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- PDB-3huf: Structure of the S. pombe Nbs1-Ctp1 complex -

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Basic information

Entry
Database: PDB / ID: 3huf
TitleStructure of the S. pombe Nbs1-Ctp1 complex
Components
  • DNA repair and telomere maintenance protein nbs1
  • Double-strand break repair protein ctp1
KeywordsCELL CYCLE / Nbs1 / FHA domain / BRCT domain / phosphoprotein binding / phosphoserine binding / DNA repair / Ctp1 / Chromosomal protein / DNA damage / Nucleus / Phosphoprotein / Telomere / Meiosis
Function / homology
Function and homology information


double-strand/single-strand DNA junction binding / DNA-DNA tethering activity / endodeoxyribonuclease activator activity / stalled replication fork localization to nuclear periphery / HDR through MMEJ (alt-NHEJ) / meiotic DNA double-strand break processing / gene conversion at mating-type locus / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends ...double-strand/single-strand DNA junction binding / DNA-DNA tethering activity / endodeoxyribonuclease activator activity / stalled replication fork localization to nuclear periphery / HDR through MMEJ (alt-NHEJ) / meiotic DNA double-strand break processing / gene conversion at mating-type locus / DNA Damage/Telomere Stress Induced Senescence / 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 / flap-structured DNA binding / Mre11 complex / chromosome, telomeric repeat region / mitotic recombination-dependent replication fork processing / DNA end binding / Y-form DNA binding / phosphorylation-dependent protein binding / double-strand break repair involved in meiotic recombination / bubble DNA binding / DNA double-strand break processing / chromatin-protein adaptor activity / telomere maintenance via recombination / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / mitotic G2 DNA damage checkpoint signaling / replication fork processing / telomere maintenance / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / double-strand break repair / single-stranded DNA binding / site of double-strand break / double-stranded DNA binding / endonuclease activity / molecular adaptor activity / damaged DNA binding / Hydrolases; Acting on ester bonds / DNA repair / identical protein binding / nucleus
Similarity search - Function
Rossmann fold - #11080 / DNA endonuclease activator Ctp1, C-terminal / DNA endonuclease activator SAE2/CtIP C-terminus / Nibrin-related / Tumour Suppressor Smad4 - #20 / BRCT domain / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain ...Rossmann fold - #11080 / DNA endonuclease activator Ctp1, C-terminal / DNA endonuclease activator SAE2/CtIP C-terminus / 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
THIOCYANATE ION / DNA repair and telomere maintenance protein nbs1 / DNA endonuclease ctp1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWilliams, R.S. / Guenther, G. / Tainer, J.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Nbs1 flexibly tethers Ctp1 and Mre11-Rad50 to coordinate DNA double-strand break processing and repair.
Authors: Williams, R.S. / Dodson, G.E. / Limbo, O. / Yamada, Y. / Williams, J.S. / Guenther, G. / Classen, S. / Glover, J.N. / Iwasaki, H. / Russell, P. / Tainer, J.A.
History
DepositionJun 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: DNA repair and telomere maintenance protein nbs1
B: DNA repair and telomere maintenance protein nbs1
C: DNA repair and telomere maintenance protein nbs1
E: Double-strand break repair protein ctp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0196
Polymers111,9024
Non-polymers1162
Water7,710428
1
A: DNA repair and telomere maintenance protein nbs1
E: Double-strand break repair protein ctp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4713
Polymers38,4122
Non-polymers581
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-8 kcal/mol
Surface area15250 Å2
MethodPISA
2
B: DNA repair and telomere maintenance protein nbs1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8032
Polymers36,7451
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA repair and telomere maintenance protein nbs1


Theoretical massNumber of molelcules
Total (without water)36,7451
Polymers36,7451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: DNA repair and telomere maintenance protein nbs1
C: DNA repair and telomere maintenance protein nbs1
E: Double-strand break repair protein ctp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2154
Polymers75,1573
Non-polymers581
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-14 kcal/mol
Surface area28830 Å2
MethodPISA
5
B: DNA repair and telomere maintenance protein nbs1
hetero molecules

B: DNA repair and telomere maintenance protein nbs1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6064
Polymers73,4902
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_355-x-2,-y,z1
Buried area3100 Å2
ΔGint-12 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.430, 244.627, 51.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA repair and telomere maintenance protein nbs1


Mass: 36744.961 Da / Num. of mol.: 3
Fragment: N-terminal FHA-BRCT1-BRCT2 domains (residues 1-321)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: nbs1, SPBC6B1.09c / Production host: Escherichia coli (E. coli) / References: UniProt: O43070
#2: Protein/peptide Double-strand break repair protein ctp1 / Nbs1-interacting protein 1 / Meiotically up-regulated gene 38 protein


Mass: 1667.467 Da / Num. of mol.: 1 / Fragment: SXT sites (residues 72-84) / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74986
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 281 K
Details: 18% polyethylene glycol 3350, 100 mM MES pH 6.1-6.5, 260 mM potassium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 281K
PH range: 6.1-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2008
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 66677 / % possible obs: 97.1 % / Observed criterion σ(I): 2.3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 23
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.3 / % possible all: 86.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.54 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3374 5.1 %RANDOM
Rwork0.215 ---
obs0.218 63231 96.9 %-
all-63231 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---1.69 Å20 Å2
3---1.86 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7254 0 6 428 7688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227384
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9629974
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.15324.984309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.495151323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2611530
X-RAY DIFFRACTIONr_chiral_restr0.10.21156
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025403
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.33312
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.55020
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.5770
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.394
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.538
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6661.54642
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28527486
X-RAY DIFFRACTIONr_scbond_it1.94932742
X-RAY DIFFRACTIONr_scangle_it3.2254.52488
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 208 -
Rwork0.248 3961 -
obs--83.58 %
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)
11.078-0.37450.45142.2395-0.56882.9690.00620.12680.0764-0.2843-0.0281-0.0049-0.22870.11680.0219-0.12980.00240.0303-0.0766-0.0387-0.1687-47.054732.8841-20.5302
22.3089-2.2510.52953.3863-0.75820.76750.0816-0.0494-0.014-0.01940.01940.1176-0.00140.0486-0.1009-0.1816-0.02120.0011-0.1223-0.0081-0.1047-86.71486.9325-31.9335
31.86072.0823-1.00773.6957-1.75481.0534-0.038-0.00480.15640.04030.0680.2988-0.1075-0.0399-0.03-0.06840.01540.0059-0.0747-0.028-0.0849-59.837948.7476-4.5943
49.0896-26.893520.028114.8195-3.6633131.8108-0.1053-0.5102-0.77160.02420.6006-0.12091.95350.6723-0.49530.00170-0.00090.0010.00040.0003-39.59883.6959.3409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 320
2X-RAY DIFFRACTION2B1 - 325
3X-RAY DIFFRACTION3C1 - 325
4X-RAY DIFFRACTION4E77 - 81

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