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- EMDB-50277: CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R ... -

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Entry
Database: EMDB / ID: EMD-50277
TitleCryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 and Megabody38 in a closed state (StateC1)
Map data
Sample
  • Complex: CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 and Megabody38 in a closed state (StateC1)
    • Protein or peptide: x 6 types
  • Ligand: x 10 types
KeywordsGABA / Neurotransmission / Ternary complex / Inhibitory postsynapse / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of inhibitory synapse assembly / symmetric, GABA-ergic, inhibitory synapse / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / positive regulation of synaptic vesicle clustering / postsynaptic membrane assembly ...regulation of inhibitory synapse assembly / symmetric, GABA-ergic, inhibitory synapse / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / positive regulation of synaptic vesicle clustering / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / cell-cell junction maintenance / presynaptic membrane assembly / postsynaptic specialization / thigmotaxis / ribbon synapse / neuron cell-cell adhesion / insulin metabolic process / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / benzodiazepine receptor activity / inhibitory synapse / presynapse assembly / GABA receptor binding / GABA receptor complex / protein localization to synapse / dopaminergic synapse / glycinergic synapse / regulation of AMPA receptor activity / positive regulation of inhibitory postsynaptic potential / cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / positive regulation of synapse assembly / protein localization to cell surface / Neurexins and neuroligins / positive regulation of dendritic spine development / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of protein localization to synapse / postsynaptic specialization membrane / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / chloride channel activity / social behavior / adult behavior / locomotory exploration behavior / roof of mouth development / Signaling by ERBB4 / neuromuscular process controlling balance / excitatory synapse / positive regulation of excitatory postsynaptic potential / regulation of presynapse assembly / chloride channel complex / synapse assembly / cell adhesion molecule binding / sensory perception of pain / dendrite membrane / cytoplasmic vesicle membrane / positive regulation of synaptic transmission, glutamatergic / chloride transmembrane transport / dendritic shaft / post-embryonic development / positive regulation of synaptic transmission, GABAergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / sensory perception of sound / synapse organization / modulation of chemical synaptic transmission / positive regulation of insulin secretion / cell-cell adhesion / presynaptic membrane / dendritic spine / postsynaptic membrane / postsynapse / axon / positive regulation of cell population proliferation / synapse / dendrite / cell surface / signal transduction / identical protein binding / membrane / plasma membrane
Similarity search - Function
Lipoma HMGIC fusion partner-like protein / Lipoma HMGIC fusion partner-like protein / Neuroligin / : / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / : ...Lipoma HMGIC fusion partner-like protein / Lipoma HMGIC fusion partner-like protein / Neuroligin / : / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / : / Gamma-aminobutyric-acid A receptor, beta subunit / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / 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 / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor subunit alpha-1 / Gamma-aminobutyric acid receptor subunit gamma-2 / Gamma-aminobutyric acid receptor subunit beta-3 / LHFPL tetraspan subfamily member 4 protein / Neuroligin-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKasaragod VB / Aricescu AR
Funding support United Kingdom, European Union, United States, 7 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/15 United Kingdom
European Molecular Biology Organization (EMBO)ALTF137-2019European Union
H2020 Marie Curie Actions of the European CommissionGABAARComp-897707European Union
Medical Research Council (MRC, United Kingdom)MR/L009609/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_EX_MR/T046279/1 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01-GM135550 United States
National Science Foundation (NSF, United States)NeuroNex 2014862 United States
CitationJournal: To Be Published
Title: CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 and Megabody38 in a closed state (StateC1)
Authors: Kasaragod VB / Aricescu AR
History
DepositionMay 10, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50277.png

Downloads & links

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Map

FileDownload / File: emd_50277.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 296 pix.
= 234.719 Å		0.79 Å/pix.
x 296 pix.
= 234.719 Å		0.79 Å/pix.
x 296 pix.
= 234.719 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.79297 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.022120433 - 0.05491021
Average (Standard dev.)0.00021780144 (±0.002415523)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 234.71912 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50277_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Postprocessed map

Fileemd_50277_additional_1.map
AnnotationPostprocessed map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the halfmaps

Fileemd_50277_half_map_1.map
AnnotationOne of the halfmaps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the halfmaps

Fileemd_50277_half_map_2.map
AnnotationOne of the halfmaps
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Sample components

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Entire : CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R ...

EntireName: CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 and Megabody38 in a closed state (StateC1)
Components
  • Complex: CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 and Megabody38 in a closed state (StateC1)
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
    • Protein or peptide: Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2
    • Protein or peptide: Neuroligin-2
    • Protein or peptide: LHFPL tetraspan subfamily member 4 protein
    • Protein or peptide: Megabody38
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: PALMITIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
  • Ligand: DECANE
  • Ligand: HEXANE
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R ...

SupramoleculeName: CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 and Megabody38 in a closed state (StateC1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Gamma-aminobutyric acid receptor subunit alpha-1

MacromoleculeName: Gamma-aminobutyric acid receptor subunit alpha-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.085117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TTVFTRILDR LLDGYDNRLR PGLGERVTEV KTDIFVTSFG PVSDHDMEYT IDVFFRQSWK DERLKFKGPM TVLRLNNLMA SKIWTPDTF FHNGKKSVAH NMTMPNKLLR ITEDGTLLYT MRLTVRAECP MHLEDFPMDA HACPLKFGSY AYTRAEVVYE W TREPARSV ...String:
TTVFTRILDR LLDGYDNRLR PGLGERVTEV KTDIFVTSFG PVSDHDMEYT IDVFFRQSWK DERLKFKGPM TVLRLNNLMA SKIWTPDTF FHNGKKSVAH NMTMPNKLLR ITEDGTLLYT MRLTVRAECP MHLEDFPMDA HACPLKFGSY AYTRAEVVYE W TREPARSV VVAEDGSRLN QYDLLGQTVD SGIVQSSTGE YVVMTTHFHL KRKIGYFVIQ TYLPCIMTVI LSQVSFWLNR ES VPARTVF GVTTVLTMTT LSISARNSLP KVAYATAMDW FIAVCYAFVF SALIEFATVN YFTKRGYAWD GKSVVPEKPK KVK DPLIKK NNTYAPTATS YTPNLARGDP GLATIAKSAT IEPKEVKPET KPPEPKKTFN SVSKIDRLSR IAFPLLFGIF NLVY WATYL

UniProtKB: Gamma-aminobutyric acid receptor subunit alpha-1

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Macromolecule #2: Gamma-aminobutyric acid receptor subunit beta-3

MacromoleculeName: Gamma-aminobutyric acid receptor subunit beta-3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.733375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSFVKETVDK LLKGYDIRLR PDFGGPPVCV GMNIDIASID MVSEVNMDYT LTMYFQQYWR DKRLAYSGIP LNLTLDNRVA DQLWVPDTY FLNDKKSFVH GVTVKNRMIR LHPDGTVLYG LRITTTAACM MDLRRYPLDE QNCTLEIESY GYTTDDIEFY W RGGDKAVT ...String:
MSFVKETVDK LLKGYDIRLR PDFGGPPVCV GMNIDIASID MVSEVNMDYT LTMYFQQYWR DKRLAYSGIP LNLTLDNRVA DQLWVPDTY FLNDKKSFVH GVTVKNRMIR LHPDGTVLYG LRITTTAACM MDLRRYPLDE QNCTLEIESY GYTTDDIEFY W RGGDKAVT GVERIELPQF SIVEHRLVSR NVVFATGAYP RLSLSFRLKR NIGYFILQTY MPSILITILS WVSFWINYDA SA ARVALGI TTVLTMTTIN THLRETLPKI PYVKAIDMYL MGCFVFVFLA LLEYAFVNYI FFGRGPQRQK KLAEKTAKAK NDR SKSESN RVDAHGNILL TSLEVHNEMN EVSGGIGDTR NSAISFDNSG IQYRKQSMPR EGHGRFLGDR SLPHKKTHLR RRSS QLKIK IPDLTDVNAI DRWSRIVFPF TFSLFNLVYW LYYV

UniProtKB: Gamma-aminobutyric acid receptor subunit beta-3

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Macromolecule #3: Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2

MacromoleculeName: Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.698262 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VTVILNNLLE GYDNKLRPDI GVKPTLIHTD MYVNSIGPVN AINMEYTIDI FFAQTWYDRR LKFNSTIKVL RLNSNMVGKI WIPDTFFRN SKKADAHWIT TPNRMLRIWN DGRVLYTLRL TIDAECQLQL HNFPMDEHSC PLEFSSYGYP REEIVYQWKR S SVEVGDTR ...String:
VTVILNNLLE GYDNKLRPDI GVKPTLIHTD MYVNSIGPVN AINMEYTIDI FFAQTWYDRR LKFNSTIKVL RLNSNMVGKI WIPDTFFRN SKKADAHWIT TPNRMLRIWN DGRVLYTLRL TIDAECQLQL HNFPMDEHSC PLEFSSYGYP REEIVYQWKR S SVEVGDTR SWRLYQFSFV GLRNTTEVVK TTSGDYVVMS VYFDLSRRMG YFTIQTYIPC TLIVVLSWVS FWINKDAVPA RT SLGITTV LTMTTLSTIA RKSLPKVSYV TAMDLFVSVC FIFVFSALVE YGTLHYFVSN RKPSKDKDKK KKNPAPTIDI RPR SATIQM NNATHLQERD EEYGYECLDG KDCASFF(P1L)(P1L)F ED(P1L)RTGAWRH GRIHIRIAKM DSYARIFFPT AF CLFNLVY WVSYLYLG

UniProtKB: Gamma-aminobutyric acid receptor subunit gamma-2

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Macromolecule #4: Neuroligin-2

MacromoleculeName: Neuroligin-2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.614107 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DSRDYSTELS VTVAVGASLL FLNILAFAAL YYK

UniProtKB: Neuroligin-2

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Macromolecule #5: LHFPL tetraspan subfamily member 4 protein

MacromoleculeName: LHFPL tetraspan subfamily member 4 protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.366189 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YHEHYMRNSR AIGVLWAIFT ICFAIINVVV FIQPYWVGDS VSTPKPGYFG LFHYCVGSGL AGRELTCRGS FTDFSTIPSS AFKAAAFFV LLSMVLILGC ITCFSLFFFC NTATVYKICA WMQLLAALCL VLGCMIFPDG WDAETIRDMC GAKTGKYSLG D CSVRWAYI ...String:
YHEHYMRNSR AIGVLWAIFT ICFAIINVVV FIQPYWVGDS VSTPKPGYFG LFHYCVGSGL AGRELTCRGS FTDFSTIPSS AFKAAAFFV LLSMVLILGC ITCFSLFFFC NTATVYKICA WMQLLAALCL VLGCMIFPDG WDAETIRDMC GAKTGKYSLG D CSVRWAYI LAIIGILNAL ILSFLAFVLG NRQTD

UniProtKB: LHFPL tetraspan subfamily member 4 protein

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Macromolecule #6: Megabody38

MacromoleculeName: Megabody38 / type: protein_or_peptide / ID: 6
Details: This megabody is a chimeric protein designed and constructed based on a circular permutation of a nanobody (raised against GABA(A) receptor subunits, in Llama) and Helicobacter pylori ...Details: This megabody is a chimeric protein designed and constructed based on a circular permutation of a nanobody (raised against GABA(A) receptor subunits, in Llama) and Helicobacter pylori protein, HopQ (Uniprot Id: B5Z8H1).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 57.784301 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QVQLQESGGG LVQTKTTTSV IDTTNDAQNL LTQAQTIVNT LKDYCPILIA KSSSSNGGTN NANTPSWQTA GGGKNSCATF GAEFSAASD MINNAQKIVQ ETQQLSANQP KNITQPHNLN LNSPSSLTAL AQKMLKNAQS QAEILKLANQ VESDFNKLSS G HLKDYIGK ...String:
QVQLQESGGG LVQTKTTTSV IDTTNDAQNL LTQAQTIVNT LKDYCPILIA KSSSSNGGTN NANTPSWQTA GGGKNSCATF GAEFSAASD MINNAQKIVQ ETQQLSANQP KNITQPHNLN LNSPSSLTAL AQKMLKNAQS QAEILKLANQ VESDFNKLSS G HLKDYIGK CDASAISSAN MTMQNQKNNW GNGCAGVEET QSLLKTSAAD FNNQTPQINQ AQNLANTLIQ ELGNNPFRAS GG GSGGGGS GKLSDTYEQL SRLLTNDNGT NSKTSAQAIN QAVNNLNERA KTLAGGTTNS PAYQATLLAL RSVLGLWNSM GYA VICGGY TKSPGENNQK DFHYTDENGN GTTINCGGST NSNGTHSYNG TNTLKADKNV SLSIEQYEKI HEAYQILSKA LKQA GLAPL NSKGEKLEAH VTTSKYGSLR VSCAASGRTF TTYIMAWFRQ APGKEREFLA AMDQGRIQYY GDSVRGRFTI SRDYA KNSV DLQLDGLRPE DTAVYYCAAG AGFWGLRTAS SYHYWGQGTQ VTVSSHHHHH HEPEA

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Macromolecule #11: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
type: ligand / ID: 11 / Number of copies: 2 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-PIO:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

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Macromolecule #12: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...

MacromoleculeName: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
type: ligand / ID: 12 / Number of copies: 5 / Formula: PGW
Molecular weightTheoretical: 749.007 Da

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Macromolecule #13: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 13 / Number of copies: 2 / Formula: PX2
Molecular weightTheoretical: 535.671 Da
Chemical component information

ChemComp-PX2:
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

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Macromolecule #14: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 14 / Number of copies: 5 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #15: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 15 / 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 #16: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 16 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #17: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 17 / Number of copies: 1 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #18: HEXANE

MacromoleculeName: HEXANE / type: ligand / ID: 18 / Number of copies: 2 / Formula: HEX
Molecular weightTheoretical: 86.175 Da
Chemical component information

ChemComp-HEX:
HEXANE

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Macromolecule #19: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #20: water

MacromoleculeName: water / type: ligand / ID: 20 / Number of copies: 64 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
15.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClSodium chloride

Details: 15 mM Hepes pH 7.4, 150 mM NaCl
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: Current: 30 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 287 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9004 / Average electron dose: 46.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1365454
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 41368
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6huo


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 25 / Target criteria: FSC at 0.5
Output model

PDB-9fap:
CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 and Megabody38 in a closed state (StateC1)

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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