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- EMDB-44763: Cryo-EM structure of human heteromeric Glycine Receptor alpha3S34... -

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Basic information

Entry
Database: EMDB / ID: EMD-44763
TitleCryo-EM structure of human heteromeric Glycine Receptor alpha3S346E-beta in presence of glycine and 2,6-DTBP
Map datastructure of human heteromeric Glycine Receptor alpha3S346E-beta in presence of glycine and 2,6-DTBP
Sample
  • Complex: heteromeric glycine receptor alpha3S346E and beta with glycine in presence of glycine and 2,6-DTBP
    • Protein or peptide: Glycine receptor subunit alpha-3
    • Protein or peptide: Glycine receptor subunit beta,Green fluorescent protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLYCINE
Keywordsglycine receptor subunit alpha-3 / glycine receptor subunit beta / Green fluorescent protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


synaptic transmission, glycinergic / glycine-gated chloride ion channel activity / acrosome reaction / glycine-gated chloride channel complex / gamma-aminobutyric acid receptor clustering / Neurotransmitter receptors and postsynaptic signal transmission / postsynaptic specialization / extracellularly glycine-gated ion channel activity / righting reflex / extracellularly glycine-gated chloride channel activity ...synaptic transmission, glycinergic / glycine-gated chloride ion channel activity / acrosome reaction / glycine-gated chloride channel complex / gamma-aminobutyric acid receptor clustering / Neurotransmitter receptors and postsynaptic signal transmission / postsynaptic specialization / extracellularly glycine-gated ion channel activity / righting reflex / extracellularly glycine-gated chloride channel activity / glycinergic synapse / adult walking behavior / glycine binding / startle response / neuropeptide signaling pathway / monoatomic ion transport / visual perception / chloride transmembrane transport / bioluminescence / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / generation of precursor metabolites and energy / protein homooligomerization / transmembrane signaling receptor activity / nervous system development / chemical synaptic transmission / perikaryon / postsynaptic membrane / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / Glycine receptor alpha3 / Glycine receptor beta / : / Glycine receptor alpha / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. ...: / Glycine receptor alpha3 / Glycine receptor beta / : / Glycine receptor alpha / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Green fluorescent protein, GFP / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Glycine receptor subunit alpha-3 / Glycine receptor subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu X / Wang W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R35GM146860 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of human heteromeric Glycine Receptor alpha3S346E-beta in presence of glycine and 2,6-DTBP
Authors: Liu X / Wang W
History
DepositionMay 7, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44763.png

Downloads & links

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Map

FileDownload / File: emd_44763.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of human heteromeric Glycine Receptor alpha3S346E-beta in presence of glycine and 2,6-DTBP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.36
Minimum - Maximum-2.6382606 - 3.1733317
Average (Standard dev.)0.009536479 (±0.105293795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_44763_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_44763_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : heteromeric glycine receptor alpha3S346E and beta with glycine in...

EntireName: heteromeric glycine receptor alpha3S346E and beta with glycine in presence of glycine and 2,6-DTBP
Components
  • Complex: heteromeric glycine receptor alpha3S346E and beta with glycine in presence of glycine and 2,6-DTBP
    • Protein or peptide: Glycine receptor subunit alpha-3
    • Protein or peptide: Glycine receptor subunit beta,Green fluorescent protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLYCINE

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Supramolecule #1: heteromeric glycine receptor alpha3S346E and beta with glycine in...

SupramoleculeName: heteromeric glycine receptor alpha3S346E and beta with glycine in presence of glycine and 2,6-DTBP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 260 KDa

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Macromolecule #1: Glycine receptor subunit alpha-3

MacromoleculeName: Glycine receptor subunit alpha-3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.978555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ARSRSAPMSP SDFLDKLMGR TSGYDARIRP NFKGPPVNVT CNIFINSFGS IAETTMDYRV NIFLRQKWND PRLAYSEYPD DSLDLDPSM LDSIWKPDLF FANEKGANFH EVTTDNKLLR IFKNGNVLYS IRLTLTLSCP MDLKNFPMDV QTCIMQLESF G YTMNDLIF ...String:
ARSRSAPMSP SDFLDKLMGR TSGYDARIRP NFKGPPVNVT CNIFINSFGS IAETTMDYRV NIFLRQKWND PRLAYSEYPD DSLDLDPSM LDSIWKPDLF FANEKGANFH EVTTDNKLLR IFKNGNVLYS IRLTLTLSCP MDLKNFPMDV QTCIMQLESF G YTMNDLIF EWQDEAPVQV AEGLTLPQFL LKEEKDLRYC TKHYNTGKFT CIEVRFHLER QMGYYLIQMY IPSLLIVILS WV SFWINMD AAPARVALGI TTVLTMTTQS SGSRASLPKV SYVKAIDIWM AVCLLFVFSA LLEYAAVNFV SRQHKELLRF RRK RKNKTE AFDMDDEVRE ERFSFTAYGM GPCLQAKDGM TPKGPNHPVQ VMPKSPDEMR KVFIDRAKKI DTISRACFPL AFLI FNIFY WVIYKILRHE DIHQQQD

UniProtKB: Glycine receptor subunit alpha-3

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Macromolecule #2: Glycine receptor subunit beta,Green fluorescent protein

MacromoleculeName: Glycine receptor subunit beta,Green fluorescent protein
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.584531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KSSKKGKGKK KQYLCPSQQS AEDLARVPAN STSNILNRLL VSYDPRIRPN FKGIPVDVVV NIFINSFGSI QETTMDYRVN IFLRQKWND PRLKLPSDFR GSDALTVDPT MYKCLWKPDL FFANEKSANF HDVTQENILL FIFRDGDVLV SMRLSITLSC P LDLTLFPM ...String:
KSSKKGKGKK KQYLCPSQQS AEDLARVPAN STSNILNRLL VSYDPRIRPN FKGIPVDVVV NIFINSFGSI QETTMDYRVN IFLRQKWND PRLKLPSDFR GSDALTVDPT MYKCLWKPDL FFANEKSANF HDVTQENILL FIFRDGDVLV SMRLSITLSC P LDLTLFPM DTQRCKMQLE SFGYTTDDLR FIWQSGDPVQ LEKIALPQFD IKKEDIEYGN CTKYYKGTGY YTCVEVIFTL RR QVGFYMM GVYAPTLLIV VLSWLSFWIN PDASAARVPL GIFSVLSLAS ECTTLAAELP KVSYVKALDV WLIACLLFGF ASL VEYAVV QVMLNGGSSA AAVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVT TFSYG VQCFSRYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD TLVNRIELKG IDFKEDGNIL GHKLE YNYN SHNVYIMADK QKNGIKVNFK IRHNIEDGSV QLADHYQQNT PIGDGPVLLP DNHYLSTQSA LSKDPNEKRD HMVLLE FVT AAGITHGMDE LYKSGSGSGV GETRCKKVCT SKSDLRSNDF SIVGSLPRDF ELSNYDCYGK PIEVNNGLGK SQAKNNK KP PPAKPVIPTA AKRIDLYARA LFPFCFLFFN VIYWSIYL

UniProtKB: Glycine receptor subunit beta, Green fluorescent protein, Glycine receptor subunit beta

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 4 / Number of copies: 3 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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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

Concentration6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
20.0 mMTris-HClTris-HCl
0.06 %(w/v)digitonindigitonin
GridModel: Quantifoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 69.6 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
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN
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: PDB ENTRY
PDB model - PDB ID:

8dn2

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22755
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

8dn2


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-9bp7:
Cryo-EM structure of human heteromeric Glycine Receptor alpha3S346E-beta in presence of glycine and 2,6-DTBP

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