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

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Entry
Database: PDB / ID: 5y3r
TitleCryo-EM structure of Human DNA-PK Holoenzyme
DescriptorPRKDC-Helix
DNA-dependent protein kinase catalytic subunit/DNA Complex
(X-ray repair cross-complementing protein ...) x 2
KeywordsDNA BINDING PROTEIN / Cryo-EM structure / DNA-PK / DNAPKcs / activation / NHEJ
Specimen sourceHomo sapiens / human
MethodElectron microscopy (6.6 Å resolution / Particle / Single particle)
AuthorsYin, X. / Liu, M. / Tian, Y. / Wang, J. / Xu, Y.
CitationCell Res., 2017

Cell Res., 2017 StrPapers
Cryo-EM structure of human DNA-PK holoenzyme.
Xiaotong Yin / Mengjie Liu / Yuan Tian / Jiawei Wang / Yanhui Xu

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 29, 2017 / Release: Sep 6, 2017

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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: Polypeptide(L)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 / References: UniProt: P12956, EC: 3.6.4.-, EC: 4.2.99.-
#2: Polypeptide(L)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 / References: UniProt: P13010, EC: 3.6.4.-

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Polypeptide(L) , 2 types, 2 molecules KC

#3: Polypeptide(L)PRKDC-Helix


Mass: 1084.182 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens
#6: Polypeptide(L)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 / References: UniProt: P78527, EC: 2.7.11.1

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DNA chain , 2 types, 2 molecules DE

#4: DNA chainDNA (34-MER)


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


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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
Source (recombinant)Organism: Homo sapiens
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 FIELD / 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
IDNameVersionCategoryImage processing ID
1RELION1.4PARTICLE SELECTION1
2CTFFIND33CTF CORRECTION1
3RELION2.0FINAL EULER ASSIGNMENT1
4RELION2.0CLASSIFICATION1
5RELION2.0RECONSTRUCTION1
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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