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- EMDB-60987: CryoEM structure of a transmembrane protein -

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Basic information

Entry
Database: EMDB / ID: EMD-60987
TitleCryoEM structure of a transmembrane protein
Map dataPost-processing cryoEM map from cryoSPARC
Sample
  • Complex: Human full-length SERT complexed with ketamine
    • Protein or peptide: x 1 types
  • Ligand: x 10 types
KeywordsSERT / ketamine / antidepressant / TRANSPORT 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 / negative regulation of organ growth / sodium ion binding / neurotransmitter transmembrane transporter activity / serotonin uptake / vasoconstriction / monoamine transmembrane transporter activity / monoamine transport / serotonin binding / brain morphogenesis / syntaxin-1 binding / antiporter activity / negative regulation of neuron differentiation / male mating behavior / neurotransmitter transport / 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 / endomembrane system / sodium ion transmembrane transport / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsNing Y / Ge J
Funding support1 items
OrganizationGrant numberCountry
Other governmentLG-QS-202203-05; 22PJ1410300
CitationJournal: To Be Published
Title: CryoEM structure of a transmembrane protein
Authors: Ning Y / Ge J
History
DepositionJul 30, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60987.png

Downloads & links

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Map

FileDownload / File: emd_60987.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processing cryoEM map from cryoSPARC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 253.2 Å		1.06 Å/pix.
x 240 pix.
= 253.2 Å		1.06 Å/pix.
x 240 pix.
= 253.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-3.4023883 - 3.9367561
Average (Standard dev.)0.0013365451 (±0.06596044)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 253.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60987_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60987_half_map_2.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 : Human full-length SERT complexed with ketamine

EntireName: Human full-length SERT complexed with ketamine
Components
  • Complex: Human full-length SERT complexed with ketamine
    • Protein or peptide: Sodium-dependent serotonin transporter
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one
  • Ligand: nonane
  • Ligand: DODECANE
  • Ligand: DECANE
  • Ligand: N-OCTANE

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Supramolecule #1: Human full-length SERT complexed with ketamine

SupramoleculeName: Human full-length SERT complexed with ketamine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 71.101172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METTPLNSQK QLSACEDGED CQENGVLQKV VPTPGDKVES GQISNGYSAV PSPGAGDDTR HSIPATTTTL VAELHQGERE TWGKKVDFL LSVIGYAVDL GNVWRFPYIC YQNGGGAFLL PYTIMAIFGG IPLFYMELAL GQYHRNGCIS IWRKICPIFK G IGYAICII ...String:
METTPLNSQK QLSACEDGED CQENGVLQKV VPTPGDKVES GQISNGYSAV PSPGAGDDTR HSIPATTTTL VAELHQGERE TWGKKVDFL LSVIGYAVDL GNVWRFPYIC YQNGGGAFLL PYTIMAIFGG IPLFYMELAL GQYHRNGCIS IWRKICPIFK G IGYAICII AFYIASYYNT IMAWALYYLI SSFTDQLPWT SCKNSWNTGN CTNYFSEDNI TWTLHSTSPA EEFYTRHVLQ IH RSKGLQD LGGISWQLAL CIMLIFTVIY FSIWKGVKTS GKVVWVTATF PYIILSVLLV RGATLPGAWR GVLFYLKPNW QKL LETGVW IDAAAQIFFS LGPGFGVLLA FASYNKFNNN CYQDALVTSV VNCMTSFVSG FVIFTVLGYM AEMRNEDVSE VAKD AGPSL LFITYAEAIA NMPASTFFAI IFFLMLITLG LDSTFAGLEG VITAVLDEFP HVWAKRRERF VLAVVITCFF GSLVT LTFG GAYVVKLLEE YATGPAVLTV ALIEAVAVSW FYGITQFCRD VKEMLGFSPG WFWRICWVAI SPLFLLFIIC SFLMSP PQL RLFQYNYPYW SIILGYCIGT SSFICIPTYI AYRLIITPGT FKERIIKSIT PETPTEIPCG DIRLNAVLEV LFQ

UniProtKB: Sodium-dependent serotonin transporter

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Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #5: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 5 / 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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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one

MacromoleculeName: (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one
type: ligand / ID: 7 / Number of copies: 1 / Formula: JC9
Molecular weightTheoretical: 237.725 Da
Chemical component information

ChemComp-JC9:
(2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one

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Macromolecule #8: nonane

MacromoleculeName: nonane / type: ligand / ID: 8 / Number of copies: 5 / Formula: DD9
Molecular weightTheoretical: 128.255 Da
Chemical component information

ChemComp-DD9:
nonane

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Macromolecule #9: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 9 / Number of copies: 6 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #10: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 10 / Number of copies: 2 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #11: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 11 / Number of copies: 5 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

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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: 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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 557141
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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