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- EMDB-53948: CryoEM structure of human alpha1beta3gamma2L GABA(A)R in CL47a -

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Basic information

Entry
Database: EMDB / ID: EMD-53948
TitleCryoEM structure of human alpha1beta3gamma2L GABA(A)R in CL47a
Map dataUnsharpened map from the Refine3D
Sample
  • Complex: CryoEM structure of human alpha1beta3gamma2L GABA(A)R in CL47a
    • Protein or peptide: x 3 types
  • Ligand: x 12 types
KeywordsGABA / Neurotransmission / Inhibitory synapse / MEMBRANE PROTEIN
Function / homology
Function and homology information


benzodiazepine receptor activity / circadian sleep/wake cycle, REM sleep / reproductive behavior / GABA receptor complex / hard palate development / cellular response to histamine / GABA receptor activation / inner ear receptor cell development / GABA-gated chloride ion channel activity / GABA-A receptor complex ...benzodiazepine receptor activity / circadian sleep/wake cycle, REM sleep / reproductive behavior / GABA receptor complex / hard palate development / cellular response to histamine / GABA receptor activation / inner ear receptor cell development / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / GABA-A receptor activity / innervation / response to anesthetic / postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / inhibitory postsynaptic potential / cellular response to zinc ion / motor behavior / roof of mouth development / adult behavior / chloride channel activity / exploration behavior / Signaling by ERBB4 / cochlea development / social behavior / chloride channel complex / dendrite membrane / cerebellum development / cytoplasmic vesicle membrane / chloride transmembrane transport / learning / post-embryonic development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / memory / dendritic spine / postsynaptic membrane / postsynapse / response to xenobiotic stimulus / axon / cell surface / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
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 / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel, conserved site ...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 / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel transmembrane region / 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
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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 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
Medical Research Council (MRC, United Kingdom)MR/L009609/1 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)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 alpha1beta3gamma2L GABA(A)R in CL47a
Authors: Kasaragod VB / Aricescu AR
History
DepositionJun 6, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53948.png

Downloads & links

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Map

FileDownload / File: emd_53948.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map from the Refine3D
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 480 pix.
= 349.92 Å		0.73 Å/pix.
x 480 pix.
= 349.92 Å		0.73 Å/pix.
x 480 pix.
= 349.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0025
Minimum - Maximum-0.012432646 - 0.0356318
Average (Standard dev.)0.000011805657 (±0.00071828463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 349.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53948_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_53948_additional_1.map
AnnotationPostprocessed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the halfmaps

Fileemd_53948_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_53948_half_map_2.map
AnnotationOne of the halfmaps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM structure of human alpha1beta3gamma2L GABA(A)R in CL47a

EntireName: CryoEM structure of human alpha1beta3gamma2L GABA(A)R in CL47a
Components
  • Complex: CryoEM structure of human alpha1beta3gamma2L GABA(A)R in CL47a
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit gamma-2
  • Ligand: DECANE
  • Ligand: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
  • Ligand: HEXADECANE
  • Ligand: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
  • Ligand: PALMITIC ACID
  • Ligand: HEXANE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: CryoEM structure of human alpha1beta3gamma2L GABA(A)R in CL47a

SupramoleculeName: CryoEM structure of human alpha1beta3gamma2L GABA(A)R in CL47a
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 250 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: 46.585602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DNTTVFTRIL DRLLDGYDNR LRPGLGERVT EVKTDIFVTS FGPVSDHDME YTIDVFFRQS WKDERLKFKG PMTVLRLNNL MASKIWTPD TFFHNGKKSV AHNMTMPNKL LRITEDGTLL YTMRLTVRAE CPMHLEDFPM DAHACPLKFG SYAYTRAEVV Y EWTREPAR ...String:
DNTTVFTRIL DRLLDGYDNR LRPGLGERVT EVKTDIFVTS FGPVSDHDME YTIDVFFRQS WKDERLKFKG PMTVLRLNNL MASKIWTPD TFFHNGKKSV AHNMTMPNKL LRITEDGTLL YTMRLTVRAE CPMHLEDFPM DAHACPLKFG SYAYTRAEVV Y EWTREPAR SVVVAEDGSR LNQYDLLGQT VDSGIVQSST GEYVVMTTHF HLKRKIGYFV IQTYLPCIMT VILSQVSFWL NR ESVPART VFGVTTVLTM TTLSISARNS LPKVAYATAM DWFIAVCYAF VFSALIEFAT VNYFTKRGYA WDGKSVVPEK PKK VKDPLI KKNNTYAPTA TSYTPNLARG DPGLATIAKS ATIEPKEVKP ETKPPEPKKT FNSVSKIDRL SRIAFPLLFG IFNL VYWAT YLNR

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: 50.904527 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GNMSFVKETV DKLLKGYDIR LRPDFGGPPV CVGMNIDIAS IDMVSEVNMD YTLTMYFQQY WRDKRLAYSG IPLNLTLDNR VADQLWVPD TYFLNDKKSF VHGVTVKNRM IRLHPDGTVL YGLRITTTAA CMMDLRRYPL DEQNCTLEIE SYGYTTDDIE F YWRGGDKA ...String:
GNMSFVKETV DKLLKGYDIR LRPDFGGPPV CVGMNIDIAS IDMVSEVNMD YTLTMYFQQY WRDKRLAYSG IPLNLTLDNR VADQLWVPD TYFLNDKKSF VHGVTVKNRM IRLHPDGTVL YGLRITTTAA CMMDLRRYPL DEQNCTLEIE SYGYTTDDIE F YWRGGDKA VTGVERIELP QFSIVEHRLV SRNVVFATGA YPRLSLSFRL KRNIGYFILQ TYMPSILITI LSWVSFWINY DA SAARVAL GITTVLTMTT INTHLRETLP KIPYVKAIDM YLMGCFVFVF LALLEYAFVN YIFFGRGPQR QKKLAEKTAK AKN DRSKSE SNRVDAHGNI LLTSLEVHNE MNEVSGGIGD TRNSAISFDN SGIQYRKQSM PREGHGRFLG DRSLPHKKTH LRRR SSQLK IKIPDLTDVN AIDRWSRIVF PFTFSLFNLV YWLYYV

UniProtKB: Gamma-aminobutyric acid receptor subunit beta-3

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

MacromoleculeName: 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: 48.448785 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VPEGDVTVIL NNLLEGYDNK LRPDIGVKPT LIHTDMYVNS IGPVNAINME YTIDIFFAQT WYDRRLKFNS TIKVLRLNSN MVGKIWIPD TFFRNSKKAD AHWITTPNRM LRIWNDGRVL YTLRLTIDAE CQLQLHNFPM DEHSCPLEFS SYGYPREEIV Y QWKRSSVE ...String:
VPEGDVTVIL NNLLEGYDNK LRPDIGVKPT LIHTDMYVNS IGPVNAINME YTIDIFFAQT WYDRRLKFNS TIKVLRLNSN MVGKIWIPD TFFRNSKKAD AHWITTPNRM LRIWNDGRVL YTLRLTIDAE CQLQLHNFPM DEHSCPLEFS SYGYPREEIV Y QWKRSSVE VGDTRSWRLY QFSFVGLRNT TEVVKTTSGD YVVMSVYFDL SRRMGYFTIQ TYIPCTLIVV LSWVSFWINK DA VPARTSL GITTVLTMTT LSTIARKSLP KVSYVTAMDL FVSVCFIFVF SALVEYGTLH YFVSNRKPSK DKDKKKKNPL LRM FSFKAP TIDIRPRSAT IQMNNATHLQ ERDEEYGYEC LDGKDCASFF CCFEDCRTGA WRHGRIHIRI AKMDSYARIF FPTA FCLFN LVYWVSYLYL

UniProtKB: Gamma-aminobutyric acid receptor subunit gamma-2

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Macromolecule #8: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 8 / Number of copies: 10 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #9: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tr...

MacromoleculeName: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
type: ligand / ID: 9 / Number of copies: 2 / Formula: PT5
Molecular weightTheoretical: 1.047088 KDa

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Macromolecule #10: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 10 / Number of copies: 5 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Macromolecule #11: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

MacromoleculeName: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / type: ligand / ID: 11 / Number of copies: 1 / Formula: EPE
Molecular weightTheoretical: 238.305 Da
Chemical component information

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM

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Macromolecule #12: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 12 / Number of copies: 3 / Formula: PX2
Molecular weightTheoretical: 535.671 Da
Chemical component information

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

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Macromolecule #13: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate

MacromoleculeName: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / type: ligand / ID: 13 / Number of copies: 3 / Formula: OLC
Molecular weightTheoretical: 356.54 Da
Chemical component information

ChemComp-OLC:
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate

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Macromolecule #14: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 14 / Number of copies: 3 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #15: HEXANE

MacromoleculeName: HEXANE / type: ligand / ID: 15 / Number of copies: 11 / Formula: HEX
Molecular weightTheoretical: 86.175 Da
Chemical component information

ChemComp-HEX:
HEXANE

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Macromolecule #16: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 16 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #17: (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: 17 / Number of copies: 1 / Formula: PGW
Molecular weightTheoretical: 749.007 Da

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Macromolecule #18: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #19: water

MacromoleculeName: water / type: ligand / ID: 19 / Number of copies: 642 / 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

Concentration3.6 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
10.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClSodium chloride
0.01 %CL47aCL47a

Details: 10 mM Hepes pH 7.4, 150 mM NaCl, 0.01 % CL47a
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: Current: 30 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4098 pixel / Digitization - Dimensions - Height: 4098 pixel / Number grids imaged: 1 / Number real images: 10940 / Average electron dose: 53.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 165000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
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: 1465798
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 232597
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9eqg


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 20 / Target criteria: FSC at 0.5
Output model

PDB-9rgd:
CryoEM structure of human alpha1beta3gamma2L GABA(A)R in CL47a

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