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- EMDB-60096: Human GPR103 -Gq complex bound to QRFP26 -

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Entry
Database: EMDB / ID: EMD-60096
TitleHuman GPR103 -Gq complex bound to QRFP26
Map data
Sample
  • Complex: Human GPR103 -Gq complex bound to QRFP26
    • Protein or peptide: Pyroglutamylated RF-amide peptide receptor
    • Protein or peptide: nanobody Nb35
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
    • Protein or peptide: scFv16
    • Protein or peptide: QRF-amide
KeywordsGPCR / MEMBRANE PROTEIN / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


orexigenic neuropeptide QRFP receptor binding / neuropeptide Y receptor activity / adenylate cyclase-activating serotonin receptor signaling pathway / Orexin and neuropeptides FF and QRFP bind to their respective receptors / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of feeding behavior / sensory perception of chemical stimulus / negative regulation of calcium ion-dependent exocytosis / grooming behavior / G protein-coupled adenosine receptor signaling pathway ...orexigenic neuropeptide QRFP receptor binding / neuropeptide Y receptor activity / adenylate cyclase-activating serotonin receptor signaling pathway / Orexin and neuropeptides FF and QRFP bind to their respective receptors / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of feeding behavior / sensory perception of chemical stimulus / negative regulation of calcium ion-dependent exocytosis / grooming behavior / G protein-coupled adenosine receptor signaling pathway / mu-type opioid receptor binding / positive regulation of blood pressure / corticotropin-releasing hormone receptor 1 binding / positive regulation of urine volume / negative regulation of adenylate cyclase activity / neuropeptide hormone activity / positive regulation of neural precursor cell proliferation / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / negative regulation of synaptic transmission / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / gamma-aminobutyric acid signaling pathway / G alpha (i) signalling events / beta-2 adrenergic receptor binding / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / Thrombin signalling through proteinase activated receptors (PARs) / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / photoreceptor outer segment membrane / G alpha (q) signalling events / G alpha (i) signalling events / spectrin binding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / neuronal dense core vesicle / alkylglycerophosphoethanolamine phosphodiesterase activity / PKA activation in glucagon signalling / regulation of calcium ion transport / negative regulation of apoptotic signaling pathway / developmental growth / photoreceptor outer segment / D1 dopamine receptor binding / neuropeptide signaling pathway / Hedgehog 'off' state / positive regulation of insulin receptor signaling pathway / Adenylate cyclase inhibitory pathway / cellular response to hormone stimulus / response to prostaglandin E / ionotropic glutamate receptor binding / adenylate cyclase regulator activity / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / photoreceptor inner segment / cardiac muscle cell apoptotic process / response to nutrient / adenylate cyclase activator activity / hippocampal mossy fiber to CA3 synapse / positive regulation of superoxide anion generation / locomotory behavior / Regulation of insulin secretion / G protein-coupled receptor binding / G protein-coupled receptor activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / bone development / G-protein beta/gamma-subunit complex binding / platelet aggregation
Similarity search - Function
Orexigenic neuropeptide QRFP/P518 / Orexigenic neuropeptide Qrfp/P518 / Neuropeptide Y receptor family / G-protein alpha subunit, group S / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit ...Orexigenic neuropeptide QRFP/P518 / Orexigenic neuropeptide Qrfp/P518 / Neuropeptide Y receptor family / G-protein alpha subunit, group S / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(i) subunit alpha-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Orexigenic neuropeptide QRFP / Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas / Pyroglutamylated RF-amide peptide receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama) / Rattus norvegicus (Norway rat) / Bos taurus (domestic cattle) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsIwama A / Akasaka H / Sano FK / Oshima HS / Shihoya W / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H05037 Japan
CitationJournal: Nat Commun / Year: 2024
Title: Structure and dynamics of the pyroglutamylated RF-amide peptide QRFP receptor GPR103.
Authors: Aika Iwama / Ryoji Kise / Hiroaki Akasaka / Fumiya K Sano / Hidetaka S Oshima / Asuka Inoue / Wataru Shihoya / Osamu Nureki /
Abstract: Pyroglutamylated RF-amide peptide (QRFP) is a peptide hormone with a C-terminal RF-amide motif. QRFP selectively activates a class A G-protein-coupled receptor (GPCR) GPR103 to exert various ...Pyroglutamylated RF-amide peptide (QRFP) is a peptide hormone with a C-terminal RF-amide motif. QRFP selectively activates a class A G-protein-coupled receptor (GPCR) GPR103 to exert various physiological functions such as energy metabolism and appetite regulation. Here, we report the cryo-electron microscopy structure of the QRFP26-GPR103-G complex at 3.19 Å resolution. QRFP26 adopts an extended structure bearing no secondary structure, with its N-terminal and C-terminal sides recognized by extracellular and transmembrane domains of GPR103 respectively. This movement, reminiscent of class B1 GPCRs except for orientation and structure of the ligand, is critical for the high-affinity binding and receptor specificity of QRFP26. Mutagenesis experiments validate the functional importance of the binding mode of QRFP26 by GPR103. Structural comparisons with closely related receptors, including RY-amide peptide-recognizing GPCRs, revealed conserved and diversified peptide recognition mechanisms, providing profound insights into the biological significance of RF-amide peptides. Collectively, this study not only advances our understanding of GPCR-ligand interactions, but also paves the way for the development of novel therapeutics targeting metabolic and appetite disorders and emergency medical care.
History
DepositionMay 10, 2024-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60096.png

Downloads & links

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Map

FileDownload / File: emd_60096.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 260 pix.
= 265.59 Å		1.02 Å/pix.
x 260 pix.
= 265.59 Å		1.02 Å/pix.
x 260 pix.
= 265.59 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0215 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.2
Minimum - Maximum-19.046403999999999 - 36.746943999999999
Average (Standard dev.)-0.0011371021 (±1.0337278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 265.59 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60096_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_60096_half_map_2.map
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Sample components

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Entire : Human GPR103 -Gq complex bound to QRFP26

EntireName: Human GPR103 -Gq complex bound to QRFP26
Components
  • Complex: Human GPR103 -Gq complex bound to QRFP26
    • Protein or peptide: Pyroglutamylated RF-amide peptide receptor
    • Protein or peptide: nanobody Nb35
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
    • Protein or peptide: scFv16
    • Protein or peptide: QRF-amide

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Supramolecule #1: Human GPR103 -Gq complex bound to QRFP26

SupramoleculeName: Human GPR103 -Gq complex bound to QRFP26 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Pyroglutamylated RF-amide peptide receptor

MacromoleculeName: Pyroglutamylated RF-amide peptide receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.652039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKQALNIT PEQFSRLLRD HNLTREQFIA LYRLRPLVYT PELPGRAKLA LVLTGVLIFA LALFGNALV FYVVTRSKAM RTVTNIFICS LALSDLLITF FCIPVTMLQN ISDNWLGGAF ICKMVPFVQS TAVVTEILTM T CIAVERHQ ...String:
MKTIIALSYI FCLVFADYKD DDDKQALNIT PEQFSRLLRD HNLTREQFIA LYRLRPLVYT PELPGRAKLA LVLTGVLIFA LALFGNALV FYVVTRSKAM RTVTNIFICS LALSDLLITF FCIPVTMLQN ISDNWLGGAF ICKMVPFVQS TAVVTEILTM T CIAVERHQ GLVHPFKMKW QYTNRRAFTM LGVVWLVAVI VGSPMWHVQQ LEIKYDFLYE KEHICCLEEW TSPVHQKIYT TF ILVILFL LPLMVMLILY SKIGYELWIK KRVGDGSVLR TIHGKEMSKI ARKKKRAVIM MVTVVALFAV CWAPFHVVHM MIE YSNFEK EYDDVTIKMI FAIVQIIGFS NSICNPIVYA FMNENFKKNV LSAVCYCIVN KTFSPAQRHG NSGSGGGGSG GSSS GG

UniProtKB: Pyroglutamylated RF-amide peptide receptor

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Macromolecule #2: nanobody Nb35

MacromoleculeName: nanobody Nb35 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15.015728 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGQVQLQESG GGLVQPGGSL RLSCAASGFT FSNYKMNWVR QAPGKGLEWV SDISQSGASI SYTGSVKGRF TISRDNAKNT LYLQMNSLK PEDTAVYYCA RCPAPFTRDC FDVTSTTYAY RGQGTQVTVS SLHHHHHH

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 38.744371 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI ...String:
MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI VTSSGDTTCA LWDIETGQQT TTFTGHTGDV MSLSLAPDTR LFVSGACDAS AKLWDVREGM CRQTFTGHES DI NAICFFP NGNAFATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGYDDFNCNV WDALKADRAG VLA GHDNRV SCLGVTDDGM AVATGSWDSF LKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 7.547685 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFS

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2...

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.573531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI LGSAGSAGSA MGSTVSAED KAAAERSKMI DKNLREDGEK ARRTLRLLLL GADNSGKSTI VKQMRILHGG SGGSGGTSGI FETKFQVDKV N FHMFDVGG ...String:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI LGSAGSAGSA MGSTVSAED KAAAERSKMI DKNLREDGEK ARRTLRLLLL GADNSGKSTI VKQMRILHGG SGGSGGTSGI FETKFQVDKV N FHMFDVGG QRDERRKWIQ CFNDVTAIIF VVDSSDYNRL QEALNDFKSI WNNRWLRTIS VILFLNKQDL LAEKVLAGKS KI EDYFPEF ARYTTPEDAT PEPGEDPRVT RAKYFIRKEF VDISTASGDG RHICYPHFTC AVDTENARRI FNDCKDIILQ MNL REYNLV

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(i) subunit alpha-2, Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas

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Macromolecule #6: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.720795 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KAAAASSEDL YFQ

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Macromolecule #7: QRF-amide

MacromoleculeName: QRF-amide / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.835161 KDa
SequenceString:
TSGPLGNLAE ELNGYSRKKG GFSFRF(NH2)

UniProtKB: Orexigenic neuropeptide QRFP

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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: 0.83 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142831
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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