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- PDB-4bj6: Crystal structure Rif2 in complex with the C-terminal domain of R... -

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Basic information

Entry
Database: PDB / ID: 4bj6
TitleCrystal structure Rif2 in complex with the C-terminal domain of Rap1 (Rap1-RCT)
Components
  • (RAP1-INTERACTING FACTOR 2) x 2
  • DNA-BINDING PROTEIN RAP1
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 / regulation of glycolytic process / DNA binding, bending / 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: 3.26 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: RAP1-INTERACTING FACTOR 2
B: RAP1-INTERACTING FACTOR 2
C: DNA-BINDING PROTEIN RAP1
D: RAP1-INTERACTING FACTOR 2
E: DNA-BINDING PROTEIN RAP1
F: RAP1-INTERACTING FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,83816
Polymers133,8776
Non-polymers96110
Water00
1
B: RAP1-INTERACTING FACTOR 2
C: DNA-BINDING PROTEIN RAP1
D: RAP1-INTERACTING FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4198
Polymers66,9393
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-94.5 kcal/mol
Surface area22300 Å2
MethodPISA
2
A: RAP1-INTERACTING FACTOR 2
E: DNA-BINDING PROTEIN RAP1
F: RAP1-INTERACTING FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4198
Polymers66,9393
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-95.4 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.250, 112.680, 140.790
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 RAP1-INTERACTING FACTOR 2


Mass: 42145.809 Da / Num. of mol.: 2 / Fragment: N-TERMINALLY TRUNCATED, RESIDUES 35-395
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 RAP1-INTERACTING FACTOR 2


Mass: 1543.956 Da / Num. of mol.: 2
Fragment: RAP1 C-TERMINAL DOMAIN BINDING MODULE, 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.: 10 / 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: Sep 19, 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: 3.26→48.8 Å / Num. obs: 27519 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 113.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.1
Reflection shellResolution: 3.26→3.27 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

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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: 3.26→48.79 Å / Cor.coef. Fo:Fc: 0.9418 / Cor.coef. Fo:Fc free: 0.9241 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.322
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 1361 4.96 %RANDOM
Rwork0.1719 ---
obs0.1731 27419 99.65 %-
Displacement parametersBiso mean: 110.75 Å2
Baniso -1Baniso -2Baniso -3
1-19.7177 Å20 Å20 Å2
2---30.0411 Å20 Å2
3---10.3234 Å2
Refine analyzeLuzzati coordinate error obs: 0.716 Å
Refinement stepCycle: LAST / Resolution: 3.26→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 50 0 7370
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017513HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1210169HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3505SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes200HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1052HARMONIC5
X-RAY DIFFRACTIONt_it7513HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion3.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1005SEMIHARMONIC5
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_contact8562SEMIHARMONIC4
LS refinement shellResolution: 3.26→3.38 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2324 120 4.25 %
Rwork0.2306 2704 -
all0.2307 2824 -
obs--99.65 %
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)
11.2073-1.4587-0.97764.5032.95563.18830.15020.0115-0.1011-0.2072-0.28750.21540.1522-0.16470.1373-0.04110.0010.07-0.19610.0181-0.1221-3.247-15.226730.3213
22.62671.73342.54992.92912.3296.09430.2042-0.07250.23810.1044-0.1187-0.22610.10340.1494-0.0855-0.2626-0.056-0.1061-0.27180.0671-0.126-30.62271.948112.0182
38.99761.3917-3.82541.7698-0.7195.2139-0.1778-0.56670.15860.25220.29780.46910.2261-0.0899-0.12-0.29330.023-0.0006-0.05110.1146-0.0742-54.78153.112832.8149
47.372.1427-0.70813.925-0.37012.0959-0.15530.18910.5432-0.1473-0.1216-0.39190.05380.6210.2769-0.20960.05220.1748-0.09920.1686-0.039621.03175.083931.0463
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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