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- PDB-3i0n: Structure of the S. pombe Nbs1 FHA/BRCT-repeat domain -

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Basic information

Entry
Database: PDB / ID: 3i0n
TitleStructure of the S. pombe Nbs1 FHA/BRCT-repeat domain
ComponentsDNA repair and telomere maintenance protein nbs1
KeywordsCELL CYCLE / Nbs1 / FHA / BRCT-repeat / DNA-damage / Chromosomal protein / DNA damage / DNA repair / Nucleus / Phosphoprotein / Telomere / GENE REGULATION
Function / homology
Function and homology information


DNA Damage/Telomere Stress Induced Senescence / HDR through MMEJ (alt-NHEJ) / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Mre11 complex / chromosome, telomeric repeat region / DNA double-strand break processing / chromatin-protein adaptor activity / telomere maintenance via recombination ...DNA Damage/Telomere Stress Induced Senescence / HDR through MMEJ (alt-NHEJ) / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Mre11 complex / chromosome, telomeric repeat region / DNA double-strand break processing / chromatin-protein adaptor activity / telomere maintenance via recombination / mitotic intra-S DNA damage checkpoint signaling / DNA duplex unwinding / protein localization to chromosome, telomeric region / mitotic G2 DNA damage checkpoint signaling / telomere maintenance / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / damaged DNA binding / molecular adaptor activity / DNA repair / nucleus
Similarity search - Function
Rossmann fold - #11080 / Nibrin-related / Tumour Suppressor Smad4 - #20 / BRCT domain / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily ...Rossmann fold - #11080 / Nibrin-related / Tumour Suppressor Smad4 - #20 / BRCT domain / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / BRCT domain superfamily / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA repair and telomere maintenance protein nbs1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsClapperton, J.A. / Lloyd, J. / Chapman, J.R. / Jackson, S.P. / Smerdon, S.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: A supramodular FHA/BRCT-repeat architecture mediates Nbs1 adaptor function in response to DNA damage
Authors: Lloyd, J. / Chapman, J.R. / Clapperton, J.A. / Haire, L.F. / Hartsuiker, E. / Li, J. / Carr, A.M. / Jackson, S.P. / Smerdon, S.J.
History
DepositionJun 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair and telomere maintenance protein nbs1
B: DNA repair and telomere maintenance protein nbs1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5844
Polymers74,3992
Non-polymers1842
Water3,765209
1
A: DNA repair and telomere maintenance protein nbs1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2922
Polymers37,2001
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA repair and telomere maintenance protein nbs1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2922
Polymers37,2001
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.189, 64.898, 106.363
Angle α, β, γ (deg.)90.00, 105.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETSERSER2AA1 - 2301 - 230
21METMETSERSER2BB1 - 2301 - 230
12CYSCYSALAALA5AA231 - 320231 - 320
22CYSCYSTYRTYR5BB231 - 319231 - 319

NCS ensembles :
ID
1
2

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Components

#1: Protein DNA repair and telomere maintenance protein nbs1 / Nbs1


Mass: 37199.727 Da / Num. of mol.: 2
Fragment: N-terminal FHA/BRCT-repeat domain, UNP residues 1-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: nbs1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43070
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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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: 50.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG3000, 0.1M sodium citrate, Protein reductively methylated/carboxypeptidase-treated, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9757 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2008
RadiationMonochromator: 0.97 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9757 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 32600 / Num. obs: 30800 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.404

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I0M

3i0m


Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 16.891 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.435 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 1550 5.1 %RANDOM
Rwork0.21495 ---
obs0.21731 29067 94.64 %-
all-0 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.428 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20.01 Å2
2---0.15 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5163 0 12 209 5384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215265
X-RAY DIFFRACTIONr_angle_refined_deg1.1282.0237117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.745637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06725.221226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35715766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9791520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213988
X-RAY DIFFRACTIONr_mcbond_it0.3981.53177
X-RAY DIFFRACTIONr_mcangle_it0.77525161
X-RAY DIFFRACTIONr_scbond_it1.14732088
X-RAY DIFFRACTIONr_scangle_it1.9184.51956
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A920tight positional0.010.05
11B926medium positional0.010.5
22A356medium positional0.250.5
22B376loose positional0.555
11A920tight thermal0.030.5
11B926medium thermal0.042
22A356medium thermal0.152
22B376loose thermal0.1610
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 82 -
Rwork0.24 1409 -
obs--64.32 %
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)
12.7030.1458-0.97832.12010.74567.85650.0339-0.5245-0.17060.3174-0.07930.04870.2223-0.12940.04550.0506-0.0198-0.00280.11610.03920.07629.903-15.16771.357
22.20970.01830.76981.33581.38386.3007-0.02080.21260.2443-0.177-0.0027-0.0503-0.43790.00540.02360.03940.0033-0.00810.0220.01690.099512.969-9.45343.837
34.6464-0.6174-0.92476.77322.09967.391-0.17040.9116-0.1511-0.65170.0524-0.44970.32750.14970.11790.2109-0.09050.05280.3746-0.0170.14188.136-20.42717.521
42.6386-0.13960.89822.30411.08478.07810.02230.51210.2466-0.3653-0.07320.0992-0.2-0.17790.0510.05820.0128-0.01270.11540.04780.083437.308-14.20831.162
51.9206-0.1725-0.87461.83781.74466.3162-0.0322-0.1656-0.17220.15370.0085-0.02570.4459-0.05810.02370.0339-0.00720.00840.01860.00860.092840.194-19.99358.6
64.7097-0.28741.07687.01922.14148.2675-0.1994-0.94930.21470.74470.0739-0.5296-0.32860.15770.12550.21450.0835-0.06570.3631-0.02120.121335.677-8.97885.244
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 114
2X-RAY DIFFRACTION2A115 - 216
3X-RAY DIFFRACTION3A217 - 319
4X-RAY DIFFRACTION4B1 - 114
5X-RAY DIFFRACTION5B115 - 216
6X-RAY DIFFRACTION6B217 - 319

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