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- EMDB-14545: DNA-PK in the active state -

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Basic information

Entry
Database: EMDB / ID: EMD-14545
TitleDNA-PK in the active state
Map data
Sample
  • Complex: Human DNA-dependent protein kinase
    • Protein or peptide: DNA-dependent protein kinase catalytic subunit
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • DNA: DNA (26-MER)
    • DNA: DNA (26-MER)
  • Ligand: (~{S})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-yl)phenyl]-(6-methoxypyridazin-3-yl)methanol
  • Ligand: water
KeywordsDNA-dependent protein kinase / DNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of platelet formation / Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / immature B cell differentiation ...positive regulation of platelet formation / Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / immature B cell differentiation / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / immunoglobulin V(D)J recombination / regulation of smooth muscle cell proliferation / nuclear telomere cap complex / double-strand break repair via alternative nonhomologous end joining / telomere capping / double-strand break repair via classical nonhomologous end joining / regulation of epithelial cell proliferation / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / regulation of hematopoietic stem cell differentiation / regulation of telomere maintenance / recombinational repair / U3 snoRNA binding / protein localization to chromosome, telomeric region / cellular response to fatty acid / cellular hyperosmotic salinity response / positive regulation of neurogenesis / T cell lineage commitment / maturation of 5.8S rRNA / positive regulation of double-strand break repair via nonhomologous end joining / B cell lineage commitment / negative regulation of cGAS/STING signaling pathway / telomeric DNA binding / 2-LTR circle formation / hematopoietic stem cell proliferation / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / negative regulation of protein phosphorylation / 5'-deoxyribose-5-phosphate lyase activity / ATP-dependent activity, acting on DNA / positive regulation of protein kinase activity / hematopoietic stem cell differentiation / ectopic germ cell programmed cell death / telomere maintenance via telomerase / somitogenesis / DNA helicase activity / neurogenesis / mitotic G1 DNA damage checkpoint signaling / peptidyl-threonine phosphorylation / telomere maintenance / activation of innate immune response / cyclin binding / cellular response to leukemia inhibitory factor / enzyme activator activity / positive regulation of erythrocyte differentiation / positive regulation of translation / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / small-subunit processome / regulation of circadian rhythm / cellular response to gamma radiation / protein destabilization / brain development / protein-DNA complex / protein modification process / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via nonhomologous end joining / cellular response to insulin stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / rhythmic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / peptidyl-serine phosphorylation / T cell differentiation in thymus / heart development / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / ficolin-1-rich granule lumen / damaged DNA binding / eukaryotic translation initiation factor 2alpha kinase activity / chromosome, telomeric region / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity
Similarity search - Function
Ku70, bridge and pillars domain superfamily / : / Ku70 / 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 ...Ku70, bridge and pillars domain superfamily / : / Ku70 / 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 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 N-terminal alpha/beta domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / : / FATC domain / PIK-related kinase, FAT / FAT 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 / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
X-ray repair cross-complementing protein 6 / X-ray repair cross-complementing protein 5 / DNA-dependent protein kinase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsLiang S / Blundell TL
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Human DNA-dependent protein kinase activation mechanism.
Authors: Shikang Liang / Tom L Blundell /
Abstract: DNA-dependent protein kinase (DNA-PK), a multicomponent complex including the DNA-PK catalytic subunit and Ku70/80 heterodimer together with DNA, is central to human DNA damage response and repair. ...DNA-dependent protein kinase (DNA-PK), a multicomponent complex including the DNA-PK catalytic subunit and Ku70/80 heterodimer together with DNA, is central to human DNA damage response and repair. Using a DNA-PK-selective inhibitor (M3814), we identified from one dataset two cryo-EM structures of the human DNA-PK complex in different states, the intermediate state and the active state. Here we show that activation of the kinase is regulated through conformational changes caused by the binding ligand and the string region (residues 802-846) of the DNA-PK catalytic subunit, particularly the helix-hairpin-helix motif (residues 816-836) that interacts with DNA. These observations demonstrate the regulatory role of the ligand and explain why DNA-PK is DNA dependent. Cooperation and coordination among binding partners, disordered flexible regions and mechanically flexible HEAT repeats modulate the activation of the kinase. Together with previous findings, these results provide a better molecular understanding of DNA-PK catalysis.
History
DepositionMar 16, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14545.png

Downloads & links

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Map

FileDownload / File: emd_14545.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 350 pix.
= 456.4 Å		1.3 Å/pix.
x 350 pix.
= 456.4 Å		1.3 Å/pix.
x 350 pix.
= 456.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.304 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-2.0018477 - 3.0337958
Average (Standard dev.)0.0000063514535 (±0.036521766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 456.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14545_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_14545_half_map_2.map
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Sample components

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Entire : Human DNA-dependent protein kinase

EntireName: Human DNA-dependent protein kinase
Components
  • Complex: Human DNA-dependent protein kinase
    • Protein or peptide: DNA-dependent protein kinase catalytic subunit
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • DNA: DNA (26-MER)
    • DNA: DNA (26-MER)
  • Ligand: (~{S})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-yl)phenyl]-(6-methoxypyridazin-3-yl)methanol
  • Ligand: water

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Supramolecule #1: Human DNA-dependent protein kinase

SupramoleculeName: Human DNA-dependent protein kinase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA-dependent protein kinase catalytic subunit

MacromoleculeName: DNA-dependent protein kinase catalytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 469.673219 KDa
SequenceString: MAGSGAGVRC SLLRLQETLS AADRCGAALA GHQLIRGLGQ ECVLSSSPAV LALQTSLVFS RDFGLLVFVR KSLNSIEFRE CREEILKFL CIFLEKMGQK IAPYSVEIKN TCTSVYTKDR AAKCKIPALD LLIKLLQTFR SSRLMDEFKI GELFSKFYGE L ALKKKIPD ...String:
MAGSGAGVRC SLLRLQETLS AADRCGAALA GHQLIRGLGQ ECVLSSSPAV LALQTSLVFS RDFGLLVFVR KSLNSIEFRE CREEILKFL CIFLEKMGQK IAPYSVEIKN TCTSVYTKDR AAKCKIPALD LLIKLLQTFR SSRLMDEFKI GELFSKFYGE L ALKKKIPD TVLEKVYELL GLLGEVHPSE MINNAENLFR AFLGELKTQM TSAVREPKLP VLAGCLKGLS SLLCNFTKSM EE DPQTSRE IFNFVLKAIR PQIDLKRYAV PSAGLRLFAL HASQFSTCLL DNYVSLFEVL LKWCAHTNVE LKKAALSALE SFL KQVSNM VAKNAEMHKN KLQYFMEQFY GIIRNVDSNN KELSIAIRGY GLFAGPCKVI NAKDVDFMYV ELIQRCKQMF LTQT DTGDD RVYQMPSFLQ SVASVLLYLD TVPEVYTPVL EHLVVMQIDS FPQYSPKMQL VCCRAIVKVF LALAAKGPVL RNCIS TVVH QGLIRICSKP VVLPKGPESE SEDHRASGEV RTGKWKVPTY KDYVDLFRHL LSSDQMMDSI LADEAFFSVN SSSESL NHL LYDEFVKSVL KIVEKLDLTL EIQTVGEQEN GDEAPGVWMI PTSDPAANLH PAKPKDFSAF INLVEFCREI LPEKQAE FF EPWVYSFSYE LILQSTRLPL ISGFYKLLSI TVRNAKKIKY FEGVSPKSLK HSPEDPEKYS CFALFVKFGK EVAVKMKQ Y KDELLASCLT FLLSLPHNII ELDVRAYVPA LQMAFKLGLS YTPLAEVGLN ALEEWSIYID RHVMQPYYKD ILPCLDGYL KTSALSDETK NNWEVSALSR AAQKGFNKVV LKHLKKTKNL SSNEAISLEE IRIRVVQMLG SLGGQINKNL LTVTSSDEMM KSYVAWDRE KRLSFAVPFR EMKPVIFLDV FLPRVTELAL TASDRQTKVA ACELLHSMVM FMLGKATQMP EGGQGAPPMY Q LYKRTFPV LLRLACDVDQ VTRQLYEPLV MQLIHWFTNN KKFESQDTVA LLEAILDGIV DPVDSTLRDF CGRCIREFLK WS IKQITPQ QQEKSPVNTK SLFKRLYSLA LHPNAFKRLG ASLAFNNIYR EFREEESLVE QFVFEALVIY MESLALAHAD EKS LGTIQQ CCDAIDHLCR IIEKKHVSLN KAKKRRLPRG FPPSASLCLL DLVKWLLAHC GRPQTECRHK SIELFYKFVP LLPG NRSPN LWLKDVLKEE GVSFLINTFE GGGCGQPSGI LAQPTLLYLR GPFSLQATLC WLDLLLAALE CYNTFIGERT VGALQ VLGT EAQSSLLKAV AFFLESIAMH DIIAAEKCFG TGAAGNRTSP QEGERYNYSK CTVVVRIMEF TTTLLNTSPE GWKLLK KDL CNTHLMRVLV QTLCEPASIG FNIGDVQVMA HLPDVCVNLM KALKMSPYKD ILETHLREKI TAQSIEELCA VNLYGPD AQ VDRSRLAAVV SACKQLHRAG LLHNILPSQS TDLHHSVGTE LLSLVYKGIA PGDERQCLPS LDLSCKQLAS GLLELAFA F GGLCERLVSL LLNPAVLSTA SLGSSQGSVI HFSHGEYFYS LFSETINTEL LKNLDLAVLE LMQSSVDNTK MVSAVLNGM LDQSFRERAN QKHQGLKLAT TILQHWKKCD SWWAKDSPLE TKMAVLALLA KILQIDSSVS FNTSHGSFPE VFTTYISLLA DTKLDLHLK GQAVTLLPFF TSLTGGSLEE LRRVLEQLIV AHFPMQSREF PPGTPRFNNY VDCMKKFLDA LELSQSPMLL E LMTEVLCR EQQHVMEELF QSSFRRIARR GSCVTQVGLL ESVYEMFRKD DPRLSFTRQS FVDRSLLTLL WHCSLDALRE FF STIVVDA IDVLKSRFTK LNESTFDTQI TKKMGYYKIL DVMYSRLPKD DVHAKESKIN QVFHGSCITE GNELTKTLIK LCY DAFTEN MAGENQLLER RRLYHCAAYN CAISVICCVF NELKFYQGFL FSEKPEKNLL IFENLIDLKR RYNFPVEVEV PMER KKKYI EIRKEAREAA NGDSDGPSYM SSLSYLADST LSEEMSQFDF STGVQSYSYS SQDPRPATGR FRRREQRDPT VHDDV LELE MDELNRHECM APLTALVKHM HRSLGPPQGE EDSVPRDLPS WMKFLHGKLG NPIVPLNIRL FLAKLVINTE EVFRPY AKH WLSPLLQLAA SENNGGEGIH YMVVEIVATI LSWTGLATPT GVPKDEVLAN RLLNFLMKHV FHPKRAVFRH NLEIIKT LV ECWKDCLSIP YRLIFEKFSG KDPNSKDNSV GIQLLGIVMA NDLPPYDPQC GIQSSEYFQA LVNNMSFVRY KEVYAAAA E VLGLILRYVM ERKNILEESL CELVAKQLKQ HQNTMEDKFI VCLNKVTKSF PPLADRFMNA VFFLLPKFHG VLKTLCLEV VLCRVEGMTE LYFQLKSKDF VQVMRHRDDE RQKVCLDIIY KMMPKLKPVE LRELLNPVVE FVSHPSTTCR EQMYNILMWI HDNYRDPES ETDNDSQEIF KLAKDVLIQG LIDENPGLQL IIRNFWSHET RLPSNTLDRL LALNSLYSPK IEVHFLSLAT N FLLEMTSM SPDYPNPMFE HPLSECEFQE YTIDSDWRFR STVLTPMFVE TQASQGTLQT RTQEGSLSAR WPVAGQIRAT QQ QHDFTLT QTADGRSSFD WLTGSSTDPL VDHTSPSSDS LLFAHKRSER LQRAPLKSVG PDFGKKRLGL PGDEVDNKVK GAA GRTDLL RLRRRFMRDQ EKLSLMYARK GVAEQKREKE IKSELKMKQD AQVVLYRSYR HGDLPDIQIK HSSLITPLQA VAQR DPIIA KQLFSSLFSG ILKEMDKFKT LSEKNNITQK LLQDFNRFLN TTFSFFPPFV SCIQDISCQH AALLSLDPAA VSAGC LASL QQPVGIRLLE EALLRLLPAE LPAKRVRGKA RLPPDVLRWV ELAKLYRSIG EYDVLRGIFT SEIGTKQITQ SALLAE ARS DYSEAAKQYD EALNKQDWVD GEPTEAEKDF WELASLDCYN HLAEWKSLEY CSTASIDSEN PPDLNKIWSE PFYQETY LP YMIRSKLKLL LQGEADQSLL TFIDKAMHGE LQKAILELHY SQELSLLYLL QDDVDRAKYY IQNGIQSFMQ NYSSIDVL L HQSRLTKLQS VQALTEIQEF ISFISKQGNL SSQVPLKRLL NTWTNRYPDA KMDPMNIWDD IITNRCFFLS KIEEKLTPL PEDNSMNVDQ DGDPSDRMEV QEQEEDISSL IRSCKFSMKM KMIDSARKQN NFSLAMKLLK ELHKESKTRD DWLVSWVQSY CRLSHCRSR SQGCSEQVLT VLKTVSLLDE NNVSSYLSKN ILAFRDQNIL LGTTYRIIAN ALSSEPACLA EIEEDKARRI L ELSGSSSE DSEKVIAGLY QRAFQHLSEA VQAAEEEAQP PSWSCGPAAG VIDAYMTLAD FCDQQLRKEE ENASVIDSAE LQ AYPALVV EKMLKALKLN SNEARLKFPR LLQIIERYPE ETLSLMTKEI SSVPCWQFIS WISHMVALLD KDQAVAVQHS VEE ITDNYP QAIVYPFIIS SESYSFKDTS TGHKNKEFVA RIKSKLDQGG VIQDFINALD QLSNPELLFK DWSNDVRAEL AKTP VNKKN IEKMYERMYA ALGDPKAPGL GAFRRKFIQT FGKEFDKHFG KGGSKLLRMK LSDFNDITNM LLLKMNKDSK PPGNL KECS PWMSDFKVEF LRNELEIPGQ YDGRGKPLPE YHVRIAGFDE RVTVMASLRR PKRIIIRGHD EREHPFLVKG GEDLRQ DQR VEQLFQVMNG ILAQDSACSQ RALQLRTYSV VPMTSRLGLI EWLENTVTLK DLLLNTMSQE EKAAYLSDPR APPCEYK DW LTKMSGKHDV GAYMLMYKGA NRTETVTSFR KRESKVPADL LKRAFVRMST SPEAFLALRS HFASSHALIC ISHWILGI G DRHLNNFMVA METGGVIGID FGHAFGSATQ FLPVPELMPF RLTRQFINLM LPMKETGLMY SIMVHALRAF RSDPGLLTN TMDVFVKEPS FDWKNFEQKM LKKGGSWIQE INVAEKNWYP RQKICYAKRK LAGANPAVIT CDELLLGHEK APAFRDYVAV ARGSKDHNI RAQEPESGLS EETQVKCLMD QATDPNILGR TWEGWEPWM

UniProtKB: DNA-dependent protein kinase catalytic subunit

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Macromolecule #2: X-ray repair cross-complementing protein 6

MacromoleculeName: X-ray repair cross-complementing protein 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.945039 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSGWESYYKT EGDEEAEEEQ EENLEASGDY KYSGRDSLIF LVDASKAMFE SQSEDELTPF DMSIQCIQSV YISKIISSDR DLLAVVFYG TEKDKNSVNF KNIYVLQELD NPGAKRILEL DQFKGQQGQK RFQDMMGHGS DYSLSEVLWV CANLFSDVQF K MSHKRIML ...String:
MSGWESYYKT EGDEEAEEEQ EENLEASGDY KYSGRDSLIF LVDASKAMFE SQSEDELTPF DMSIQCIQSV YISKIISSDR DLLAVVFYG TEKDKNSVNF KNIYVLQELD NPGAKRILEL DQFKGQQGQK RFQDMMGHGS DYSLSEVLWV CANLFSDVQF K MSHKRIML FTNEDNPHGN DSAKASRART KAGDLRDTGI FLDLMHLKKP GGFDISLFYR DIISIAEDED LRVHFEESSK LE DLLRKVR AKETRKRALS RLKLKLNKDI VISVGIYNLV QKALKPPPIK LYRETNEPVK TKTRTFNTST GGLLLPSDTK RSQ IYGSRQ IILEKEETEE LKRFDDPGLM LMGFKPLVLL KKHHYLRPSL FVYPEESLVI GSSTLFSALL IKCLEKEVAA LCRY TPRRN IPPYFVALVP QEEELDDQKI QVTPPGFQLV FLPFADDKRK MPFTEKIMAT PEQVGKMKAI VEKLRFTYRS DSFEN PVLQ QHFRNLEALA LDLMEPEQAV DLTLPKVEAM NKRLGSLVDE FKELVYPPDY NPEGKVTKRK HDNEGSGSKR PKVEYS EEE LKTHISKGTL GKFTVPMLKE ACRAYGLKSG LKKQELLEAL TKHFQD

UniProtKB: X-ray repair cross-complementing protein 6

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Macromolecule #3: X-ray repair cross-complementing protein 5

MacromoleculeName: X-ray repair cross-complementing protein 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.812438 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLSG GDQYQNITVH RHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ HETIGKKFEK RHIEIFTDLS SRFSKSQLDI IIHSLKKCDI S LQFFLPFS ...String:
MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLSG GDQYQNITVH RHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ HETIGKKFEK RHIEIFTDLS SRFSKSQLDI IIHSLKKCDI S LQFFLPFS LGKEDGSGDR GDGPFRLGGH GPSFPLKGIT EQQKEGLEIV KMVMISLEGE DGLDEIYSFS ESLRKLCVFK KI ERHSIHW PCRLTIGSNL SIRIAAYKSI LQERVKKTWT VVDAKTLKKE DIQKETVYCL NDDDETEVLK EDIIQGFRYG SDI VPFSKV DEEQMKYKSE GKCFSVLGFC KSSQVQRRFF MGNQVLKVFA ARDDEAAAVA LSSLIHALDD LDMVAIVRYA YDKR ANPQV GVAFPHIKHN YECLVYVQLP FMEDLRQYMF SSLKNSKKYA PTEAQLNAVD ALIDSMSLAK KDEKTDTLED LFPTT KIPN PRFQRLFQCL LHRALHPREP LPPIQQHIWN MLNPPAEVTT KSQIPLSKIK TLFPLIEAKK KDQVTAQEIF QDNHED GPT AKKLKTEQGG AHFSVSSLAE GSVTSVGSVN PAENFRVLVK QKKASFEEAS NQLINHIEQF LDTNETPYFM KSIDCIR AF REEAIKFSEE QRFNNFLKAL QEKVEIKQLN HFWEIVVQDG ITLITKEEAS GSSVTAEEAK KFLAPKDKPS GDTAAVFE E GGDVDDLLDM I

UniProtKB: X-ray repair cross-complementing protein 5

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Macromolecule #4: DNA (26-MER)

MacromoleculeName: DNA (26-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.900079 KDa
SequenceString:
(DC)(DC)(DC)(DG)(DC)(DT)(DG)(DC)(DC)(DG) (DA)(DT)(DT)(DC)(DC)(DG)(DC)(DT)(DG)(DG) (DA)(DA)(DC)(DA)(DT)(DT)

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Macromolecule #5: DNA (26-MER)

MacromoleculeName: DNA (26-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.078203 KDa
SequenceString:
(DA)(DA)(DT)(DG)(DT)(DT)(DC)(DC)(DA)(DG) (DC)(DG)(DG)(DA)(DA)(DT)(DC)(DG)(DG)(DC) (DA)(DG)(DC)(DG)(DG)(DG)

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Macromolecule #6: (~{S})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-y...

MacromoleculeName: (~{S})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-yl)phenyl]-(6-methoxypyridazin-3-yl)methanol
type: ligand / ID: 6 / Number of copies: 1 / Formula: 1IX
Molecular weightTheoretical: 481.907 Da
Chemical component information

ChemComp-1IX:
(~{S})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-yl)phenyl]-(6-methoxypyridazin-3-yl)methanol

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 194 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.22 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: PDB entry 6ZHA and 7K1N were used as the startup model.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 275300
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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