[English] 日本語
Yorodumi
- EMDB-34305: the human PTH1 receptor bound to an intracellular biased agonist -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34305
Titlethe human PTH1 receptor bound to an intracellular biased agonist
Map data
Sample
  • Complex: the human PTH1 receptor bound to an intracellular biased agonist
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • Protein or peptide: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Complex: 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(T) subunit beta-1
    • Complex: 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
    • Complex: nanobody Nb35
      • Protein or peptide: Nanobody-35Single-domain antibody
    • Complex: Parathyroid hormone/parathyroid hormone-related peptide receptor
      • Protein or peptide: Parathyroid hormone/parathyroid hormone-related peptide receptor
  • Ligand: PCO-371
KeywordsG protein-coupled receptor / membrane protein / SIGNALING PROTEIN
Function / homology
Function and homology information


parathyroid hormone receptor activity / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding ...parathyroid hormone receptor activity / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Activation of G protein gated Potassium channels / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G protein-coupled peptide receptor activity / G alpha (z) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / G alpha (i) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / Class B/2 (Secretin family receptors) / 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 / Glucagon-type ligand receptors / alkylglycerophosphoethanolamine phosphodiesterase activity / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / osteoblast development / G alpha (s) signalling events / G alpha (q) signalling events / positive regulation of inositol phosphate biosynthetic process / photoreceptor outer segment membrane / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / spectrin binding / Vasopressin regulates renal water homeostasis via Aquaporins / bone mineralization / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / PKA activation in glucagon signalling / peptide hormone binding / hair follicle placode formation / intracellular transport / photoreceptor outer segment / D1 dopamine receptor binding / developmental growth / chondrocyte differentiation / Hedgehog 'off' state / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating adrenergic receptor signaling pathway / cell maturation / bone resorption / cardiac muscle cell apoptotic process / activation of adenylate cyclase activity / photoreceptor inner segment / adenylate cyclase activator activity / trans-Golgi network membrane / skeletal system development / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / bone development / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / platelet aggregation / Glucagon-type ligand receptors / cognition / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of GTPase activity / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / heterotrimeric G-protein complex / : / signaling receptor complex adaptor activity / sensory perception of smell
Similarity search - Function
GPCR, family 2, parathyroid hormone receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like ...GPCR, family 2, parathyroid hormone receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / G-protein alpha subunit, group S / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Parathyroid hormone/parathyroid hormone-related peptide receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus norvegicus (Norway rat) / Bos taurus (cattle) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKobayashi K / Kusakizako T / Okamoto HH / Nureki O / Yamashita K / Nishizawa T / Kato HE
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nature / Year: 2023
Title: Class B1 GPCR activation by an intracellular agonist.
Authors: Kazuhiro Kobayashi / Kouki Kawakami / Tsukasa Kusakizako / Atsuhiro Tomita / Michihiro Nishimura / Kazuhiro Sawada / Hiroyuki H Okamoto / Suzune Hiratsuka / Gaku Nakamura / Riku Kuwabara / ...Authors: Kazuhiro Kobayashi / Kouki Kawakami / Tsukasa Kusakizako / Atsuhiro Tomita / Michihiro Nishimura / Kazuhiro Sawada / Hiroyuki H Okamoto / Suzune Hiratsuka / Gaku Nakamura / Riku Kuwabara / Hiroshi Noda / Hiroyasu Muramatsu / Masaru Shimizu / Tomohiko Taguchi / Asuka Inoue / Takeshi Murata / Osamu Nureki /
Abstract: G protein-coupled receptors (GPCRs) generally accommodate specific ligands in the orthosteric-binding pockets. Ligand binding triggers a receptor allosteric conformational change that leads to the ...G protein-coupled receptors (GPCRs) generally accommodate specific ligands in the orthosteric-binding pockets. Ligand binding triggers a receptor allosteric conformational change that leads to the activation of intracellular transducers, G proteins and β-arrestins. Because these signals often induce adverse effects, the selective activation mechanism for each transducer must be elucidated. Thus, many orthosteric-biased agonists have been developed, and intracellular-biased agonists have recently attracted broad interest. These agonists bind within the receptor intracellular cavity and preferentially tune the specific signalling pathway over other signalling pathways, without allosteric rearrangement of the receptor from the extracellular side. However, only antagonist-bound structures are currently available, and there is no evidence to support that biased agonist binding occurs within the intracellular cavity. This limits the comprehension of intracellular-biased agonism and potential drug development. Here we report the cryogenic electron microscopy structure of a complex of G and the human parathyroid hormone type 1 receptor (PTH1R) bound to a PTH1R agonist, PCO371. PCO371 binds within an intracellular pocket of PTH1R and directly interacts with G. The PCO371-binding mode rearranges the intracellular region towards the active conformation without extracellularly induced allosteric signal propagation. PCO371 stabilizes the significantly outward-bent conformation of transmembrane helix 6, which facilitates binding to G proteins rather than β-arrestins. Furthermore, PCO371 binds within the highly conserved intracellular pocket, activating 7 out of the 15 class B1 GPCRs. Our study identifies a new and conserved intracellular agonist-binding pocket and provides evidence of a biased signalling mechanism that targets the receptor-transducer interface.
History
DepositionSep 16, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34305.png

Downloads & links

-
Map

FileDownload / File: emd_34305.map.gz / Format: CCP4 / Size: 12.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.10667 Å
Density
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.14162266 - 0.23974013
Average (Standard dev.)0.0006183178 (±0.009341711)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions148148148
Spacing148148148
CellA=B=C: 163.78717 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_34305_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_34305_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34305_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : the human PTH1 receptor bound to an intracellular biased agonist

EntireName: the human PTH1 receptor bound to an intracellular biased agonist
Components
  • Complex: the human PTH1 receptor bound to an intracellular biased agonist
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • Protein or peptide: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Complex: 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(T) subunit beta-1
    • Complex: 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
    • Complex: nanobody Nb35
      • Protein or peptide: Nanobody-35Single-domain antibody
    • Complex: Parathyroid hormone/parathyroid hormone-related peptide receptor
      • Protein or peptide: Parathyroid hormone/parathyroid hormone-related peptide receptor
  • Ligand: PCO-371

+
Supramolecule #1: the human PTH1 receptor bound to an intracellular biased agonist

SupramoleculeName: the human PTH1 receptor bound to an intracellular biased agonist
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

+
Supramolecule #2: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

SupramoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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

SupramoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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

SupramoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Bos taurus (cattle)

+
Supramolecule #5: nanobody Nb35

SupramoleculeName: nanobody Nb35 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: unidentified (others)

+
Supramolecule #6: Parathyroid hormone/parathyroid hormone-related peptide receptor

SupramoleculeName: Parathyroid hormone/parathyroid hormone-related peptide receptor
type: complex / ID: 6 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit...

MacromoleculeName: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.073574 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QRNEEKAQRE ANKKIEKQLQ KDKQVYRATH RLLLLGADNS GKSTIVKQMR ILHVNGFNGD SEKATKVQDI KNNLKEAIET IVAAMSNLV PPVELANPEN QFRVDYILSV MNVPDFDFPP EFYEHAKALW EDEGVRACYE RSNEYQLIDC AQYFLDKIDV I KQADYVPS ...String:
QRNEEKAQRE ANKKIEKQLQ KDKQVYRATH RLLLLGADNS GKSTIVKQMR ILHVNGFNGD SEKATKVQDI KNNLKEAIET IVAAMSNLV PPVELANPEN QFRVDYILSV MNVPDFDFPP EFYEHAKALW EDEGVRACYE RSNEYQLIDC AQYFLDKIDV I KQADYVPS DQDLLRCRVL TSGIFETKFQ VDKVNFHMFD VGGQRDERRK WIQCFNDVTA IIFVVDSSDY NRLQEALNLF KS IWNNRWL RTISVILFLN KQDLLAEKVL AGKSKIEDYF PEFARYTTPE DATPEPGEDP RVTRAKYFIR DEFLRISTAS GDG RHYCYP HFTCAVDTEN ARRIFNDCRD IIQRMHLRQY ELL

UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

+
Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 38.744371 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

+
Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 7.547685 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFS

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

+
Macromolecule #4: Nanobody-35

MacromoleculeName: Nanobody-35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 13.885439 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSS

+
Macromolecule #5: Parathyroid hormone/parathyroid hormone-related peptide receptor

MacromoleculeName: Parathyroid hormone/parathyroid hormone-related peptide receptor
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.264359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKDA DDVMTKEEQI FLLHRAQAQC EKRLKEVLQR PASIMESDKG WTSASTSGKP RKDKASGKLY PESEEDKEAP TGSRYRGRP CLPEWDHILC WPLGAPGEVV AVPCPDYIYD FNHKGHAYRR CDRNGSWELV PGHNRTWANY SECVKFLTNE T REREVFDR ...String:
DYKDDDDKDA DDVMTKEEQI FLLHRAQAQC EKRLKEVLQR PASIMESDKG WTSASTSGKP RKDKASGKLY PESEEDKEAP TGSRYRGRP CLPEWDHILC WPLGAPGEVV AVPCPDYIYD FNHKGHAYRR CDRNGSWELV PGHNRTWANY SECVKFLTNE T REREVFDR LGMIYTVGYS VSLASLTVAV LILAYFRRLH CTRNYIHMHL FLSFMLRAVS IFVKDAVLYS GATLDEAERL TE EELRAIA QAPPPPATAA AGYAGCRVAV TFFLYFLATN YYWILVEGLY LHSLIFMAFF SEKKYLWGFT VFGWGLPAVF VAV WVSVRA TLANTGCWDL SSGNKKWIIQ VPILASIVLN FILFINIVRV LATKLRETNA GRCDTRQQYR KLLKSTLVLM PLFG VHYIV FMATPYTEVS GTLWQVQMHY EMLFNSFQGF FVAIIYCFCN GEVQAEIKKS WSRWTLALDF KRKARSGS

UniProtKB: Parathyroid hormone/parathyroid hormone-related peptide receptor

+
Macromolecule #6: PCO-371

MacromoleculeName: PCO-371 / type: ligand / ID: 6 / Number of copies: 1 / Formula: KHF
Molecular weightTheoretical: 635.654 Da
Chemical component information

ChemComp-KHF:
PCO-371

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration7 mg/mL
BufferpH: 9
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.578 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7vvn

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 109422
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more