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- EMDB-3313: Cryo-EM structure of CSN-N8-CRL4A at 6.7 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-3313
TitleCryo-EM structure of CSN-N8-CRL4A at 6.7 A resolution
Map dataCryo-EM structure of CSN-N8-CRL4 at 6.7 A resolution
Sample
  • Sample: Recombinant human CSN-N8-CRL4A complex
  • Protein or peptide: x 12 types
KeywordsCOP9 Signalosome / Cullin-RING ligases / Cryo-EM
Function / homology
Function and homology information


Prolactin receptor signaling / Recognition of DNA damage by PCNA-containing replication complex / Formation of TC-NER Pre-Incision Complex / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Dual incision in TC-NER / Regulation of BACH1 activity / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of Incision Complex in GG-NER / Regulation of RAS by GAPs ...Prolactin receptor signaling / Recognition of DNA damage by PCNA-containing replication complex / Formation of TC-NER Pre-Incision Complex / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Dual incision in TC-NER / Regulation of BACH1 activity / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of Incision Complex in GG-NER / Regulation of RAS by GAPs / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Regulation of RUNX2 expression and activity / COP9 signalosome assembly / Degradation of GLI1 by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Hedgehog 'on' state / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / miRNA-mediated gene silencing by mRNA destabilization / Degradation of beta-catenin by the destruction complex / eukaryotic initiation factor 4E binding / regulation of IRE1-mediated unfolded protein response / negative regulation of granulocyte differentiation / base-excision repair, AP site formation via deaminated base removal / Interleukin-1 signaling / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity / anaphase-promoting complex / GLI3 is processed to GLI3R by the proteasome / protein deneddylation / regulation of protein neddylation / activation of NF-kappaB-inducing kinase activity / eukaryotic translation initiation factor 3 complex / Neddylation / cellular response to camptothecin / cullin-RING-type E3 NEDD8 transferase / COP9 signalosome / KEAP1-NFE2L2 pathway / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / regulation of DNA damage checkpoint / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation by virus of viral protein levels in host cell / positive regulation of protein autoubiquitination / regulation of nucleotide-excision repair / RNA polymerase II transcription initiation surveillance / protein neddylation / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / positive regulation of epithelial cell apoptotic process / NEDD8 ligase activity / Hydrolases; Acting on peptide bonds (peptidases) / regulation of JNK cascade / metal-dependent deubiquitinase activity / negative regulation of response to oxidative stress / RHOBTB1 GTPase cycle / regulation of DNA damage response, signal transduction by p53 class mediator / UV-damage excision repair / VCB complex / inner cell mass cell proliferation / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / SCF ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / biological process involved in interaction with symbiont / Cul2-RING ubiquitin ligase complex / regulation of mitotic cell cycle phase transition / lysosome organization / Cul3-RING ubiquitin ligase complex / negative regulation of type I interferon production / type I interferon-mediated signaling pathway / WD40-repeat domain binding / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / p38MAPK cascade / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / TGF-beta receptor signaling activates SMADs / negative regulation of signal transduction by p53 class mediator / hemopoiesis / TORC1 signaling / regulation of proteolysis / viral release from host cell / somatic stem cell population maintenance / skeletal muscle cell differentiation / : / epithelial to mesenchymal transition / regulation of postsynapse assembly / cullin family protein binding / response to light stimulus / anatomical structure morphogenesis / protein monoubiquitination
Similarity search - Function
COP9 signalosome complex subunit 7, helix I / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 3-like, C-terminal helix / CSN7 helical bundle subdomain / COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 4, helix turn helix domain / : / CSN4/RPN5/eIF3a helix turn helix domain / COP9 signalosome complex subunit 3, N-terminal helical repeats ...COP9 signalosome complex subunit 7, helix I / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 3-like, C-terminal helix / CSN7 helical bundle subdomain / COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 4, helix turn helix domain / : / CSN4/RPN5/eIF3a helix turn helix domain / COP9 signalosome complex subunit 3, N-terminal helical repeats / COP9 signalosome subunit 6 / : / : / COP9 signalosome complex subunit 1, C-terminal helix / COP9 signalosome complex subunit 2, C-terminal helix / Cop9 signalosome subunit 5 C-terminal domain / Cop9 signalosome subunit 5 C-terminal domain / Nedd8-like ubiquitin / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin, N-terminal / Cullin protein neddylation domain / : / : / Cullin, conserved site / : / : / Cullin alpha solenoid domain / PSMD12/CSN4, N-terminal / Cullin family signature. / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / PCI/PINT associated module / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Tetratricopeptide-like helical domain superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / COP9 signalosome complex subunit 1 / Cullin-4A / Ubiquitin-like protein NEDD8 / DNA damage-binding protein 1 / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 5 / COP9 signalosome complex subunit 8 / COP9 signalosome complex subunit 4 ...COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / COP9 signalosome complex subunit 1 / Cullin-4A / Ubiquitin-like protein NEDD8 / DNA damage-binding protein 1 / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 5 / COP9 signalosome complex subunit 8 / COP9 signalosome complex subunit 4 / COP9 signalosome complex subunit 7a / COP9 signalosome complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsCavadini S / Fischer ES / Bunker RD / Potenza A / Lingaraju GM / Goldie KN / Mohamed WI / Faty M / Petzold G / Beckwith REJ ...Cavadini S / Fischer ES / Bunker RD / Potenza A / Lingaraju GM / Goldie KN / Mohamed WI / Faty M / Petzold G / Beckwith REJ / Tichkule R / Hassiepen U / Abdulrahman W / Pantelic RS / Matsumoto S / Sugasawa K / Stahlberg H / Thoma NH
CitationJournal: Nature / Year: 2016
Title: Cullin-RING ubiquitin E3 ligase regulation by the COP9 signalosome.
Authors: Simone Cavadini / Eric S Fischer / Richard D Bunker / Alessandro Potenza / Gondichatnahalli M Lingaraju / Kenneth N Goldie / Weaam I Mohamed / Mahamadou Faty / Georg Petzold / Rohan E J ...Authors: Simone Cavadini / Eric S Fischer / Richard D Bunker / Alessandro Potenza / Gondichatnahalli M Lingaraju / Kenneth N Goldie / Weaam I Mohamed / Mahamadou Faty / Georg Petzold / Rohan E J Beckwith / Ritesh B Tichkule / Ulrich Hassiepen / Wassim Abdulrahman / Radosav S Pantelic / Syota Matsumoto / Kaoru Sugasawa / Henning Stahlberg / Nicolas H Thomä /
Abstract: The cullin-RING ubiquitin E3 ligase (CRL) family comprises over 200 members in humans. The COP9 signalosome complex (CSN) regulates CRLs by removing their ubiquitin-like activator NEDD8. The CUL4A- ...The cullin-RING ubiquitin E3 ligase (CRL) family comprises over 200 members in humans. The COP9 signalosome complex (CSN) regulates CRLs by removing their ubiquitin-like activator NEDD8. The CUL4A-RBX1-DDB1-DDB2 complex (CRL4A(DDB2)) monitors the genome for ultraviolet-light-induced DNA damage. CRL4A(DBB2) is inactive in the absence of damaged DNA and requires CSN to regulate the repair process. The structural basis of CSN binding to CRL4A(DDB2) and the principles of CSN activation are poorly understood. Here we present cryo-electron microscopy structures for CSN in complex with neddylated CRL4A ligases to 6.4 Å resolution. The CSN conformers defined by cryo-electron microscopy and a novel apo-CSN crystal structure indicate an induced-fit mechanism that drives CSN activation by neddylated CRLs. We find that CSN and a substrate cannot bind simultaneously to CRL4A, favouring a deneddylated, inactive state for substrate-free CRL4 complexes. These architectural and regulatory principles appear conserved across CRL families, allowing global regulation by CSN.
History
DepositionJan 30, 2016-
Header (metadata) releaseFeb 24, 2016-
Map releaseApr 6, 2016-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3313.png

Downloads & links

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Map

FileDownload / File: emd_3313.map.gz / Format: CCP4 / Size: 39.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of CSN-N8-CRL4 at 6.7 A resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 220 pix.
= 290.4 Å		1.32 Å/pix.
x 220 pix.
= 290.4 Å		1.32 Å/pix.
x 220 pix.
= 290.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.02112711 - 0.07154658
Average (Standard dev.)-0.00001917 (±0.00438419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-110-110-110
Dimensions220220220
Spacing220220220
CellA=B=C: 290.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z290.400290.400290.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-64
NX/NY/NZ6161129
MAP C/R/S123
start NC/NR/NS-110-110-110
NC/NR/NS220220220
D min/max/mean-0.0210.072-0.000

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Supplemental data

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Sample components

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Entire : Recombinant human CSN-N8-CRL4A complex

EntireName: Recombinant human CSN-N8-CRL4A complex
Components
  • Sample: Recombinant human CSN-N8-CRL4A complex
  • Protein or peptide: COP9 signalosome subunit 1
  • Protein or peptide: COP9 signalosome subunit 2
  • Protein or peptide: COP9 signalosome subunit 3
  • Protein or peptide: COP9 signalosome subunit 4
  • Protein or peptide: COP9 signalosome subunit 5
  • Protein or peptide: COP9 signalosome subunit 6
  • Protein or peptide: COP9 signalosome subunit 7A
  • Protein or peptide: COP9 signalosome subunit 8
  • Protein or peptide: CUL4A
  • Protein or peptide: DNA DAMAGE-BINDING PROTEIN 1
  • Protein or peptide: E3 UBIQUITIN-PROTEIN LIGASE RBX1
  • Protein or peptide: NEDD8

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Supramolecule #1000: Recombinant human CSN-N8-CRL4A complex

SupramoleculeName: Recombinant human CSN-N8-CRL4A complex / type: sample / ID: 1000 / Number unique components: 12
Molecular weightTheoretical: 493 KDa

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Macromolecule #1: COP9 signalosome subunit 1

MacromoleculeName: COP9 signalosome subunit 1 / type: protein_or_peptide / ID: 1 / Name.synonym: CSN1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 1

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Macromolecule #2: COP9 signalosome subunit 2

MacromoleculeName: COP9 signalosome subunit 2 / type: protein_or_peptide / ID: 2 / Name.synonym: CSN2 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 2

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Macromolecule #3: COP9 signalosome subunit 3

MacromoleculeName: COP9 signalosome subunit 3 / type: protein_or_peptide / ID: 3 / Name.synonym: CSN3 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 3

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Macromolecule #4: COP9 signalosome subunit 4

MacromoleculeName: COP9 signalosome subunit 4 / type: protein_or_peptide / ID: 4 / Name.synonym: CSN4 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.6 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 4

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Macromolecule #5: COP9 signalosome subunit 5

MacromoleculeName: COP9 signalosome subunit 5 / type: protein_or_peptide / ID: 5 / Name.synonym: CSN5 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.4 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 5

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Macromolecule #6: COP9 signalosome subunit 6

MacromoleculeName: COP9 signalosome subunit 6 / type: protein_or_peptide / ID: 6 / Name.synonym: CSN6 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.6 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 6

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Macromolecule #7: COP9 signalosome subunit 7A

MacromoleculeName: COP9 signalosome subunit 7A / type: protein_or_peptide / ID: 7 / Name.synonym: CSN7A / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 7a

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Macromolecule #8: COP9 signalosome subunit 8

MacromoleculeName: COP9 signalosome subunit 8 / type: protein_or_peptide / ID: 8 / Name.synonym: CSN8 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 8

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Macromolecule #9: CUL4A

MacromoleculeName: CUL4A / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 79.3 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: Cullin-4A

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Macromolecule #10: DNA DAMAGE-BINDING PROTEIN 1

MacromoleculeName: DNA DAMAGE-BINDING PROTEIN 1 / type: protein_or_peptide / ID: 10 / Name.synonym: DDB1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 125.4 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: DNA damage-binding protein 1

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Macromolecule #11: E3 UBIQUITIN-PROTEIN LIGASE RBX1

MacromoleculeName: E3 UBIQUITIN-PROTEIN LIGASE RBX1 / type: protein_or_peptide / ID: 11 / Name.synonym: RBX1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.8 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #12: NEDD8

MacromoleculeName: NEDD8 / type: protein_or_peptide / ID: 12 / Name.synonym: NEDD8 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.9 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Ubiquitin-like protein NEDD8

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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

Concentration0.1 mg/mL
BufferpH: 7.4 / Details: 50mM HEPES, 200mM NaCl, 0.25mM TCEP
GridDetails: Quantifoil holey carbon grids (R1.2/1.3, Cu 400 mesh) and Lacey carbons films
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: LEICA EM GP / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: Gatan Image Filter Quantum LS / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateJun 1, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 2626
Details: Every image is the average of 38 frames recorded by the direct electron detector
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: OTHER / Software - Name: EMAN2, RELION / Number images used: 63269

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Atomic model buiding 1

Initial modelPDB ID:

4d10

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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Atomic model buiding 2

Initial modelPDB ID:

4d18

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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Atomic model buiding 3

Initial modelPDB ID:

4a0k

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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