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- PDB-5y3r: Cryo-EM structure of Human DNA-PK Holoenzyme -

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Basic information

Entry
Database: PDB / ID: 5y3r
TitleCryo-EM structure of Human DNA-PK Holoenzyme
Components
  • (X-ray repair cross-complementing protein ...) x 2
  • DNA (34-MER)
  • DNA (36-MER)
  • DNA-dependent protein kinase catalytic subunit
  • PRKDC-Helix
KeywordsDNA BINDING PROTEIN / Cryo-EM structure / DNA-PK / DNAPKcs / activation / NHEJ
Function / homologyKu, C-terminal / von Willebrand factor, type A / Phosphatidylinositol 3- and 4-kinases signature 2. / Armadillo-type fold / Ku70/Ku80 C-terminal arm / FATC domain / PIK-related kinase, FAT / Phosphatidylinositol 3- and 4-kinases signature 1. / SAP domain / Ku C terminal domain like ...Ku, C-terminal / von Willebrand factor, type A / Phosphatidylinositol 3- and 4-kinases signature 2. / Armadillo-type fold / Ku70/Ku80 C-terminal arm / FATC domain / PIK-related kinase, FAT / Phosphatidylinositol 3- and 4-kinases signature 1. / SAP domain / Ku C terminal domain like / NUC194 domain / Phosphatidylinositol 3-/4-kinase, catalytic domain / SAP motif profile. / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 C-terminal arm / Ku70/Ku80 beta-barrel domain / von Willebrand factor A-like domain superfamily / Ku, C-terminal domain superfamily / FATC domain / FAT domain / SAP domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphatidylinositol 3- and 4-kinases family profile. / DNA-dependent protein kinase catalytic subunit, catalytic domain / Ku70/Ku80, N-terminal alpha/beta / Neutrophil degranulation / SPOC-like, C-terminal domain superfamily / Protein kinase-like domain superfamily / Ku80 / PIK-related kinase / E3 ubiquitin ligases ubiquitinate target proteins / Ku70 / Ku70/Ku80 beta-barrel domain / SAP domain superfamily / Ku70, bridge and pillars domain superfamily / Nonhomologous End-Joining (NHEJ) / IRF3-mediated induction of type I IFN / NUC194 / Cytosolic sensors of pathogen-associated DNA / Phosphatidylinositol 3/4-kinase, conserved site / 2-LTR circle formation / FATC domain profile. / FAT domain profile. / signal transduction involved in mitotic G1 DNA damage checkpoint / negative regulation of response to gamma radiation / DNA-dependent protein kinase activity / negative regulation of immunoglobulin production / Ku70:Ku80 complex / double-strand break repair via alternative nonhomologous end joining / double-strand break repair via classical nonhomologous end joining / T cell receptor V(D)J recombination / negative regulation of t-circle formation / immunoglobulin V(D)J recombination / pro-B cell differentiation / DNA-dependent protein kinase-DNA ligase 4 complex / T cell lineage commitment / cellular response to X-ray / nonhomologous end joining complex / positive regulation of developmental growth / DNA ligation / regulation of smooth muscle cell proliferation / B cell lineage commitment / positive regulation of neurogenesis / hematopoietic stem cell differentiation / nuclear telomere cap complex / 5'-deoxyribose-5-phosphate lyase activity / ectopic germ cell programmed cell death / site of DNA damage / somitogenesis / cellular hyperosmotic salinity response / regulation of telomere maintenance / ec:3.6.4.-: / ATP-dependent DNA helicase activity / negative regulation of cellular senescence / activation of innate immune response / cellular response to fatty acid / protein localization to chromosome, telomeric region / telomeric DNA binding / telomere capping / positive regulation of catalytic activity / positive regulation of type I interferon production / Other Carbon-Oxygen Lyases / positive regulation of protein kinase activity / regulation of circadian rhythm / positive regulation of telomere maintenance via telomerase / telomere maintenance / cellular response to leukemia inhibitory factor / cyclin binding / double-strand break repair / response to activity / positive regulation of telomerase activity / thymus development / spleen development / cellular protein modification process / negative regulation of protein phosphorylation / enzyme activator activity / protein destabilization / ribonucleoprotein complex / rhythmic process
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.6 Å resolution
AuthorsYin, X. / Liu, M. / Tian, Y. / Wang, J. / Xu, Y.
CitationJournal: Cell Res. / Year: 2017
Title: Cryo-EM structure of human DNA-PK holoenzyme.
Authors: Xiaotong Yin / Mengjie Liu / Yuan Tian / Jiawei Wang / Yanhui Xu
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 29, 2017 / Release: Sep 6, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 6, 2017Structure modelrepositoryInitial release
1.1Nov 15, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last
1.2Jun 13, 2018Structure modelData collection / Source and taxonomyentity_src_gen_entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

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Assembly

Deposited unit
A: X-ray repair cross-complementing protein 6
B: X-ray repair cross-complementing protein 5
K: PRKDC-Helix
D: DNA (34-MER)
E: DNA (36-MER)
C: DNA-dependent protein kinase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)610,1076
Polyers610,1076
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)27230
ΔGint (kcal/M)-158
Surface area (Å2)214470

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Components

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X-ray repair cross-complementing protein ... , 2 types, 2 molecules AB

#1: Protein/peptide X-ray repair cross-complementing protein 6 / 5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 1 / ATP-dependent DNA helicase II 70 kDa subunit / CTC box-binding factor 75 kDa subunit / CTCBF / DNA repair protein XRCC6 / Lupus Ku autoantigen protein p70 / Ku70 / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 6


Mass: 57619.352 Da / Num. of mol.: 1 / Fragment: UNP residues 34-534 / Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC6, G22P1 / Production host: Homo sapiens (human)
References: UniProt: P12956, EC: 3.6.4.-, Other Carbon-Oxygen Lyases
#2: Protein/peptide X-ray repair cross-complementing protein 5 / 86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase II 80 kDa subunit / CTC box-binding factor 85 kDa subunit / CTCBF / DNA repair protein XRCC5 / Ku80 / Ku86 / Lupus Ku autoantigen protein p86 / Nuclear factor IV / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)


Mass: 60972.969 Da / Num. of mol.: 1 / Fragment: UNP residues 6-541 / Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5, G22P2 / Production host: Homo sapiens (human) / References: UniProt: P13010, EC: 3.6.4.-

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Protein/peptide , 2 types, 2 molecules KC

#3: Protein/peptide PRKDC-Helix


Mass: 1084.182 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Protein/peptide DNA-dependent protein kinase catalytic subunit / DNA-PKcs / DNPK1 / p460


Mass: 468885.344 Da / Num. of mol.: 1 / Fragment: UNP residues 10-4128 / Source: (gene. exp.) Homo sapiens (human) / Gene: PRKDC, HYRC, HYRC1 / Cell line (production host): HEK293F / Organ (production host): KIDNEY / Production host: Homo sapiens (human)
References: UniProt: P78527, non-specific serine/threonine protein kinase

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DNA chain , 2 types, 2 molecules DE

#4: DNA chain DNA (34-MER)


Mass: 10502.785 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: DNA chain DNA (36-MER)


Mass: 11042.164 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PRKDC-Helix / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 18000 / Nominal defocus max: 4700 nm / Nominal defocus min: 1700 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 3496
Image scansMovie frames/image: 32 / Used frames/image: 1-32

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155 / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
2CTFFIND33CTF correction
3RELION2.0final Euler assignment
4RELION2.0classification
5RELION2.03D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 53451 / Number of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01139702
ELECTRON MICROSCOPYf_angle_d1.50053937
ELECTRON MICROSCOPYf_dihedral_angle_d12.27424059
ELECTRON MICROSCOPYf_chiral_restr0.0696075
ELECTRON MICROSCOPYf_plane_restr0.0096647

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