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- PDB-4bjt: Crystal structure of the Rap1 C-terminal domain (Rap1-RCT) in com... -

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Basic information

Entry
Database: PDB / ID: 4bjt
TitleCrystal structure of the Rap1 C-terminal domain (Rap1-RCT) in complex with the Rap1 binding module of Rif1 (Rif1-RBM)
Components
  • DNA-BINDING PROTEIN RAP1
  • TELOMERE LENGTH REGULATOR PROTEIN RIF1
KeywordsTRANSCRIPTION / GENOME STABILITY / TELOMERE ASSOCIATED PROTEINS
Function / homology
Function and homology information


negative regulation of mitotic DNA replication initiation from late origin / positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / regulation of DNA stability / 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 ...negative regulation of mitotic DNA replication initiation from late origin / positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / regulation of DNA stability / 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 / centromeric DNA binding / G-quadruplex DNA binding / double-stranded telomeric DNA binding / DNA double-strand break processing / telomere capping / regulation of glycolytic process / silent mating-type cassette heterochromatin formation / DNA binding, bending / protein localization to chromosome, telomeric region / nuclear chromosome / telomeric DNA binding / DNA replication origin binding / TFIID-class transcription factor complex binding / DNA replication initiation / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / nucleosomal DNA binding / negative regulation of DNA-templated DNA replication initiation / TBP-class protein binding / telomere maintenance / protein-DNA complex / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / 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
Telomere-associated protein Rif1, N-terminal / Rap1-interacting factor 1 N terminal / Arc Repressor Mutant, subunit A - #2170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1480 / 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 ...Telomere-associated protein Rif1, N-terminal / Rap1-interacting factor 1 N terminal / Arc Repressor Mutant, subunit A - #2170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1480 / 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 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding protein RAP1 / Telomere length regulator protein RIF1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsShi, T. / Bunker, R.D. / Gut, H. / Scrima, A. / Thoma, N.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Rif1 and Rif2 Shape Telomere Funcation and Architecture Through Multivalent RAP1 Interactions
Authors: Shi, T. / Bunker, R.D. / Mattarocci, S. / Ribeyre, C. / Faty, M. / Gut, H. / Scrima, A. / Rass, U. / Rubin, S.M. / Shore, D. / Thoma, N.H.
History
DepositionApr 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Atomic model / Other
Revision 1.2Mar 27, 2019Group: Data collection / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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-BINDING PROTEIN RAP1
B: DNA-BINDING PROTEIN RAP1
C: DNA-BINDING PROTEIN RAP1
D: TELOMERE LENGTH REGULATOR PROTEIN RIF1
E: TELOMERE LENGTH REGULATOR PROTEIN RIF1
F: TELOMERE LENGTH REGULATOR PROTEIN RIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7939
Polymers76,6076
Non-polymers1863
Water11,638646
1
C: DNA-BINDING PROTEIN RAP1
F: TELOMERE LENGTH REGULATOR PROTEIN RIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5983
Polymers25,5362
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-10.6 kcal/mol
Surface area8960 Å2
MethodPISA
2
A: DNA-BINDING PROTEIN RAP1
D: TELOMERE LENGTH REGULATOR PROTEIN RIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5983
Polymers25,5362
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-7.4 kcal/mol
Surface area8760 Å2
MethodPISA
3
B: DNA-BINDING PROTEIN RAP1
E: TELOMERE LENGTH REGULATOR PROTEIN RIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5983
Polymers25,5362
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-7.4 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.010, 88.900, 57.580
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2085-

HOH

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Components

#1: Protein DNA-BINDING PROTEIN RAP1 / RAP1 / REPRESSOR/ACTIVATOR SITE-BINDING PROTEIN / SBF-E / TUF


Mass: 23248.975 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN RAP1-RCT, RESIDUES 672-827
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE S288C (yeast) / Plasmid: PAD DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P11938
#2: Protein/peptide TELOMERE LENGTH REGULATOR PROTEIN RIF1 / RAP1-INTERACTING FACTOR 1


Mass: 2286.732 Da / Num. of mol.: 3 / Fragment: RAP1 BINDING MODULE, RESIDUES 1752-1771 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE S288C (yeast) / References: UniProt: P29539
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 3.8 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growDetails: 2.4-2.5 M AMMONIUM SULFATE, 100 MM NA CITRATE PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→47 Å / Num. obs: 103829 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 23.98 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.7
Reflection shellResolution: 1.61→1.62 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 88.4

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OWT

3owt


Resolution: 1.61→47.16 Å / Cor.coef. Fo:Fc: 0.9515 / Cor.coef. Fo:Fc free: 0.9378 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.064 / SU Rfree Blow DPI: 0.064 / SU Rfree Cruickshank DPI: 0.064
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 5133 4.97 %RANDOM
Rwork0.1664 ---
obs0.1673 103339 96.81 %-
Displacement parametersBiso mean: 31.03 Å2
Baniso -1Baniso -2Baniso -3
1--2.8147 Å20 Å21.1606 Å2
2---4.3469 Å20 Å2
3---7.1616 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.61→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 12 646 4560
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018004HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9514493HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1741SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes125HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1165HARMONIC5
X-RAY DIFFRACTIONt_it8004HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion13.48
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion534SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies17HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9151SEMIHARMONIC4
LS refinement shellResolution: 1.61→1.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 351 4.7 %
Rwork0.1915 7120 -
all0.1919 7471 -
obs--96.81 %
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)
10.80740.8331-0.58971.6017-0.48581.93520.0189-0.00520.0211-0.01430.00260.017-0.25040.1188-0.0215-0.007-0.0340.0053-0.08430.0108-0.0593-44.210916.2628-23.7192
21.09961.0602-0.06291.8596-0.3650.6159-0.0049-0.0082-0.0072-0.01540.0106-0.00370.0921-0.0236-0.00580.0012-0.02650.0361-0.0655-0.0114-0.0444-37.021526.89814.4626
32.9549-0.00060.60780.2990.24451.59870.0019-0.0092-0.03170.0020.01370.00580.01430.2795-0.0155-0.09420.0020.01010.01370.0213-0.0826-6.480544.7226-14.5928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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