcium-mediated signaling / signaling receptor activity / molecular adaptor activity / calmodulin binding / calcium ion binding / identical protein binding / plasma membrane
Similarity search - Function
Receptor for retinol uptake STRA6 / Retinol binding protein receptor / Calmodulin / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin / Receptor for retinol uptake stra6 / Receptor for retinol uptake stra6
Similarity search - Component
Biological speciesDanio rerio (zebrafish) / Spodoptera frugiperda (fall armyworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsClarke OB / Chen Y
CitationJournal: Science / Year: 2016
Title: Structure of the STRA6 receptor for retinol uptake.
Authors: Yunting Chen / Oliver B Clarke / Jonathan Kim / Sean Stowe / Youn-Kyung Kim / Zahra Assur / Michael Cavalier / Raquel Godoy-Ruiz / Desiree C von Alpen / Chiara Manzini / William S Blaner / ...Authors: Yunting Chen / Oliver B Clarke / Jonathan Kim / Sean Stowe / Youn-Kyung Kim / Zahra Assur / Michael Cavalier / Raquel Godoy-Ruiz / Desiree C von Alpen / Chiara Manzini / William S Blaner / Joachim Frank / Loredana Quadro / David J Weber / Lawrence Shapiro / Wayne A Hendrickson / Filippo Mancia /
Abstract: Vitamin A homeostasis is critical to normal cellular function. Retinol-binding protein (RBP) is the sole specific carrier in the bloodstream for hydrophobic retinol, the main form in which vitamin A ...Vitamin A homeostasis is critical to normal cellular function. Retinol-binding protein (RBP) is the sole specific carrier in the bloodstream for hydrophobic retinol, the main form in which vitamin A is transported. The integral membrane receptor STRA6 mediates cellular uptake of vitamin A by recognizing RBP-retinol to trigger release and internalization of retinol. We present the structure of zebrafish STRA6 determined to 3.9-angstrom resolution by single-particle cryo-electron microscopy. STRA6 has one intramembrane and nine transmembrane helices in an intricate dimeric assembly. Unexpectedly, calmodulin is bound tightly to STRA6 in a noncanonical arrangement. Residues involved with RBP binding map to an archlike structure that covers a deep lipophilic cleft. This cleft is open to the membrane, suggesting a possible mode for internalization of retinol through direct diffusion into the lipid bilayer.
History
DepositionAug 12, 2016-
Header (metadata) releaseAug 24, 2016-
Map releaseAug 24, 2016-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5sy1
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8315.png

Downloads & links

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Map

FileDownload / File: emd_8315.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of STRA6/CaM complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 200 pix.
= 251. Å		1.26 Å/pix.
x 200 pix.
= 251. Å		1.26 Å/pix.
x 200 pix.
= 251. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.255 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.07116239 - 0.12414183
Average (Standard dev.)0.00019051395 (±0.005057728)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 251.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2551.2551.255
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z251.000251.000251.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0710.1240.000

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Supplemental data

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Mask #1

Fileemd_8315_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Reconstruction of STRA6/CaM complex, half map 1

Fileemd_8315_half_map_1.map
AnnotationReconstruction of STRA6/CaM complex, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Reconstruction of STRA6/CaM complex, half map 2

Fileemd_8315_half_map_2.map
AnnotationReconstruction of STRA6/CaM complex, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of zebrafish (D. rerio) STRA6 with copurified calmodulin ...

EntireName: Complex of zebrafish (D. rerio) STRA6 with copurified calmodulin reconstituted in amphipol A8-35
Components
  • Complex: Complex of zebrafish (D. rerio) STRA6 with copurified calmodulin reconstituted in amphipol A8-35
    • Protein or peptide: Calmodulin
    • Protein or peptide: STRA6Vitamin A receptor
  • Ligand: CALCIUM IONCalcium
  • Ligand: CHOLESTEROL

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Supramolecule #1: Complex of zebrafish (D. rerio) STRA6 with copurified calmodulin ...

SupramoleculeName: Complex of zebrafish (D. rerio) STRA6 with copurified calmodulin reconstituted in amphipol A8-35
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Danio rerio (zebrafish)

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Macromolecule #1: Calmodulin

MacromoleculeName: Calmodulin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 16.82552 KDa
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG FISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVTMMTSK

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Macromolecule #2: STRA6

MacromoleculeName: STRA6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 75.551523 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAETVNNYD YSDWYENAAP TKAPVEVIPP CDPTADEGLF HICIAAISLV VMLVLAILAR RQKLSDNQRG LTGLLSPVNF LDHTQHKGL AVAVYGVLFC KLVGMVLSHH PLPFTKEVAN KEFWMILALL YYPTLYYPLL ACGTLHNKVG YVLGSLLSWT H FGILVWQK ...String:
MSAETVNNYD YSDWYENAAP TKAPVEVIPP CDPTADEGLF HICIAAISLV VMLVLAILAR RQKLSDNQRG LTGLLSPVNF LDHTQHKGL AVAVYGVLFC KLVGMVLSHH PLPFTKEVAN KEFWMILALL YYPTLYYPLL ACGTLHNKVG YVLGSLLSWT H FGILVWQK VDCPKTPQIY KYYALFGSLP QIACLAFLSF QYPLLLFKGL QNTETANASE DLSSSYYRDY VKKILKKKKP TK ISSSTSK PKLFDRLRDA VKSYIYTPED VFRFPLKLAI SVVVAFIALY QMALLLISGV LPTLHIVRRG VDENIAFLLA GFN IILSND RQEVVRIVVY YLWCVEICYV SAVTLSCLVN LLMLMRSMVL HRSNLKGLYR GDSLNVFNCH RSIRPSRPAL VCWM GFTSY QAAFLCLGMA IQTLVFFICI LFAVFLIIIP ILWGTNLMLF HIIGNLWPFW LTLVLAALIQ HVASRFLFIR KDGGT RDLN NRGSLFLLSY ILFLVNVMIG VVLGIWRVVI TALFNIVHLG RLDISLLNRN VEAFDPGYRC YSHYLKIEVS QSHPVM KAF CGLLLQSSGQ DGLSAQRIRD AEEGIQLVQQ EKKQNKVSNA KRARAHWQLL YTLVNNPSLV GSRKHFQCQS SESFING AL SRTSKEGSKK DGSVKEPNKE AESAAASN

UniProtKB: Receptor for retinol uptake stra6

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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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

Concentration0.6 mg/mL
BufferpH: 7
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 3 uL sample applied, 3-4 second blot time, 30 second wait time, blot force 3, grid blotted from both sides, plunged into liquid ethane (FEI VITROBOT MARK IV)..

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 100.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: An initial model was generated using e2initialmodel.py starting from 2D class averages created in Relion 1.3.
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 56615
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-5sy1:
Structure of the STRA6 receptor for retinol uptake in complex with calmodulin

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