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- EMDB-19334: SPNS2 in complex with homo Di-Gluebody GbD12 - SPNS2 local refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-19334
TitleSPNS2 in complex with homo Di-Gluebody GbD12 - SPNS2 local refinement
Map dataEMhancer: SPNS2 in complex with Di-Gluebody GbD12- SPNS2 local refinement
Sample
  • Complex: Local refinement of the SPNS2 part of SPNS2 homodimer assembled by GbD12 homo Di-Gluebody
    • Protein or peptide: Sphingosine-1-phosphate transporter SPNS2
  • Ligand: DODECYL-BETA-D-MALTOSIDE
KeywordsSPNS2 / Di-Gluebody / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of eye pigmentation / regulation of humoral immune response / regulation of T cell migration / sphingolipid transporter activity / lymphocyte migration / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / sphingosine-1-phosphate receptor signaling pathway / lipid transport / T cell homeostasis ...regulation of eye pigmentation / regulation of humoral immune response / regulation of T cell migration / sphingolipid transporter activity / lymphocyte migration / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / sphingosine-1-phosphate receptor signaling pathway / lipid transport / T cell homeostasis / B cell homeostasis / transmembrane transporter activity / lymph node development / sensory perception of sound / bone development / endosome membrane / membrane / plasma membrane
Similarity search - Function
Protein spinster-like / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Sphingosine-1-phosphate transporter SPNS2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsYi G / Ye M / Mamalis D / Sauer DB / von Delft F / Davis BG / Gilbert RJC
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: To Be Published
Title: Di-Gluebodies: Rigid modular nanobody protein assemblies enabling simultaneous determination of high-resolution cryo-EM structures
Authors: Yi G / Mamalis D / Ye M / Carrique L / Fairhead M / Li H / Duerr K / Zhang P / Sauer DB / von Delft F / Davis BG / Gilbert RJC
History
DepositionJan 2, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19334.png

Downloads & links

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Map

FileDownload / File: emd_19334.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEMhancer: SPNS2 in complex with Di-Gluebody GbD12- SPNS2 local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 331.6 Å		0.83 Å/pix.
x 400 pix.
= 331.6 Å		0.83 Å/pix.
x 400 pix.
= 331.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.07863395 - 2.6478407
Average (Standard dev.)0.00043901685 (±0.010571596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19334_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: SPNS2 in complex with Di-Gluebody GbD12 - SPNS2 local refinement

Fileemd_19334_additional_1.map
AnnotationSPNS2 in complex with Di-Gluebody GbD12 - SPNS2 local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_19334_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_19334_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Local refinement of the SPNS2 part of SPNS2 homodimer assembled b...

EntireName: Local refinement of the SPNS2 part of SPNS2 homodimer assembled by GbD12 homo Di-Gluebody
Components
  • Complex: Local refinement of the SPNS2 part of SPNS2 homodimer assembled by GbD12 homo Di-Gluebody
    • Protein or peptide: Sphingosine-1-phosphate transporter SPNS2
  • Ligand: DODECYL-BETA-D-MALTOSIDE

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Supramolecule #1: Local refinement of the SPNS2 part of SPNS2 homodimer assembled b...

SupramoleculeName: Local refinement of the SPNS2 part of SPNS2 homodimer assembled by GbD12 homo Di-Gluebody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 146 KDa

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Macromolecule #1: Sphingosine-1-phosphate transporter SPNS2

MacromoleculeName: Sphingosine-1-phosphate transporter SPNS2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.962211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MMCLECASAA AGGAEEEEAD AERRRRRRGA QRGAGGSGCC GARGAGGAGV SAAGDEVQTL SGSVRRAPTG PPGTPGTPGC AATAKGPGA QQPKPASLGR GRGAAAAILS LGNVLNYLDR YTVAGVLLDI QQHFGVKDRG AGLLQSVFIC SFMVAAPIFG Y LGDRFNRK ...String:
MMCLECASAA AGGAEEEEAD AERRRRRRGA QRGAGGSGCC GARGAGGAGV SAAGDEVQTL SGSVRRAPTG PPGTPGTPGC AATAKGPGA QQPKPASLGR GRGAAAAILS LGNVLNYLDR YTVAGVLLDI QQHFGVKDRG AGLLQSVFIC SFMVAAPIFG Y LGDRFNRK VILSCGIFFW SAVTFSSSFI PQQYFWLLVL SRGLVGIGEA SYSTIAPTII GDLFTKNTRT LMLSVFYFAI PL GSGLGYI TGSSVKQAAG DWHWALRVSP VLGMITGTLI LILVPATKRG HADQLGDQLK ARTSWLRDMK ALIRNRSYVF SSL ATSAVS FATGALGMWI PLYLHRAQVV QKTAETCNSP PCGAKDSLIF GAITCFTGFL GVVTGAGATR WCRLKTQRAD PLVC AVGML GSAIFICLIF VAAKSSIVGA YICIFVGETL LFSNWAITAD ILMYVVIPTR RATAVALQSF TSHLLGDAGS PYLIG FISD LIRQSTKDSP LWEFLSLGYA LMLCPFVVVL GGMFFLATAL FFVSDRARAE QQVNQLAMPP ASVKVAENLY FQ

UniProtKB: Sphingosine-1-phosphate transporter SPNS2

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Macromolecule #2: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 2 / Number of copies: 1 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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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

Concentration9.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
0.025 %C24H46O11DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 12013 / Average electron dose: 50.0 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 871094
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio reconstruction in cryoSPARC
Final reconstructionNumber classes used: 6 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 570074
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0) / Details: Non-uniform refinement in cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0) / Details: Local refinement in cryoSPARC
Final 3D classificationNumber classes: 10 / Software - Name: cryoSPARC (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8qv6


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Overall B value: 100.8
Output model

PDB-8rl8:
SPNS2 in complex with homo Di-Gluebody GbD12 - SPNS2 local refinement

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