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- PDB-4bj5: Crystal structure of Rif2 in complex with the C-terminal domain o... -

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Basic information

Entry
Database: PDB / ID: 4bj5
TitleCrystal structure of Rif2 in complex with the C-terminal domain of Rap1 (Rap1-RCT)
Components
  • (DNA-BINDING PROTEIN RAP1) x 2
  • PROTEIN RIF2
KeywordsTRANSCRIPTION / GENOME STABILITY / TELOMERE ASSOCIATED PROTEINS / AAA+ FOLD
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 / establishment of protein localization to chromatin / telomere maintenance via telomere lengthening / shelterin complex / double-stranded telomeric DNA binding / G-quadruplex 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 / establishment of protein localization to chromatin / telomere maintenance via telomere lengthening / shelterin complex / double-stranded telomeric DNA binding / G-quadruplex DNA binding / telomere capping / silent mating-type cassette heterochromatin formation / DNA binding, bending / regulation of glycolytic process / nucleosomal DNA binding / nuclear chromosome / telomeric DNA binding / TFIID-class transcription factor complex binding / telomere maintenance via telomerase / subtelomeric heterochromatin formation / cis-regulatory region sequence-specific DNA binding / telomere maintenance / TBP-class protein binding / protein-DNA complex / histone binding / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / 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
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1650 / Rossmann fold - #12060 / : / : / RIF2, ASCE domain / RIF2, AAA+ lid domain / Arc Repressor Mutant, subunit A - #2170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1480 / Rap1, DNA-binding domain / Rap1, DNA-binding ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1650 / Rossmann fold - #12060 / : / : / RIF2, ASCE domain / RIF2, AAA+ lid domain / Arc Repressor Mutant, subunit A - #2170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1480 / Rap1, DNA-binding domain / Rap1, DNA-binding / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / BRCT domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / breast cancer carboxy-terminal domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb 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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA-binding protein RAP1 / Protein RIF2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 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 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 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 1.2Dec 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: PROTEIN RIF2
B: PROTEIN RIF2
C: DNA-BINDING PROTEIN RAP1
D: DNA-BINDING PROTEIN RAP1
E: DNA-BINDING PROTEIN RAP1
F: DNA-BINDING PROTEIN RAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,13911
Polymers141,6586
Non-polymers4805
Water00
1
B: PROTEIN RIF2
C: DNA-BINDING PROTEIN RAP1
D: DNA-BINDING PROTEIN RAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0215
Polymers70,8293
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-62.9 kcal/mol
Surface area16860 Å2
MethodPISA
2
A: PROTEIN RIF2
E: DNA-BINDING PROTEIN RAP1
F: DNA-BINDING PROTEIN RAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1176
Polymers70,8293
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-62.9 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.440, 113.860, 140.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN RIF2 / RAP1-INTERACTING FACTOR 2


Mass: 46036.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PAD DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q06208
#2: Protein DNA-BINDING PROTEIN RAP1 / REPRESSOR/ACTIVATOR SITE-BINDING PROTEIN / SBF-E / TUF


Mass: 23248.975 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 627-827
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PAD DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P11938
#3: Protein/peptide DNA-BINDING PROTEIN RAP1 / REPRESSOR/ACTIVATOR SITE-BINDING PROTEIN / SBF-E / TUF / RAP1


Mass: 1543.956 Da / Num. of mol.: 2 / Fragment: RESIDUES 36-48 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q06208
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4

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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: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growDetails: 22-25% PEG 6000, 100 MM TRIS/HCL PH 8.0, 500 MM LI2SO4

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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: Jul 30, 2010 / 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: 3.29→68.5 Å / Num. obs: 27170 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 119.43 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 3.29→3.3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4BJ1 AND 3OWT

4bj1

3owt


Resolution: 3.29→70.47 Å / Cor.coef. Fo:Fc: 0.9448 / Cor.coef. Fo:Fc free: 0.9304 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.322
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.1929 1349 5 %RANDOM
Rwork0.1757 ---
obs0.1766 26997 99.54 %-
Displacement parametersBiso mean: 115.93 Å2
Baniso -1Baniso -2Baniso -3
1-23.7348 Å20 Å20 Å2
2---22.1079 Å20 Å2
3----1.6269 Å2
Refine analyzeLuzzati coordinate error obs: 0.741 Å
Refinement stepCycle: LAST / Resolution: 3.29→70.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7280 0 25 0 7305
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017453HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1310100HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3463SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes200HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1051HARMONIC5
X-RAY DIFFRACTIONt_it7453HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion3.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1006SEMIHARMONIC5
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_contact8355SEMIHARMONIC4
LS refinement shellResolution: 3.29→3.41 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2654 122 4.42 %
Rwork0.2389 2641 -
all0.2401 2763 -
obs--99.54 %
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)
11.4202-1.5281-0.93854.81552.96133.05910.15140.0202-0.0757-0.1891-0.29410.19040.1667-0.18530.1426-0.06740.02210.0798-0.18470.0278-0.1939-3.2077-15.279430.1612
23.02011.73362.5243.81852.76656.23490.215-0.06820.35120.1122-0.1262-0.11280.02840.1474-0.0888-0.2918-0.0698-0.0849-0.27030.078-0.2136-30.84731.9311.6955
38.96831.1561-3.10731.8679-0.55235.7219-0.07-0.44630.13150.18680.31670.4790.2375-0.0839-0.2466-0.33010.03320.0156-0.04310.107-0.081-54.80783.158532.4604
46.93271.9142-0.62233.956-0.39491.8939-0.10520.10440.5449-0.1883-0.1789-0.40960.06040.58030.2841-0.24410.07470.1943-0.07910.1777-0.097121.02035.177830.6758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN E

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