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- EMDB-23361: apo SERT reconstituted in lipid nanodisc in KCl -

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Basic information

Entry
Database: EMDB / ID: EMD-23361
Titleapo SERT reconstituted in lipid nanodisc in KCl
Map datasharpened map
Sample
  • Complex: apo state of human serotonin transporter in complex with 15B8 Fab in KCl
    • Protein or peptide: Sodium-dependent serotonin transporter
    • Protein or peptide: variable domain of 15B8 antibody Fab heavy chain
    • Protein or peptide: variable domain of 15B8 antibody Fab light chain
  • Ligand: CHLORIDE ION
  • Ligand: HEXADECANE
  • Ligand: HEPTANE
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: PENTANE
Keywordsserotonin / human serotonin transporter / transport / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / Serotonin clearance from the synaptic cleft / positive regulation of serotonin secretion / serotonergic synapse / negative regulation of synaptic transmission, dopaminergic / cocaine binding / serotonin:sodium:chloride symporter activity / cellular response to cGMP / enteric nervous system development ...negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / Serotonin clearance from the synaptic cleft / positive regulation of serotonin secretion / serotonergic synapse / negative regulation of synaptic transmission, dopaminergic / cocaine binding / serotonin:sodium:chloride symporter activity / cellular response to cGMP / enteric nervous system development / sodium ion binding / negative regulation of organ growth / neurotransmitter transmembrane transporter activity / serotonin uptake / vasoconstriction / monoamine transmembrane transporter activity / monoamine transport / serotonin binding / brain morphogenesis / antiporter activity / syntaxin-1 binding / male mating behavior / neurotransmitter transport / negative regulation of neuron differentiation / nitric-oxide synthase binding / amino acid transport / conditioned place preference / membrane depolarization / monoatomic cation channel activity / behavioral response to cocaine / positive regulation of cell cycle / cellular response to retinoic acid / response to nutrient / sodium ion transmembrane transport / endomembrane system / circadian rhythm / response to toxic substance / platelet aggregation / memory / integrin binding / actin filament binding / response to estradiol / presynaptic membrane / postsynaptic membrane / response to hypoxia / neuron projection / endosome membrane / membrane raft / response to xenobiotic stimulus / focal adhesion / synapse / positive regulation of gene expression / identical protein binding / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter, serotonin, N-terminal / Serotonin (5-HT) neurotransmitter transporter, N-terminus / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
Sodium-dependent serotonin transporter
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYang D / Gouaux E
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH) United States
CitationJournal: Sci Adv / Year: 2021
Title: Illumination of serotonin transporter mechanism and role of the allosteric site.
Authors: Yang D / Gouaux E
History
DepositionJan 26, 2021-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7li6
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23361.png

Downloads & links

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Map

FileDownload / File: emd_23361.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 400 pix.
= 264.4 Å		0.66 Å/pix.
x 400 pix.
= 264.4 Å		0.66 Å/pix.
x 400 pix.
= 264.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.661 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.5454338 - 2.2662814
Average (Standard dev.)0.00089520216 (±0.040203996)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 264.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6610.6610.661
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z264.400264.400264.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.5452.2660.001

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Supplemental data

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Additional map: unsharpened map

Fileemd_23361_additional_1.map
Annotationunsharpened 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 : apo state of human serotonin transporter in complex with 15B8 Fab...

EntireName: apo state of human serotonin transporter in complex with 15B8 Fab in KCl
Components
  • Complex: apo state of human serotonin transporter in complex with 15B8 Fab in KCl
    • Protein or peptide: Sodium-dependent serotonin transporter
    • Protein or peptide: variable domain of 15B8 antibody Fab heavy chain
    • Protein or peptide: variable domain of 15B8 antibody Fab light chain
  • Ligand: CHLORIDE ION
  • Ligand: HEXADECANE
  • Ligand: HEPTANE
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: PENTANE

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Supramolecule #1: apo state of human serotonin transporter in complex with 15B8 Fab...

SupramoleculeName: apo state of human serotonin transporter in complex with 15B8 Fab in KCl
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium-dependent serotonin transporter

MacromoleculeName: Sodium-dependent serotonin transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.875957 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RETWGKKVDF LLSVIGYAVD LGNVWRFPYI CYQNGGGAFL LPYTIMAIFG GIPLFYMELA LGQYHRNGCI SIWRKICPIF KGIGYAICI IAFYIASYYN TIMAWALYYL ISSFTDQLPW TSCKNSWNTG NCTNYFSEDN ITWTLHSTSP AEEFYTRHVL Q IHRSKGLQ ...String:
RETWGKKVDF LLSVIGYAVD LGNVWRFPYI CYQNGGGAFL LPYTIMAIFG GIPLFYMELA LGQYHRNGCI SIWRKICPIF KGIGYAICI IAFYIASYYN TIMAWALYYL ISSFTDQLPW TSCKNSWNTG NCTNYFSEDN ITWTLHSTSP AEEFYTRHVL Q IHRSKGLQ DLGGISWQLA LCIMLIFTVI YFSIWKGVKT SGKVVWVTAT FPYIILSVLL VRGATLPGAW RGVLFYLKPN WQ KLLETGV WIDAAAQIFF SLGPGFGVLL AFASYNKFNN NCYQDALVTS VVNCMTSFVS GFVIFTVLGY MAEMRNEDVS EVA KDAGPS LLFITYAEAI ANMPASTFFA IIFFLMLITL GLDSTFAGLE GVITAVLDEF PHVWAKRRER FVLAVVITCF FGSL VTLTF GGAYVVKLLE EYATGPAVLT VALIEAVAVS WFYGITQFCR DVKEMLGFSP GWFWRICWVA ISPLFLLFII CSFLM SPPQ LRLFQYNYPY WSIILGYCIG TSSFICIPTY IAYRLIITPG TFKERIIKSI TPETP

UniProtKB: Sodium-dependent serotonin transporter

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Macromolecule #2: variable domain of 15B8 antibody Fab heavy chain

MacromoleculeName: variable domain of 15B8 antibody Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.980533 KDa
SequenceString:
QVQLQQSGPE LVKLGASVRI SCKASGYRFS YSWMNWVKQR PGKGLEWIGR IYPGDGDTKY SGKFKGKATL TADKSSSTVY MQLSSLTSE DSAVYFCARS AYGSEGFAMD YWGQGTSVT

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Macromolecule #3: variable domain of 15B8 antibody Fab light chain

MacromoleculeName: variable domain of 15B8 antibody Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.776065 KDa
SequenceString:
DIVLTQSPAS LAVSLGQRAT ISCRASESVD NYGISFLNWF QQKPGQPPKL LIYAASNQGS GVPARFSGSG SGTYFSLNIH PMEEDDTAV YFCQQTKGVS WTFGGGTKVE I

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Macromolecule #5: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #6: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 6 / Number of copies: 1 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Macromolecule #7: HEPTANE

MacromoleculeName: HEPTANE / type: ligand / ID: 7 / Number of copies: 9 / Formula: HP6
Molecular weightTheoretical: 100.202 Da
Chemical component information

ChemComp-HP6:
HEPTANE

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Macromolecule #8: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 8 / Number of copies: 6 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #9: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 9 / Number of copies: 3 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #10: PENTANE

MacromoleculeName: PENTANE / type: ligand / ID: 10 / Number of copies: 4 / Formula: LNK
Molecular weightTheoretical: 72.149 Da
Chemical component information

ChemComp-LNK:
PENTANE

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 707210
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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