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- PDB-6ldm: Structural basis of G-quadruplex DNA recognition by the yeast tel... -

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Basic information

Entry
Database: PDB / ID: 6ldm
TitleStructural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1
Components
  • DNA-binding protein RAP1
  • G-guadruplex DNA
KeywordsDNA BINDING PROTEIN/DNA / complex / G-quadruplex / DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / telomeric G-quadruplex DNA binding / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / telomere maintenance via telomere lengthening / establishment of protein localization to chromatin / shelterin complex / G-quadruplex DNA binding / double-stranded telomeric DNA binding ...positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / telomeric G-quadruplex DNA binding / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / telomere maintenance via telomere lengthening / establishment of protein localization to chromatin / shelterin complex / G-quadruplex DNA binding / double-stranded telomeric DNA binding / regulation of glycolytic process / silent mating-type cassette heterochromatin formation / DNA binding, bending / nuclear chromosome / telomeric DNA binding / TFIID-class transcription factor complex binding / subtelomeric heterochromatin formation / cis-regulatory region sequence-specific DNA binding / nucleosomal DNA binding / telomere maintenance / TBP-class protein binding / protein-DNA complex / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Rap1, DNA-binding domain / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / Rap1, DNA-binding / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / BRCT domain, a BRCA1 C-terminus domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain ...Rap1, DNA-binding domain / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / Rap1, DNA-binding / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / BRCT domain, a BRCA1 C-terminus domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / breast cancer carboxy-terminal domain / Homeodomain-like / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA-binding protein RAP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTraczyk, A. / Gill, D.J. / Chong, W.L. / Rhodes, D.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1.
Authors: Traczyk, A. / Liew, C.W. / Gill, D.J. / Rhodes, D.
History
DepositionNov 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein RAP1
B: G-guadruplex DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,34620
Polymers39,6832
Non-polymers66318
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-124 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.680, 70.200, 64.850
Angle α, β, γ (deg.)90.000, 97.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-103-

K

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Components

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Protein / DNA chain , 2 types, 2 molecules AB

#1: Protein DNA-binding protein RAP1 / Repressor/activator site-binding protein / SBF-E / TUF


Mass: 33648.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RAP1, GRF1, TUF1, YNL216W, N1310 / Plasmid: pET30a-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-RIPL / References: UniProt: P11938
#2: DNA chain G-guadruplex DNA


Mass: 6034.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 61 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.6, 10% isopropanol, 14% PEG 4000, 10% of glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→64.262 Å / Num. obs: 14665 / % possible obs: 99.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 71.79 Å2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.068 / Rsym value: 0.055 / Net I/av σ(I): 6.7 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.532.50.4061.8525821340.3120.5150.406299.5
2.53-2.682.80.2163.1561620150.1540.2660.2163.699.6
2.68-2.872.80.1843.6532919080.1290.2260.1844.499.5
2.87-3.12.80.0956.9494017900.0680.1180.0956.899.4
3.1-3.392.50.0616.5407416220.0470.0770.0619.699
3.39-3.792.40.0614.1353414740.0480.0770.06112.199.3
3.79-4.382.90.04811.1371513020.0330.0590.0481698.8
4.38-5.372.80.04412.6306510980.030.0540.04416.997.7
5.37-7.592.50.04412.620828440.0320.0550.04416.297.3
7.59-32.13130.0318.914394800.0210.0370.0319.497.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IGN

1ign


Resolution: 2.4→35.09 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.266 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.208
RfactorNum. reflection% reflectionSelection details
Rfree0.233 737 5.03 %RANDOM
Rwork0.203 ---
obs0.2043 14665 99.1 %-
Displacement parametersBiso max: 136.07 Å2 / Biso mean: 74.76 Å2 / Biso min: 44.08 Å2
Baniso -1Baniso -2Baniso -3
1--3.9976 Å20 Å21.0962 Å2
2--5.2599 Å20 Å2
3----1.2623 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.4→35.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 384 30 43 2055
Biso mean--81.15 64.17 -
Num. residues----209
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d667SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes302HARMONIC5
X-RAY DIFFRACTIONt_it2082HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion262SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1339SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2082HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg2898HARMONIC20.89
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion19.55
LS refinement shellResolution: 2.4→2.53 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2512 26 6.37 %
Rwork0.2356 382 -
obs--98.35 %
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)
12.63971.5887-0.03292.723-0.1882.1294-0.16-0.11190.5353-0.26890.03080.5170.12980.07230.1293-0.2382-0.0984-0.02120.026-0.0593-0.1145-5.7111-0.827620.9098
28.56810.54080.99678.8451-0.402410.3608-0.19090.31630.09770.1078-0.20480.3490.1948-0.1880.3957-0.1165-0.05980.13580.1446-0.0326-0.293-3.5171-10.89683.4609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A361 - 573
2X-RAY DIFFRACTION2{ B|* }B1 - 18

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