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- EMDB-27384: Native serotonin transporter in complex with 15B8 Fab in the pres... -

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Basic information

Entry
Database: EMDB / ID: EMD-27384
TitleNative serotonin transporter in complex with 15B8 Fab in the presence of methamphetamine
Map datathe sharpened map
Sample
  • Complex: native serotonin transporter in complex with 15B8 Fab in the presence of methamphetamine
    • Protein or peptide: Transporter
    • Protein or peptide: 15B8 Fab heavy chain variable domain
    • Protein or peptide: 15B8 Fab light chain variable domain
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION
  • Ligand: (2S)-N-methyl-1-phenylpropan-2-amine
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
Keywordsmethamphetamine / SERT / native protein / pig brain / MEMBRANE PROTEIN
Function / homology
Function and homology information


serotonin:sodium:chloride symporter activity / antiporter activity / presynapse / endosome membrane / neuron projection / focal adhesion / metal ion 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
Biological speciesSus scrofa (pig) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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 Center for Research Resources (NIH/NCRR) United States
CitationJournal: To be published
Title: Native serotonin transporter in complex with 15B8 Fab in the presence of methamphetamine
Authors: Yang D / Gouaux E
History
DepositionJun 19, 2022-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27384.png

Downloads & links

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Map

FileDownload / File: emd_27384.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 299.16 Å		0.83 Å/pix.
x 360 pix.
= 299.16 Å		0.83 Å/pix.
x 360 pix.
= 299.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-1.2697263 - 1.6441079
Average (Standard dev.)0.000001282144 (±0.024771333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 299.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: the unsharpened map

Fileemd_27384_additional_1.map
Annotationthe unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_27384_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_27384_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 : native serotonin transporter in complex with 15B8 Fab in the pres...

EntireName: native serotonin transporter in complex with 15B8 Fab in the presence of methamphetamine
Components
  • Complex: native serotonin transporter in complex with 15B8 Fab in the presence of methamphetamine
    • Protein or peptide: Transporter
    • Protein or peptide: 15B8 Fab heavy chain variable domain
    • Protein or peptide: 15B8 Fab light chain variable domain
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION
  • Ligand: (2S)-N-methyl-1-phenylpropan-2-amine
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE

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Supramolecule #1: native serotonin transporter in complex with 15B8 Fab in the pres...

SupramoleculeName: native serotonin transporter in complex with 15B8 Fab in the presence of methamphetamine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Transporter

MacromoleculeName: Transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 60.778879 KDa
SequenceString: RETWGKKVDF LLSVIGYAVD LGNVWRFPYI CYQNGGGAFL LPYTIMAIFG GIPLFYMELA LGQYHRNGCI SIWRKICPIF KGIGFAICV IAFYIASYYN TIMAWALYYL ISSFTDQLPW TSCKNSWNTG NCTNYFSEDN VTWMLHSTSP AEEFYTRHVL Q IHRSKGLQ ...String:
RETWGKKVDF LLSVIGYAVD LGNVWRFPYI CYQNGGGAFL LPYTIMAIFG GIPLFYMELA LGQYHRNGCI SIWRKICPIF KGIGFAICV IAFYIASYYN TIMAWALYYL ISSFTDQLPW TSCKNSWNTG NCTNYFSEDN VTWMLHSTSP AEEFYTRHVL Q IHRSKGLQ DLGGISWQLA LCIMLIFTII YFSIWKGVKT SGKVVWVTAT FPYIILSILL VRGATLPGAW RGVLFYLKPN WQ KLLETGV WVDAAAQIFF SLGPGFGVLL AFASYNKFNN NCYQDALVTS VVNCMTSFVS GFVIFTVLGY MAEMRNEDVS EVA KDAGPS LLFITYAEAI ANMPASTFFA IIFFLMLITL GLDSTFAGLE GVITAVLDEF PHFWSKRREW LALGVVITCF LGSL ITLTF GGAYVVKLLE EFATGPAVLT VALIEAVAVF WFYGITQFCS DVKEMLGFSP GWFWRICWVA ISPLFLVFII CSFLM SPPQ LWLFQYNYPQ WSIILGYCIG TSSFICIPTY ITYRLIITPG TLKERIVKGI TPETP

UniProtKB: Transporter

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Macromolecule #2: 15B8 Fab heavy chain variable domain

MacromoleculeName: 15B8 Fab heavy chain variable domain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.980533 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString:
QVQLQQSGPE LVKLGASVRI SCKASGYRFS YSWMNWVKQR PGKGLEWIGR IYPGDGDTKY SGKFKGKATL TADKSSSTVY MQLSSLTSE DSAVYFCARS AYGSEGFAMD YWGQGTSVT

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Macromolecule #3: 15B8 Fab light chain variable domain

MacromoleculeName: 15B8 Fab light chain variable domain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.776065 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
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: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 6 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #7: (2S)-N-methyl-1-phenylpropan-2-amine

MacromoleculeName: (2S)-N-methyl-1-phenylpropan-2-amine / type: ligand / ID: 7 / Number of copies: 1 / Formula: B40
Molecular weightTheoretical: 149.233 Da
Chemical component information

ChemComp-B40:
(2S)-N-methyl-1-phenylpropan-2-amine

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Macromolecule #8: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 8 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #9: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 9 / 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

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: 60.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 271242
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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