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- PDB-5gox: Eukaryotic Rad50 Functions as A Rod-shaped Dimer -

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Basic information

Entry
Database: PDB / ID: 5gox
TitleEukaryotic Rad50 Functions as A Rod-shaped Dimer
ComponentsDNA repair protein RAD50
KeywordsHYDROLASE / DNA repair
Function / homology
Function and homology information


chromosomal region / telomeric 3' overhang formation / Mre11 complex / negative regulation of telomere capping / BRCA1-C complex / Sensing of DNA Double Strand Breaks / regulation of mitotic recombination / R-loop processing / Hydrolases; Acting on acid anhydrides / chromosome organization involved in meiotic cell cycle ...chromosomal region / telomeric 3' overhang formation / Mre11 complex / negative regulation of telomere capping / BRCA1-C complex / Sensing of DNA Double Strand Breaks / regulation of mitotic recombination / R-loop processing / Hydrolases; Acting on acid anhydrides / chromosome organization involved in meiotic cell cycle / double-stranded telomeric DNA binding / DNA strand resection involved in replication fork processing / homologous recombination / G-quadruplex DNA binding / DNA double-strand break processing / Impaired BRCA2 binding to PALB2 / single-stranded telomeric DNA binding / telomere maintenance via recombination / mitotic G2/M transition checkpoint / HDR through MMEJ (alt-NHEJ) / reciprocal meiotic recombination / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / positive regulation of double-strand break repair / Impaired BRCA2 binding to RAD51 / positive regulation of telomere maintenance / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / telomere maintenance / protein serine/threonine kinase activator activity / condensed nuclear chromosome / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / protein-macromolecule adaptor activity / DNA recombination / Regulation of TP53 Activity through Phosphorylation / chromosome, telomeric region / DNA repair / DNA damage response / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / membrane
Similarity search - Function
DNA repair protein Rad50, eukaryotes / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / SbcC/RAD50-like, Walker B motif / Rad50/SbcC-type AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA repair protein RAD50
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.405 Å
AuthorsPark, Y.B. / Hohl, M. / Padjasek, M. / Jeong, E. / Jin, K.S. / Krezel, A. / Petrini, J.H.J. / Cho, Y.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Eukaryotic Rad50 functions as a rod-shaped dimer
Authors: Park, Y.B. / Hohl, M. / Padjasek, M. / Jeong, E. / Jin, K.S. / Krezel, A. / Petrini, J.H.J. / Cho, Y.
History
DepositionJul 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RAD50
B: DNA repair protein RAD50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0946
Polymers43,7522
Non-polymers3424
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-54 kcal/mol
Surface area24530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.180, 61.972, 81.540
Angle α, β, γ (deg.)90.00, 99.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA repair protein RAD50 / hRAD50


Mass: 21876.180 Da / Num. of mol.: 2 / Fragment: UNP residues 585-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD50 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: Q92878, Hydrolases; Acting on acid anhydrides
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.3 % / Description: hexagonal
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 28 - 30% PEG 600, 0.1 M bis-tris propane, 3% 1, 6-hexanediol, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9766 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2014
RadiationMonochromator: Si 4-crystal channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16270 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.98 / Rsym value: 0.07 / Net I/σ(I): 42.2
Reflection shellResolution: 2.4→2.44 Å

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Processing

Software
NameVersionClassification
PHENIXdev_1745refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXdev_1745phasing
RefinementMethod to determine structure: SAD / Resolution: 2.405→28.221 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.48
RfactorNum. reflection% reflection
Rfree0.2709 811 5.03 %
Rwork0.2132 --
obs0.2164 16117 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.405→28.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 19 9 2980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092991
X-RAY DIFFRACTIONf_angle_d1.3023983
X-RAY DIFFRACTIONf_dihedral_angle_d15.4391236
X-RAY DIFFRACTIONf_chiral_restr0.05444
X-RAY DIFFRACTIONf_plane_restr0.007526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4052-2.55580.36941400.29782464X-RAY DIFFRACTION97
2.5558-2.7530.40781370.27912537X-RAY DIFFRACTION99
2.753-3.02970.36521210.2582568X-RAY DIFFRACTION99
3.0297-3.46740.34191220.26382564X-RAY DIFFRACTION100
3.4674-4.3660.27771380.20132579X-RAY DIFFRACTION100
4.366-28.22250.21751530.18012594X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.00490.55066.009-0.38410.07163.48480.34911.01150.05080.0547-0.25590.20460.5074-0.13390.11370.691-0.166-0.14361.27560.11260.9865-20.394628.2819.2723
25.62590.69914.17222.98780.73126.58740.0327-0.03590.1380.5183-0.2367-0.7499-0.15410.72150.1280.5424-0.0303-0.05650.49320.15760.579734.704633.525750.6252
39.27161.82435.45490.85561.26994.3528-0.2097-0.07050.4033-0.17860.03570.10240.0275-0.40830.00440.6868-0.0547-0.00190.67950.1070.61330.868428.45126.1877
44.4321-0.51796.2330.96050.3117.08410.137-1.65560.8445-0.2669-0.35580.19040.2606-1.85120.2470.6884-0.0173-0.15151.16360.04870.7923-20.326650.322913.6201
53.7605-0.00792.51783.3366-0.94973.6362-0.35430.19390.51310.1414-0.416-0.3714-0.3480.41150.43820.51320.05130.04350.4362-0.03290.764226.520741.025147.7624
67.39730.93984.89230.36581.6849.80720.0716-0.51940.49360.1446-0.3402-0.4899-0.21280.39830.38831.0312-0.172-0.2050.74490.04540.718838.521139.723369.5464
76.7395-1.58364.48271.1144-1.0023.8408-0.20390.97840.85440.0536-0.34840.0767-0.3110.15180.70330.6901-0.0545-0.01320.7490.07020.81921.416647.909124.8866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 585 through 632 )
2X-RAY DIFFRACTION2chain 'A' and (resid 633 through 707 )
3X-RAY DIFFRACTION3chain 'A' and (resid 708 through 765 )
4X-RAY DIFFRACTION4chain 'B' and (resid 585 through 632 )
5X-RAY DIFFRACTION5chain 'B' and (resid 633 through 679 )
6X-RAY DIFFRACTION6chain 'B' and (resid 680 through 707 )
7X-RAY DIFFRACTION7chain 'B' and (resid 708 through 765 )

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