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- EMDB-53028: Cryo-EM structure of apo-CAK-CDK2-cyclin A2 -

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Basic information

Entry
Database: EMDB / ID: EMD-53028
TitleCryo-EM structure of apo-CAK-CDK2-cyclin A2
Map dataPost-processed, sharpened map.
Sample
  • Complex: CAK-CDK2-cyclin A2 complex
    • Complex: CDK-activating kinase (CAK)
      • Protein or peptide: CDK-activating kinase assembly factor MAT1
      • Protein or peptide: Cyclin-H
      • Protein or peptide: Cyclin-dependent kinase 7
    • Complex: CDK2-cyclin A2
      • Protein or peptide: Cyclin-dependent kinase 2
      • Protein or peptide: Cyclin-A2
KeywordsComplex / cell cycle / kinase / TRANSFERASE
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat S5 kinase activity / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / ventricular system development / cellular response to luteinizing hormone stimulus / snRNA transcription by RNA polymerase II / G2/M DNA replication checkpoint / transcription factor TFIIK complex / CAK-ERCC2 complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 ...RNA polymerase II CTD heptapeptide repeat S5 kinase activity / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / ventricular system development / cellular response to luteinizing hormone stimulus / snRNA transcription by RNA polymerase II / G2/M DNA replication checkpoint / transcription factor TFIIK complex / CAK-ERCC2 complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / adult heart development / male pronucleus / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / cellular response to cocaine / [RNA-polymerase]-subunit kinase / response to glucagon / RNA Polymerase I Transcription Termination / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of DNA biosynthetic process / cellular response to insulin-like growth factor stimulus / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / regulation of heterochromatin organization / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / Y chromosome / cyclin-dependent protein kinase activity / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / X chromosome / PTK6 Regulates Cell Cycle / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / regulation of DNA replication / microtubule organizing center / centrosome duplication / RNA Polymerase I Transcription Initiation / regulation of G1/S transition of mitotic cell cycle / G0 and Early G1 / RNA polymerase II transcribes snRNA genes / cochlea development / animal organ regeneration / Telomere Extension By Telomerase / Activation of the pre-replicative complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / ATP-dependent activity, acting on DNA / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin A:Cdk2-associated events at S phase entry / Cyclin A/B1/B2 associated events during G2/M transition / cyclin-dependent protein kinase holoenzyme complex / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / regulation of G2/M transition of mitotic cell cycle / condensed chromosome / negative regulation of protein localization to chromatin / cellular response to platelet-derived growth factor stimulus / mitotic G1 DNA damage checkpoint signaling / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / cellular response to nitric oxide / positive regulation of smooth muscle cell proliferation / post-translational protein modification / regulation of mitotic cell cycle / cyclin binding / positive regulation of DNA replication / male germ cell nucleus / meiotic cell cycle / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair
Similarity search - Function
CyclinH/Ccl1 / Cyclin-dependent kinase 7 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain ...CyclinH/Ccl1 / Cyclin-dependent kinase 7 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Cyclin-A2 / Cyclin-dependent kinase 2 / Cyclin-dependent kinase 7 / Cyclin-H / CDK-activating kinase assembly factor MAT1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsCushing VI / Greber BJ / McGeoch AJS / Feng J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
The Institute of Cancer Research (ICR) United Kingdom
CitationJournal: Science / Year: 2025
Title: Structural basis of T-loop-independent recognition and activation of CDKs by the CDK-activating kinase.
Authors: Victoria I Cushing / Amy J S McGeoch / Sophie L Williams / Theodoros I Roumeliotis / Junjie Feng / Lucy M Dan / Jyoti S Choudhary / Norman E Davey / Basil J Greber /
Abstract: Cyclin-dependent kinases (CDKs) are prototypical regulators of the cell cycle. The CDK-activating kinase (CAK) acts as a master regulator of CDK activity by catalyzing the activating phosphorylation ...Cyclin-dependent kinases (CDKs) are prototypical regulators of the cell cycle. The CDK-activating kinase (CAK) acts as a master regulator of CDK activity by catalyzing the activating phosphorylation of CDKs on a conserved threonine residue within the regulatory T-loop. However, structural data illuminating the mechanism by which the CAK recognizes and activates CDKs have remained elusive. In this study, we determined high-resolution structures of the CAK in complex with CDK2 and CDK2-cyclin A2 by cryogenic electron microscopy. Our structures reveal a T-loop-independent kinase-kinase interface with contributions from both kinase lobes. Computational analysis and structures of the CAK in complex with CDK1-cyclin B1 and CDK11 indicate that these structures represent the general architecture of CAK-CDK complexes. These results advance our mechanistic understanding of cell cycle regulation and kinase signaling cascades.
History
DepositionMar 5, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53028.png

Downloads & links

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Map

FileDownload / File: emd_53028.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed, sharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 196 pix.
= 225.792 Å		1.15 Å/pix.
x 196 pix.
= 225.792 Å		1.15 Å/pix.
x 196 pix.
= 225.792 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.152 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.035214175 - 0.09732983
Average (Standard dev.)0.0000093823255 (±0.0026813026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 225.79199 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53028_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map.

Fileemd_53028_half_map_1.map
AnnotationUnfiltered half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map.

Fileemd_53028_half_map_2.map
AnnotationUnfiltered half-map.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CAK-CDK2-cyclin A2 complex

EntireName: CAK-CDK2-cyclin A2 complex
Components
  • Complex: CAK-CDK2-cyclin A2 complex
    • Complex: CDK-activating kinase (CAK)
      • Protein or peptide: CDK-activating kinase assembly factor MAT1
      • Protein or peptide: Cyclin-H
      • Protein or peptide: Cyclin-dependent kinase 7
    • Complex: CDK2-cyclin A2
      • Protein or peptide: Cyclin-dependent kinase 2
      • Protein or peptide: Cyclin-A2

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Supramolecule #1: CAK-CDK2-cyclin A2 complex

SupramoleculeName: CAK-CDK2-cyclin A2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: CDK-activating kinase (CAK) in complex with CDK2-cyclin A2
Molecular weightTheoretical: 83 KDa

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Supramolecule #2: CDK-activating kinase (CAK)

SupramoleculeName: CDK-activating kinase (CAK) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: CDK2-cyclin A2

SupramoleculeName: CDK2-cyclin A2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CDK-activating kinase assembly factor MAT1

MacromoleculeName: CDK-activating kinase assembly factor MAT1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.13234 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSSHHHHHH ENLYFQSNAM DDQGCPRCKT TKYRNPSLKL MVNVCGHTLC ESCVDLLFVR GAGNCPECGT PLRKSNFRVQ LFEDPTVDK EVEIRKKVLK IYNKREEDFP SLREYNDFLE EVEEIVFNLT NNVDLDNTKK KMEIYQKENK DVIQKNKLKL T REQEELEE ...String:
MGSSHHHHHH ENLYFQSNAM DDQGCPRCKT TKYRNPSLKL MVNVCGHTLC ESCVDLLFVR GAGNCPECGT PLRKSNFRVQ LFEDPTVDK EVEIRKKVLK IYNKREEDFP SLREYNDFLE EVEEIVFNLT NNVDLDNTKK KMEIYQKENK DVIQKNKLKL T REQEELEE ALEVERQENE QRRLFIQKEE QLQQILKRKN KQAFLDELES SDLPVALLLA QHKDRSTQLE MQLEKPKPVK PV TFSTGIK MGQHISLAPI HKLEEALYEY QPLQIETYGP HVPELEMLGR LGYLNHVRAA SPQDLAGGYT SSLACHRALQ DAF SGLFWQ PS

UniProtKB: CDK-activating kinase assembly factor MAT1

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Macromolecule #2: Cyclin-H

MacromoleculeName: Cyclin-H / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.721508 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: (ACE)MYHNSSQKR HWTFSSEEQL ARLRADANRK FRCKAVANGK VLPNDPVFLE PHEEMTLCKY YEKRLLEFCS VFKPAM PRS VVGTACMYFK RFYLNNSVME YHPRIIMLTC AFLACKVDEF NVSSPQFVGN LRESPLGQEK ALEQILEYEL LLIQQLN FH LIVHNPYRPF ...String:
(ACE)MYHNSSQKR HWTFSSEEQL ARLRADANRK FRCKAVANGK VLPNDPVFLE PHEEMTLCKY YEKRLLEFCS VFKPAM PRS VVGTACMYFK RFYLNNSVME YHPRIIMLTC AFLACKVDEF NVSSPQFVGN LRESPLGQEK ALEQILEYEL LLIQQLN FH LIVHNPYRPF EGFLIDLKTR YPILENPEIL RKTADDFLNR IALTDAYLLY TPSQIALTAI LSSASRAGIT MESYLSES L MLKENRTCLS QLLDIMKSMR NLVKKYEPPR SEEVAVLKQK LERCHSAELA LNVITKKRKG YEDDDYVSKK SKHEEEEWT DDDLVESL

UniProtKB: Cyclin-H

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Macromolecule #3: Cyclin-dependent kinase 7

MacromoleculeName: Cyclin-dependent kinase 7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.65107 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASWSHPQFE KGGGSGGGSG GGSWSHPQFE KSGGGSENLY FQSNAMALDV KSRAKRYEKL DFLGEGQFAT VYKARDKNTN QIVAIKKIK LGHRSEAKDG INRTALREIK LLQELSHPNI IGLLDAFGHK SNISLVFDFM ETDLEVIIKD NSLVLTPSHI K AYMLMTLQ ...String:
MASWSHPQFE KGGGSGGGSG GGSWSHPQFE KSGGGSENLY FQSNAMALDV KSRAKRYEKL DFLGEGQFAT VYKARDKNTN QIVAIKKIK LGHRSEAKDG INRTALREIK LLQELSHPNI IGLLDAFGHK SNISLVFDFM ETDLEVIIKD NSLVLTPSHI K AYMLMTLQ GLEYLHQHWI LHRDLKPNNL LLDENGVLKL ADFGLAKSFG SPNRAYTHQV VTRWYRAPEL LFGARMYGVG VD MWAVGCI LAELLLRVPF LPGDSDLDQL TRIFETLGTP TEEQWPDMCS LPDYVTFKSF PGIPLHHIFS AAGDDLLDLI QGL FLFNPC ARITATQALK MKYFSNRPGP TPGCQLPRPN CPVETLKEQS NPALAIKRKR TEALEQGGLP KKLIF

UniProtKB: Cyclin-dependent kinase 7

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Macromolecule #4: Cyclin-dependent kinase 2

MacromoleculeName: Cyclin-dependent kinase 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.24875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMENFQKV EKIGEGTYGV VYKARNKLTG EVVALKKIRL DTETEGVPST AIREISLLKE LNHPNIVKLL DVIHTENKLY LVFEFLHQD LKKFMDASAL TGIPLPLIKS YLFQLLQGLA FCHSHRVLHR DLKPQNLLIN TEGAIKLADF GLARAFGVPV R TYTHEVVT ...String:
SNAMENFQKV EKIGEGTYGV VYKARNKLTG EVVALKKIRL DTETEGVPST AIREISLLKE LNHPNIVKLL DVIHTENKLY LVFEFLHQD LKKFMDASAL TGIPLPLIKS YLFQLLQGLA FCHSHRVLHR DLKPQNLLIN TEGAIKLADF GLARAFGVPV R TYTHEVVT LWYRAPEILL GCKYYSTAVD IWSLGCIFAE MVTRRALFPG DSEIDQLFRI FRTLGTPDEV VWPGVTSMPD YK PSFPKWA RQDFSKVVPP LDEDGRSLLS QMLHYDPNKR ISAKAALAHP FFQDVTKPVP HLRL

UniProtKB: Cyclin-dependent kinase 2

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Macromolecule #5: Cyclin-A2

MacromoleculeName: Cyclin-A2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.867805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMLGNSAP GPATREAGSA LLALQQTALQ EDQENINPEK AAPVQQPRTR AALAVLKSGN PRGLAQQQRP KTRRVAPLKD LPVNDEHVT VPPWKANSKQ PAFTIHVDEA EKEAQKKPAE SQKIEREDAL AFNSAISLPG PRKPLVPLDY PMDGSFESPH T MDMSIVLE ...String:
SNAMLGNSAP GPATREAGSA LLALQQTALQ EDQENINPEK AAPVQQPRTR AALAVLKSGN PRGLAQQQRP KTRRVAPLKD LPVNDEHVT VPPWKANSKQ PAFTIHVDEA EKEAQKKPAE SQKIEREDAL AFNSAISLPG PRKPLVPLDY PMDGSFESPH T MDMSIVLE DEKPVSVNEV PDYHEDIHTY LREMEVKCKP KVGYMKKQPD ITNSMRAILV DWLVEVGEEY KLQNETLHLA VN YIDRFLS SMSVLRGKLQ LVGTAAMLLA SKFEEIYPPE VAEFVYITDD TYTKKQVLRM EHLVLKVLTF DLAAPTVNQF LTQ YFLHQQ PANCKVESLA MFLGELSLID ADPYLKYLPS VIAGAAFHLA LYTVTGQSWP ESLIRKTGYT LESLKPCLMD LHQT YLKAP QHAQQSIREK YKNSKYHGVS LLNPPETLNL

UniProtKB: Cyclin-A2

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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

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMHEPES
150.0 mMSodium chlorideNaCl
10.0 mMMagnesium chlorideMgCl2
0.5 mMAMP-PNP
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 10934 / Average electron dose: 70.0 e/Å2
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: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 215000
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

CTF correctionSoftware: (Name: cryoSPARC, RELION (ver. 5.0)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 106829
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 5.0)

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Atomic model buiding 1

Initial model
PDB IDChain

8p6y

source_name: PDB, initial_model_type: experimental model

1okv

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qcx:
Cryo-EM structure of apo-CAK-CDK2-cyclin A2

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