[English] 日本語
Yorodumi
- EMDB-8752: Cryo-EM structure of DNAPK -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8752
TitleCryo-EM structure of DNAPK
Map dataCryo-EM structure of DNAPK
Sample
  • Organelle or cellular component: DNA-PK holoenzyme complex
    • Protein or peptide: DNA-PK
Function / homology
Function and homology information


positive regulation of platelet formation / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / immature B cell differentiation / DNA-dependent protein kinase-DNA ligase 4 complex ...positive regulation of platelet formation / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / immature B cell differentiation / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / double-strand break repair via alternative nonhomologous end joining / Cytosolic sensors of pathogen-associated DNA / regulation of epithelial cell proliferation / IRF3-mediated induction of type I IFN / telomere capping / U3 snoRNA binding / regulation of hematopoietic stem cell differentiation / maturation of 5.8S rRNA / T cell lineage commitment / negative regulation of cGAS/STING signaling pathway / B cell lineage commitment / positive regulation of double-strand break repair via nonhomologous end joining / ectopic germ cell programmed cell death / somitogenesis / mitotic G1 DNA damage checkpoint signaling / activation of innate immune response / telomere maintenance / small-subunit processome / positive regulation of translation / negative regulation of protein phosphorylation / positive regulation of erythrocyte differentiation / protein-DNA complex / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / brain development / peptidyl-threonine phosphorylation / protein destabilization / protein modification process / regulation of circadian rhythm / double-strand break repair via nonhomologous end joining / cellular response to insulin stimulus / rhythmic process / double-strand break repair / intrinsic apoptotic signaling pathway in response to DNA damage / E3 ubiquitin ligases ubiquitinate target proteins / T cell differentiation in thymus / heart development / double-stranded DNA binding / peptidyl-serine phosphorylation / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / nucleolus / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
DNA-dependent protein kinase catalytic subunit, CC3 / DNA-dependent protein kinase catalytic subunit, catalytic domain / DNA-dependent protein kinase catalytic subunit, CC5 / DNA-dependent protein kinase catalytic subunit, CC1/2 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC3 / DNA-PKcs, CC5 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC1/2 / NUC194 ...DNA-dependent protein kinase catalytic subunit, CC3 / DNA-dependent protein kinase catalytic subunit, catalytic domain / DNA-dependent protein kinase catalytic subunit, CC5 / DNA-dependent protein kinase catalytic subunit, CC1/2 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC3 / DNA-PKcs, CC5 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC1/2 / NUC194 / PIK-related kinase, FAT / FAT domain / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
DNA-dependent protein kinase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human) / human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsSharif H / Li Y / Wu H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI125535 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Cryo-EM structure of the DNA-PK holoenzyme.
Authors: Humayun Sharif / Yang Li / Yuanchen Dong / Liyi Dong / Wei Li Wang / Youdong Mao / Hao Wu /
Abstract: DNA-dependent protein kinase (DNA-PK) is a large protein complex central to the nonhomologous end joining (NHEJ) DNA-repair pathway. It comprises the DNA-PK catalytic subunit (DNA-PKcs) and the ...DNA-dependent protein kinase (DNA-PK) is a large protein complex central to the nonhomologous end joining (NHEJ) DNA-repair pathway. It comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer of DNA-binding proteins Ku70 and Ku80. Here, we report the cryo-electron microscopy (cryo-EM) structures of human DNA-PKcs at 4.4-Å resolution and the DNA-PK holoenzyme at 5.8-Å resolution. The DNA-PKcs structure contains three distinct segments: the N-terminal region with an arm and a bridge, the circular cradle, and the head that includes the kinase domain. Two perpendicular apertures exist in the structure, which are sufficiently large for the passage of dsDNA. The DNA-PK holoenzyme cryo-EM map reveals density for the C-terminal globular domain of Ku80 that interacts with the arm of DNA-PKcs. The Ku80-binding site is adjacent to the previously identified density for the DNA-binding region of the Ku70/Ku80 complex, suggesting concerted DNA interaction by DNA-PKcs and the Ku complex.
History
DepositionJun 5, 2017-
Header (metadata) releaseJun 14, 2017-
Map releaseJul 12, 2017-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8752.png

Downloads & links

-
Map

FileDownload / File: emd_8752.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of DNAPK
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.51 Å/pix.
x 160 pix.
= 241.6 Å		1.51 Å/pix.
x 160 pix.
= 241.6 Å		1.51 Å/pix.
x 160 pix.
= 241.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.51 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.02647787 - 0.061950527
Average (Standard dev.)0.00027630603 (±0.0039580823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 241.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.511.511.51
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z241.600241.600241.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0260.0620.000

-
Supplemental data

-
Sample components

-
Entire : DNA-PK holoenzyme complex

EntireName: DNA-PK holoenzyme complex
Components
  • Organelle or cellular component: DNA-PK holoenzyme complex
    • Protein or peptide: DNA-PK

-
Supramolecule #1: DNA-PK holoenzyme complex

SupramoleculeName: DNA-PK holoenzyme complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: DNA-PK (DNA-PKcs in complex with Ku80-CTR)
Source (natural)Organism: Homo sapiens (human) / Organ: Cervical / Location in cell: Nucleus

-
Macromolecule #1: DNA-PK

MacromoleculeName: DNA-PK / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human) / Organ: CERVICAL
SequenceString: MAGSGAGVR CSLLRLQETL SAADRCGAAL AGHQLIRGLG QECVLSSSPA VLALQTSLVF S RDFGLLVF VRKSLNSIEF RECREEILKF LCIFLEKMGQ KIAPYSVEIK NTCTSVYTKD RA AKCKIPA LDLLIKLLQT FRSSRLMDEF KIGELFSKFY GELALKKKIP ...String:
MAGSGAGVR CSLLRLQETL SAADRCGAAL AGHQLIRGLG QECVLSSSPA VLALQTSLVF S RDFGLLVF VRKSLNSIEF RECREEILKF LCIFLEKMGQ KIAPYSVEIK NTCTSVYTKD RA AKCKIPA LDLLIKLLQT FRSSRLMDEF KIGELFSKFY GELALKKKIP DTVLEKVYEL LGL LGEVHP SEMINNAENL FRAFLGELKT QMTSAVREPK LPVLAGCLKG LSSLLCNFTK SMEE DPQTS REIFNFVLKA IRPQIDLKRY AVPSAGLRLF ALHASQFSTC LLDNYVSLFE VLLKW CAHT NVELKKAALS ALESFLKQVS NMVAKNAEMH KNKLQYFMEQ FYGIIRNVDS NNKELS IAI RGYGLFAGPC KVINAKDVDF MYVELIQRCK QMFLTQTDTG DDRVYQMPSF LQSVASV LL YLDTVPEVYT PVLEHLVVMQ IDSFPQYSPK MQLVCCRAIV KVFLALAAKG PVLRNCIS T VVHQGLIRIC SKPVVLPKGP ESESEDHRAS GEVRTGKWKV PTYKDYVDLF RHLLSSDQM MDSILADEAF FSVNSSSESL NHLLYDEFVK SVLKIVEKLD LTLEIQTVGE QENGDEAPGV WMIPTSDPA ANLHPAKPKD FSAFINLVEF CREILPEKQA EFFEPWVYSF SYELILQSTR L PLISGFYK LLSITVRNAK KIKYFEGVSP KSLKHSPEDP EKYSCFALFV KFGKEVAVKM KQ YKDELLA SCLTFLLSLP HNIIELDVRA YVPALQMAFK LGLSYTPLAE VGLNALEEWS IYI DRHVMQ PYYKDILPCL DGYLKTSALS DETKNNWEVS ALSRAAQKGF NKVVLKHLKK TKNL SSNEA ISLEEIRIRV VQMLGSLGGQ INKNLLTVTS SDEMMKSYVA WDREKRLSFA VPFRE MKPV IFLDVFLPRV TELALTASDR QTKVAACELL HSMVMFMLGK ATQMPEGGQG APPMYQ LYK RTFPVLLRLA CDVDQVTRQL YEPLVMQLIH WFTNNKKFES QDTVALLEAI LDGIVDP VD STLRDFCGRC IREFLKWSIK QITPQQQEKS PVNTKSLFKR LYSLALHPNA FKRLGASL A FNNIYREFRE EESLVEQFVF EALVIYMESL ALAHADEKSL GTIQQCCDAI DHLCRIIEK KHVSLNKAKK RRLPRGFPPS ASLCLLDLVK WLLAHCGRPQ TECRHKSIEL FYKFVPLLPG NRSPNLWLK DVLKEEGVSF LINTFEGGGC GQPSGILAQP TLLYLRGPFS LQATLCWLDL L LAALECYN TFIGERTVGA LQVLGTEAQS SLLKAVAFFL ESIAMHDIIA AEKCFGTGAA GN RTSPQEG ERYNYSKCTV VVRIMEFTTT LLNTSPEGWK LLKKDLCNTH LMRVLVQTLC EPA SIGFNI GDVQVMAHLP DVCVNLMKAL KMSPYKDILE THLREKITAQ SIEELCAVNL YGPD AQVDR SRLAAVVSAC KQLHRAGLLH NILPSQSTDL HHSVGTELLS LVYKGIAPGD ERQCL PSLD LSCKQLASGL LELAFAFGGL CERLVSLLLN PAVLSTASLG SSQGSVIHFS HGEYFY SLF SETINTELLK NLDLAVLELM QSSVDNTKMV SAVLNGMLDQ SFRERANQKH QGLKLAT TI LQHWKKCDSW WAKDSPLETK MAVLALLAKI LQIDSSVSFN TSHGSFPEVF TTYISLLA D TKLDLHLKGQ AVTLLPFFTS LTGGSLEELR RVLEQLIVAH FPMQSREFPP GTPRFNNYV DCMKKFLDAL ELSQSPMLLE LMTEVLCREQ QHVMEELFQS SFRRIARRGS CVTQVGLLES VYEMFRKDD PRLSFTRQSF VDRSLLTLLW HCSLDALREF FSTIVVDAID VLKSRFTKLN E STFDTQIT KKMGYYKILD VMYSRLPKDD VHAKESKINQ VFHGSCITEG NELTKTLIKL CY DAFTENM AGENQLLERR RLYHCAAYNC AISVICCVFN ELKFYQGFLF SEKPEKNLLI FEN LIDLKR RYNFPVEVEV PMERKKKYIE IRKEAREAAN GDSDGPSYMS SLSYLADSTL SEEM SQFDF STGVQSYSYS SQDPRPATGR FRRREQRDPT VHDDVLELEM DELNRHECMA PLTAL VKHM HRSLGPPQGE EDSVPRDLPS WMKFLHGKLG NPIVPLNIRL FLAKLVINTE EVFRPY AKH WLSPLLQLAA SENNGGEGIH YMVVEIVATI LSWTGLATPT GVPKDEVLAN RLLNFLM KH VFHPKRAVFR HNLEIIKTLV ECWKDCLSIP YRLIFEKFSG KDPNSKDNSV GIQLLGIV M ANDLPPYDPQ CGIQSSEYFQ ALVNNMSFVR YKEVYAAAAE VLGLILRYVM ERKNILEES LCELVAKQLK QHQNTMEDKF IVCLNKVTKS FPPLADRFMN AVFFLLPKFH GVLKTLCLEV VLCRVEGMT ELYFQLKSKD FVQVMRHRDD ERQKVCLDII YKMMPKLKPV ELRELLNPVV E FVSHPSTT CREQMYNILM WIHDNYRDPE SETDNDSQEI FKLAKDVLIQ GLIDENPGLQ LI IRNFWSH ETRLPSNTLD RLLALNSLYS PKIEVHFLSL ATNFLLEMTS MSPDYPNPMF EHP LSECEF QEYTIDSDWR FRSTVLTPMF VETQASQGTL QTRTQEGSLS ARWPVAGQIR ATQQ QHDFT LTQTADGRSS FDWLTGSSTD PLVDHTSPSS DSLLFAHKRS ERLQRAPLKS VGPDF GKKR LGLPGDEVDN KVKGAAGRTD LLRLRRRFMR DQEKLSLMYA RKGVAEQKRE KEIKSE LKM KQDAQVVLYR SYRHGDLPDI QIKHSSLITP LQAVAQRDPI IAKQLFSSLF SGILKEM DK FKTLSEKNNI TQKLLQDFNR FLNTTFSFFP PFVSCIQDIS CQHAALLSLD PAAVSAGC L ASLQQPVGIR LLEEALLRLL PAELPAKRVR GKARLPPDVL RWVELAKLYR SIGEYDVLR GIFTSEIGTK QITQSALLAE ARSDYSEAAK QYDEALNKQD WVDGEPTEAE KDFWELASLD CYNHLAEWK SLEYCSTASI DSENPPDLNK IWSEPFYQET YLPYMIRSKL KLLLQGEADQ S LLTFIDKA MHGELQKAIL ELHYSQELSL LYLLQDDVDR AKYYIQNGIQ SFMQNYSSID VL LHQSRLT KLQSVQALTE IQEFISFISK QGNLSSQVPL KRLLNTWTNR YPDAKMDPMN IWD DIITNR CFFLSKIEEK LTPLPEDNSM NVDQDGDPSD RMEVQEQEED ISSLIRSCKF SMKM KMIDS ARKQNNFSLA MKLLKELHKE SKTRDDWLVS WVQSYCRLSH CRSRSQGCSE QVLTV LKTV SLLDENNVSS YLSKNILAFR DQNILLGTTY RIIANALSSE PACLAEIEED KARRIL ELS GSSSEDSEKV IAGLYQRAFQ HLSEAVQAAE EEAQPPSWSC GPAAGVIDAY MTLADFC DQ QLRKEEENAS VIDSAELQAY PALVVEKMLK ALKLNSNEAR LKFPRLLQII ERYPEETL S LMTKEISSVP CWQFISWISH MVALLDKDQA VAVQHSVEEI TDNYPQAIVY PFIISSESY SFKDTSTGHK NKEFVARIKS KLDQGGVIQD FINALDQLSN PELLFKDWSN DVRAELAKTP VNKKNIEKM YERMYAALGD PKAPGLGAFR RKFIQTFGKE FDKHFGKGGS KLLRMKLSDF N DITNMLLL KMNKDSKPPG NLKECSPWMS DFKVEFLRNE LEIPGQYDGR GKPLPEYHVR IA GFDERVT VMASLRRPKR IIIRGHDERE HPFLVKGGED LRQDQRVEQL FQVMNGILAQ DSA CSQRAL QLRTYSVVPM TSRLGLIEWL ENTVTLKDLL LNTMSQEEKA AYLSDPRAPP CEYK DWLTK MSGKHDVGAY MLMYKGANRT ETVTSFRKRE SKVPADLLKR AFVRMSTSPE AFLAL RSHF ASSHALICIS HWILGIGDRH LNNFMVAMET GGVIGIDFGH AFGSATQFLP VPELMP FRL TRQFINLMLP MKETGLMYSI MVHALRAFRS DPGLLTNTMD VFVKEPSFDW KNFEQKM LK KGGSWIQEIN VAEKNWYPRQ KICYAKRKLA GANPAVITCD ELLLGHEKAP AFRDYVAV A RGSKDHNIRA QEPESGLSEE TQVKCLMDQA TDPNILGRTW EGWEPWM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.4 / Details: 20mM Hepes pH 7.4, 150mM NaCl, 0.5mM EDTA, 1mM DTT
Sugar embeddingMaterial: ice
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsDNA-PK holoenzyme containing DNA-PKcs and Ku70/80 proteins purified from Hela cell nuclear extracts.

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46415

+
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