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- PDB-5np7: CryoEM structure of Human Rad51 on single-stranded DNA to 4.2A re... -

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Basic information

Entry
Database: PDB / ID: 5np7
TitleCryoEM structure of Human Rad51 on single-stranded DNA to 4.2A resolution.
DescriptorDNA repair protein RAD51 homolog 1
KeywordsRECOMBINATION / recombinase / cryoEM / Human Rad51 / single-stranded DNA
Specimen sourceHomo sapiens / human
MethodElectron microscopy (4.2 Å resolution / Helical array / Helical)
AuthorsShort, J.M. / Venkitaraman, A.
CitationNucleic Acids Res., 2016, 44, 9017-9030

Nucleic Acids Res., 2016, 44, 9017-9030 StrPapers
High-resolution structure of the presynaptic RAD51 filament on single-stranded DNA by electron cryo-microscopy.
Judith M Short / Yang Liu / Shaoxia Chen / Neelesh Soni / Mallur S Madhusudhan / Mahmud K K Shivji / Ashok R Venkitaraman

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 13, 2017 / Release: May 3, 2017

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Assembly

Deposited unit
A: DNA repair protein RAD51 homolog 1
B: DNA repair protein RAD51 homolog 1
C: DNA repair protein RAD51 homolog 1
D: DNA repair protein RAD51 homolog 1
E: DNA repair protein RAD51 homolog 1
F: DNA repair protein RAD51 homolog 1
G: DNA repair protein RAD51 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,60714
Polyers259,0647
Non-polymers3,5437
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)28990
ΔGint (kcal/M)-135
Surface area (Å2)88880
MethodPISA

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Components

#1: Polypeptide(L)
DNA repair protein RAD51 homolog 1 / hRAD51 / RAD51 homolog A


Mass: 37009.125 Da / Num. of mol.: 7 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: Q06609

Cellular component

Molecular function

Biological process

#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP (energy-carrying molecule analogue) *YM


Mass: 506.196 Da / Num. of mol.: 7 / Formula: C10H17N6O12P3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: HELICAL

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Sample preparation

ComponentName: Helical filament of HRAD51 on single-stranded DNA with AMPPNP
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 259 deg. / Units: KILODALTONS/NANOMETER / Experimental flag: NO
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil
VitrificationCryogen name: NITROGEN

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 / Calibrated magnification: 104477 / Nominal defocus min: 2000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansSampling size: 14 microns / Dimension width: 4096 / Dimension height: 4096 / Movie frames/image: 34

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Processing

SoftwareName: REFMAC / Version: 5.8.0166 / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1XimdispPARTICLE SELECTION1
2epuIMAGE ACQUISITION1
4gctfCTF CORRECTION1
7COOTMODEL FITTING1
11RELION1.4CLASSIFICATION1
12RELION1.4RECONSTRUCTION1
19REFMACMODEL REFINEMENT1
CTF correctionDetails: per segment / Type: NONE
EM helical entityAngular rotation per subunit: 56.2 deg. / Axial rise per subunit: 16 Å / Axial symmetry: C1
Particle selectionNumber of particles selected: 70000
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 60000
Details: Helical segments were divided in half, not drawn randomly or odd/even as this would result in some segments from the same filament in both half models. Thus, it is strictly not gold-standard.
Symmetry type: HELICAL
Atomic model buildingDetails: Backbone fitting is good but many of the sidechains cannot be relied on as the map resolution was insufficient.
Overall b value: 94.574 / Ref protocol: FLEXIBLE FIT / Ref space: RECIPROCAL / Target criteria: maximum likelihood
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLStereochemistry target valuesSolvent model details
1131.509-1.000.210.17-0.54-0.041.540.9370.283150.283154.20180.0063875100.0046.5670.572MAXIMUM LIKELIHOOD WITH PHASESPARAMETERS FOR MASK CACLULATION
ELECTRON MICROSCOPY
Number of atoms included #1Total: 16754
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0190.01917035
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg2.6471.96623140
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.7245.0002163
ELECTRON MICROSCOPYr_dihedral_angle_2_deg37.02423.434693
ELECTRON MICROSCOPYr_dihedral_angle_3_deg23.00615.0002723
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.90915.000133
ELECTRON MICROSCOPYr_chiral_restr0.2100.2002642
ELECTRON MICROSCOPYr_gen_planes_refined0.0110.02112631
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it11.50012.5798694
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it19.49218.84010843
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it15.79813.9968341
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined44.96760052
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded

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