[English] 日本語
Yorodumi
- EMDB-28734: DNA-PKcs monomer in dimer DNA-PKcs complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28734
TitleDNA-PKcs monomer in dimer DNA-PKcs complex
Map dataDPKcs in dimer
Sample
  • Complex: dimer of DNA-PKcs
    • Protein or peptide: PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit
KeywordsDimer / Kinase / Complex / NHEJ / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsChen S / He Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM135651 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
CitationJournal: Sci Adv / Year: 2023
Title: Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ.
Authors: Siyu Chen / Alex Vogt / Linda Lee / Tasmin Naila / Ryan McKeown / Alan E Tomkinson / Susan P Lees-Miller / Yuan He /
Abstract: DNA double-strand breaks (DSBs), one of the most cytotoxic forms of DNA damage, can be repaired by the tightly regulated nonhomologous end joining (NHEJ) machinery (Stinson and Loparo and Zhao ). ...DNA double-strand breaks (DSBs), one of the most cytotoxic forms of DNA damage, can be repaired by the tightly regulated nonhomologous end joining (NHEJ) machinery (Stinson and Loparo and Zhao ). Core NHEJ factors form an initial long-range (LR) synaptic complex that transitions into a DNA-PKcs (DNA-dependent protein kinase, catalytic subunit)-free, short-range state to align the DSB ends (Chen ). Using single-particle cryo-electron microscopy, we have visualized three additional key NHEJ complexes representing different transition states, with DNA-PKcs adopting distinct dimeric conformations within each of them. Upon DNA-PKcs autophosphorylation, the LR complex undergoes a substantial conformational change, with both Ku and DNA-PKcs rotating outward to promote DNA break exposure and DNA-PKcs dissociation. We also captured a dimeric state of catalytically inactive DNA-PKcs, which resembles structures of other PIKK (Phosphatidylinositol 3-kinase-related kinase) family kinases, revealing a model of the full regulatory cycle of DNA-PKcs during NHEJ.
History
DepositionOct 31, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28734.png

Downloads & links

-
Map

FileDownload / File: emd_28734.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDPKcs in dimer
Voxel sizeX=Y=Z: 1.6512 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.00054426136 - 2.2636538
Average (Standard dev.)0.013915995 (±0.0882309)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 277.4016 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half1

Fileemd_28734_half_map_1.map
Annotationhalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half2

Fileemd_28734_half_map_2.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : dimer of DNA-PKcs

EntireName: dimer of DNA-PKcs
Components
  • Complex: dimer of DNA-PKcs
    • Protein or peptide: PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit

-
Supramolecule #1: dimer of DNA-PKcs

SupramoleculeName: dimer of DNA-PKcs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 940 KDa

-
Macromolecule #1: PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit

MacromoleculeName: PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
SequenceString: MAGSGAGVRC SLLRLQETLS AADRCGAALA GHQLIRGLGQ ECVLSSSPAV LALQTSLVFS RDFGLLVFV RKSLNSIEFR ECREEILKFL CIFLEKMGQK IAPYSVEIKN TCTSVYTKDR A AKCKIPAL DLLIKLLQTF RSSRLMDEFK IGELFSKFYG ELALKKKIPD ...String:
MAGSGAGVRC SLLRLQETLS AADRCGAALA GHQLIRGLGQ ECVLSSSPAV LALQTSLVFS RDFGLLVFV RKSLNSIEFR ECREEILKFL CIFLEKMGQK IAPYSVEIKN TCTSVYTKDR A AKCKIPAL DLLIKLLQTF RSSRLMDEFK IGELFSKFYG ELALKKKIPD TVLEKVYELL GL LGEVHPS EMINNAENLF RAFLGELKTQ MTSAVREPKL PVLAGCLKGL SSLLCNFTKS MEE DPQTSR EIFNFVLKAI RPQIDLKRYA VPSAGLRLFA LHASQFSTCL LDNYVSLFEV LLKW CAHTN VELKKAALSA LESFLKQVSN MVAKNAEMHK NKLQYFMEQF YGIIRNVDSN NKELS IAIR GYGLFAGPCK VINAKDVDFM YVELIQRCKQ MFLTQTDTGD DRVYQMPSFL QSVASV LLY LDTVPEVYTP VLEHLVVMQI DSFPQYSPKM QLVCCRAIVK VFLALAAKGP VLRNCIS TV VHQGLIRICS KPVVLPKGPE SESEDHRASG EVRTGKWKVP TYKDYVDLFR HLLSSDQM M DSILADEAFF SVNSSSESLN HLLYDEFVKS VLKIVEKLDL TLEIQTVGEQ ENGDEAPGV WMIPTSDPAA NLHPAKPKDF SAFINLVEFC REILPEKQAE FFEPWVYSFS YELILQSTRL PLISGFYKL LSITVRNAKK IKYFEGVSPK SLKHSPEDPE KYSCFALFVK FGKEVAVKMK Q YKDELLAS CLTFLLSLPH NIIELDVRAY VPALQMAFKL GLSYTPLAEV GLNALEEWSI YI DRHVMQP YYKDILPCLD GYLKTSALSD ETKNNWEVSA LSRAAQKGFN KVVLKHLKKT KNL SSNEAI SLEEIRIRVV QMLGSLGGQI NKNLLTVTSS DEMMKSYVAW DREKRLSFAV PFRE MKPVI FLDVFLPRVT ELALTASDRQ TKVAACELLH SMVMFMLGKA TQMPEGGQGA PPMYQ LYKR TFPVLLRLAC DVDQVTRQLY EPLVMQLIHW FTNNKKFESQ DTVALLEAIL DGIVDP VDS TLRDFCGRCI REFLKWSIKQ ITPQQQEKSP VNTKSLFKRL YSLALHPNAF KRLGASL AF NNIYREFREE ESLVEQFVFE ALVIYMESLA LAHADEKSLG TIQQCCDAID HLCRIIEK K HVSLNKAKKR RLPRGFPPSA SLCLLDLVKW LLAHCGRPQT ECRHKSIELF YKFVPLLPG NRSPNLWLKD VLKEEGVSFL INTFEGGGCG QPSGILAQPT LLYLRGPFSL QATLCWLDLL LAALECYNT FIGERTVGAL QVLGTEAQSS LLKAVAFFLE SIAMHDIIAA EKCFGTGAAG N RTSPQEGE RYNYSKCTVV VRIMEFTTTL LNTSPEGWKL LKKDLCNTHL MRVLVQTLCE PA SIGFNIG DVQVMAHLPD VCVNLMKALK MSPYKDILET HLREKITAQS IEELCAVNLY GPD AQVDRS RLAAVVSACK QLHRAGLLHN ILPSQSTDLH HSVGTELLSL VYKGIAPGDE RQCL PSLDL SCKQLASGLL ELAFAFGGLC ERLVSLLLNP AVLSTASLGS SQGSVIHFSH GEYFY SLFS ETINTELLKN LDLAVLELMQ SSVDNTKMVS AVLNGMLDQS FRERANQKHQ GLKLAT TIL QHWKKCDSWW AKDSPLETKM AVLALLAKIL QIDSSVSFNT SHGSFPEVFT TYISLLA DT KLDLHLKGQA VTLLPFFTSL TGGSLEELRR VLEQLIVAHF PMQSREFPPG TPRFNNYV D CMKKFLDALE LSQSPMLLEL MTEVLCREQQ HVMEELFQSS FRRIARRGSC VTQVGLLES VYEMFRKDDP RLSFTRQSFV DRSLLTLLWH CSLDALREFF STIVVDAIDV LKSRFTKLNE STFDTQITK KMGYYKILDV MYSRLPKDDV HAKESKINQV FHGSCITEGN ELTKTLIKLC Y DAFTENMA GENQLLERRR LYHCAAYNCA ISVICCVFNE LKFYQGFLFS EKPEKNLLIF EN LIDLKRR YNFPVEVEVP MERKKKYIEI RKEAREAANG DSDGPSYMSS LSYLADSTLS EEM SQFDFS TGVQSYSYSS QDPRPATGRF RRREQRDPTV HDDVLELEMD ELNRHECMAP LTAL VKHMH RSLGPPQGEE DSVPRDLPSW MKFLHGKLGN PIVPLNIRLF LAKLVINTEE VFRPY AKHW LSPLLQLAAS ENNGGEGIHY MVVEIVATIL SWTGLATPTG VPKDEVLANR LLNFLM KHV FHPKRAVFRH NLEIIKTLVE CWKDCLSIPY RLIFEKFSGK DPNSKDNSVG IQLLGIV MA NDLPPYDPQC GIQSSEYFQA LVNNMSFVRY KEVYAAAAEV LGLILRYVME RKNILEES L CELVAKQLKQ HQNTMEDKFI VCLNKVTKSF PPLADRFMNA VFFLLPKFHG VLKTLCLEV VLCRVEGMTE LYFQLKSKDF VQVMRHRDDE RQKVCLDIIY KMMPKLKPVE LRELLNPVVE FVSHPSTTC REQMYNILMW IHDNYRDPES ETDNDSQEIF KLAKDVLIQG LIDENPGLQL I IRNFWSHE TRLPSNTLDR LLALNSLYSP KIEVHFLSLA TNFLLEMTSM SPDYPNPMFE HP LSECEFQ EYTIDSDWRF RSTVLTPMFV ETQASQGTLQ TRTQEGSLSA RWPVAGQIRA TQQ QHDFTL TQTADGRSSF DWLTGSSTDP LVDHTSPSSD SLLFAHKRSE RLQRAPLKSV GPDF GKKRL GLPGDEVDNK VKGAAGRTDL LRLRRRFMRD QEKLSLMYAR KGVAEQKREK EIKSE LKMK QDAQVVLYRS YRHGDLPDIQ IKHSSLITPL QAVAQRDPII AKQLFSSLFS GILKEM DKF KTLSEKNNIT QKLLQDFNRF LNTTFSFFPP FVSCIQDISC QHAALLSLDP AAVSAGC LA SLQQPVGIRL LEEALLRLLP AELPAKRVRG KARLPPDVLR WVELAKLYRS IGEYDVLR G IFTSEIGTKQ ITQSALLAEA RSDYSEAAKQ YDEALNKQDW VDGEPTEAEK DFWELASLD CYNHLAEWKS LEYCSTASID SENPPDLNKI WSEPFYQETY LPYMIRSKLK LLLQGEADQS LLTFIDKAM HGELQKAILE LHYSQELSLL YLLQDDVDRA KYYIQNGIQS FMQNYSSIDV L LHQSRLTK LQSVQALTEI QEFISFISKQ GNLSSQVPLK RLLNTWTNRY PDAKMDPMNI WD DIITNRC FFLSKIEEKL TPLPEDNSMN VDQDGDPSDR MEVQEQEEDI SSLIRSCKFS MKM KMIDSA RKQNNFSLAM KLLKELHKES KTRDDWLVSW VQSYCRLSHC RSRSQGCSEQ VLTV LKTVS LLDENNVSSY LSKNILAFRD QNILLGTTYR IIANALSSEP ACLAEIEEDK ARRIL ELSG SSSEDSEKVI AGLYQRAFQH LSEAVQAAEE EAQPPSWSCG PAAGVIDAYM TLADFC DQQ LRKEEENASV IDSAELQAYP ALVVEKMLKA LKLNSNEARL KFPRLLQIIE RYPEETL SL MTKEISSVPC WQFISWISHM VALLDKDQAV AVQHSVEEIT DNYPQAIVYP FIISSESY S FKDTSTGHKN KEFVARIKSK LDQGGVIQDF INALDQLSNP ELLFKDWSND VRAELAKTP VNKKNIEKMY ERMYAALGDP KAPGLGAFRR KFIQTFGKEF DKHFGKGGSK LLRMKLSDFN DITNMLLLK MNKDSKPPGN LKECSPWMSD FKVEFLRNEL EIPGQYDGRG KPLPEYHVRI A GFDERVTV MASLRRPKRI IIRGHDEREH PFLVKGGEDL RQDQRVEQLF QVMNGILAQD SA CSQRALQ LRTYSVVPMT SRLGLIEWLE NTVTLKDLLL NTMSQEEKAA YLSDPRAPPC EYK DWLTKM SGKHDVGAYM LMYKGANRTE TVTSFRKRES KVPADLLKRA FVRMSTSPEA FLAL RSHFA SSHALICISH WILGIGDRHL NNFMVAMETG GVIGIDFGHA FGSATQFLPV PELMP FRLT RQFINLMLPM KETGLMYSIM VHALRAFRSD PGLLTNTMDV FVKEPSFDWK NFEQKM LKK GGSWIQEINV AEKNWYPRQK ICYAKRKLAG ANPAVITCDE LLLGHEKAPA FRDYVAV AR GSKDHNIRAQ EPESGLSEET QVKCLMDQAT DPNILGRTWE GWEPWM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.3 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Support film - Film thickness: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 302 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 13132 / Average exposure time: 4.0 sec. / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 2.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1587734
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7lt3

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 64775
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: CC

+
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://pdbjlvh1.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