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- PDB-3tix: Crystal structure of the Chp1-Tas3 complex core -

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Basic information

Entry
Database: PDB / ID: 3tix
TitleCrystal structure of the Chp1-Tas3 complex core
Components
  • Chromo domain-containing protein 1
  • Ubiquitin-like protein SMT3,RNA-induced transcriptional silencing complex protein tas3
KeywordsGENE REGULATION/PROTEIN BINDING / PIN / Rossmann fold / SPOC / alpha-helical hairpin / heterochromatin / silencing / RITS / RNAi / Argonaute / ClrC / RDRC / Nucleus / GENE REGULATION-PROTEIN BINDING complex
Function / homology
Function and homology information


RITS complex / Factors involved in megakaryocyte development and platelet production / subtelomeric heterochromatin / heterochromatin island / mating-type region heterochromatin / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors ...RITS complex / Factors involved in megakaryocyte development and platelet production / subtelomeric heterochromatin / heterochromatin island / mating-type region heterochromatin / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / siRNA-mediated pericentric heterochromatin formation / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / pericentric heterochromatin formation / condensed chromosome, centromeric region / siRNA binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / spindle pole body / silent mating-type cassette heterochromatin formation / ubiquitin-like protein ligase binding / protein sumoylation / subtelomeric heterochromatin formation / pericentric heterochromatin / methylated histone binding / histone reader activity / condensed nuclear chromosome / chromosome segregation / heterochromatin formation / protein tag activity / molecular adaptor activity / single-stranded RNA binding / chromatin binding / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Ku70; Chain: A; Domain 2 - #20 / Cobalt-precorrin-4 Transmethylase; domain 1 - #30 / Rossmann fold - #11490 / Helix Hairpins - #1690 / : / : / : / : / Chromo domain-containing protein 1-like, PIN domain / Tas3, C-terminal helical domains ...Ku70; Chain: A; Domain 2 - #20 / Cobalt-precorrin-4 Transmethylase; domain 1 - #30 / Rossmann fold - #11490 / Helix Hairpins - #1690 / : / : / : / : / Chromo domain-containing protein 1-like, PIN domain / Tas3, C-terminal helical domains / Tas3-like, N-terminal domain / Chromo domain-containing protein 1-like, SPOC domain / Ku70; Chain: A; Domain 2 / : / Chromo domain, conserved site / Cobalt-precorrin-4 Transmethylase; domain 1 / Chromo domain signature. / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Helix Hairpins / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helix non-globular / RNA-binding domain superfamily / Special / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / RNA-induced transcriptional silencing complex protein tas3 / Chromo domain-containing protein 1 / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Schizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9001 Å
AuthorsSchalch, T. / Joshua-Tor, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: The Chp1-Tas3 core is a multifunctional platform critical for gene silencing by RITS.
Authors: Schalch, T. / Job, G. / Shanker, S. / Partridge, J.F. / Joshua-Tor, L.
History
DepositionAug 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Jun 7, 2017Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_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

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Assembly

Deposited unit
A: Ubiquitin-like protein SMT3,RNA-induced transcriptional silencing complex protein tas3
B: Chromo domain-containing protein 1
C: Ubiquitin-like protein SMT3,RNA-induced transcriptional silencing complex protein tas3
D: Chromo domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,79115
Polymers151,3904
Non-polymers40111
Water46826
1
A: Ubiquitin-like protein SMT3,RNA-induced transcriptional silencing complex protein tas3
B: Chromo domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8767
Polymers75,6952
Non-polymers1815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-87 kcal/mol
Surface area28830 Å2
MethodPISA
2
C: Ubiquitin-like protein SMT3,RNA-induced transcriptional silencing complex protein tas3
D: Chromo domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9158
Polymers75,6952
Non-polymers2206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-84 kcal/mol
Surface area28820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.880, 172.200, 198.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ubiquitin-like protein SMT3,RNA-induced transcriptional silencing complex protein tas3 / RITS protein tas3


Mass: 23333.049 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN,N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: ATCC 204508 / S288c, 972 / ATCC 24843 / Gene: SMT3, YDR510W, D9719.15, tas3, SPBC83.03c / Plasmid: pFL, Multibac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q12306, UniProt: O94687
#2: Protein Chromo domain-containing protein 1


Mass: 52361.988 Da / Num. of mol.: 2 / Fragment: C-TERMINAL HALF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: chp1, SPAC18G6.02c / Plasmid: pFL, Multibac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q10103
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: microseeding in 0.95 M potassium sodium tartrate, 100 mM MES, 180 mM sodium thiocyanate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2010
RadiationMonochromator: CRYOGENICALLY COOLED DOUBLE CRYSTAL MONOCHROMATOR WITH HORIZONTAL FOCUSING SAGITTAL BEND SECOND MONO CRYSTAL WITH 4:1 MAGNIFICATION RATIO AND VERTICALLY FOCUSING MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→89.7 Å / Num. all: 40228 / Num. obs: 40143 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.93 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 8.04
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 1.93 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.78 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CBASSdata collection
HKL2Mapmodel building
SHELXmodel building
SHARPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDS(VERSION February 3data reduction
XDS(VERSION February 3data scaling
HKL2Mapphasing
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9001→65.063 Å / SU ML: 0.82
Isotropic thermal model: isotropic grouped main chain and side chain, TLS.
σ(F): 1.59 / Phase error: 25.15 / Stereochemistry target values: ML / Details: used riding hydrogens
RfactorNum. reflection% reflection
Rfree0.2427 1996 4.97 %
Rwork0.2107 --
obs0.2123 40128 99.77 %
all-40228 -
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.61 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.1384 Å20 Å2-0 Å2
2--15.2281 Å2-0 Å2
3----8.0897 Å2
Refinement stepCycle: LAST / Resolution: 2.9001→65.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9272 0 11 26 9309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059464
X-RAY DIFFRACTIONf_angle_d0.52612793
X-RAY DIFFRACTIONf_dihedral_angle_d12.1493554
X-RAY DIFFRACTIONf_chiral_restr0.0341459
X-RAY DIFFRACTIONf_plane_restr0.0021625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-2.97260.37451380.30792712X-RAY DIFFRACTION100
2.9726-3.0530.33221480.29592676X-RAY DIFFRACTION100
3.053-3.14280.32381460.28172708X-RAY DIFFRACTION100
3.1428-3.24420.3111470.25882677X-RAY DIFFRACTION100
3.2442-3.36020.27971370.24522711X-RAY DIFFRACTION100
3.3602-3.49470.28141330.23712699X-RAY DIFFRACTION100
3.4947-3.65380.26741430.21972697X-RAY DIFFRACTION100
3.6538-3.84640.24581410.20262705X-RAY DIFFRACTION100
3.8464-4.08730.20221470.18932713X-RAY DIFFRACTION100
4.0873-4.40280.20721350.16792739X-RAY DIFFRACTION100
4.4028-4.84580.20721500.16022725X-RAY DIFFRACTION100
4.8458-5.54670.23921430.192747X-RAY DIFFRACTION100
5.5467-6.98690.25741370.23462769X-RAY DIFFRACTION100
6.9869-65.07940.20221510.20122854X-RAY DIFFRACTION99
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)
13.54970.5283-1.96883.028-1.0754.71770.2650.5099-0.25120.0243-0.21120.1012-0.2495-0.01890.02420.4807-0.04230.05080.71390.05120.6627-27.5729-26.179356.0326
21.39810.5742-0.65722.5843-0.71032.72740.15060.01030.35650.3390.46111.0346-0.3145-0.46820.00010.96250.10690.16921.41080.50471.3801-39.341-3.778541.7386
32.33620.7635-0.38671.27260.14192.14980.69470.40241.8045-0.2436-0.31470.0273-0.2402-0.0698-01.16350.06750.48170.97620.16161.6026-51.1557-14.07428.5321
44.75520.9018-0.433.2011-2.60124.0540.09010.10430.44070.07850.36090.20360.1692-0.19070.02590.6381-0.0198-0.00110.43860.08750.7659-28.8804-23.9582-5.4617
56.0751.3185-2.16873.18050.48224.3760.00540.16990.18480.22610.22480.5847-0.0407-0.280900.6513-0.03780.07820.51950.12720.7972-43.1973-32.304277.0913
61.2910.381-1.53160.75560.2111.9813-0.45410.004-0.61370.05720.20270.01240.46780.108200.67160.00910.02830.7430.10630.6423-20.7622-32.786357.5372
74.16390.7283-0.18264.1649-0.29564.8034-0.02330.41090.1327-0.17770.12980.2429-0.2961-0.1939-00.5137-0.02280.03570.73740.0790.4007-9.3968-20.644737.3158
81.7646-0.19040.67054.55062.13141.2841-0.48450.3686-0.3527-0.00130.253-0.2430.93571.23670.00060.60570.10320.03311.20460.04410.61440.732-33.058618.8833
90.9401-0.07450.44440.83240.96471.2489-0.37710.12870.0103-0.8270.4044-0.81240.8645-0.6899-00.98630.10280.09551.4362-0.23981.1456-0.267-36.0161-2.402
103.0033-1.2741-0.08363.1208-0.24715.2355-0.00390.83480.17430.2756-0.0108-0.0952-0.01410.892400.627-0.11090.04271.0631-0.06840.5414-3.1604-26.950614.5551
112.50831.03211.46687.2095-3.16514.15260.20740.27980.2202-0.431300.0490.09990.177600.7115-0.04560.06210.74430.13740.8425-22.1282-7.7441-27.6656
121.4113-0.86470.74221.1542-1.65732.52930.29380.5696-0.289-0.1038-0.3124-0.42570.29180.2278-0.00010.6415-0.0913-0.00750.5551-0.07320.7152-22.0801-30.7333-8.9075
135.19820.6302-0.48465.2525-1.30094.56850.0216-0.06640.08940.21940.2640.14780.3684-0.458-0.00010.7148-0.083-0.05040.63720.060.6929-32.5443-43.509111.0467
142.86560.82791.71811.90871.61371.60760.7209-0.4347-0.95530.4044-0.1974-0.39721.56380.26070.07811.29380.0448-0.23580.68610.33711.2379-18.1985-53.958727.6773
150.14320.19210.14030.34420.36180.30180.4532-0.0019-0.93060.2847-0.8268-0.49290.16150.04810.00011.75830.1158-0.42771.47780.28431.6739-14.0366-54.926947.357
163.73030.0381.08561.56620.33222.86640.6092-0.4865-0.62950.3366-0.6453-0.04650.5431-0.28270.00011.2443-0.1411-0.26560.85490.28940.9907-24.0583-51.438332.518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid -4:100
2X-RAY DIFFRACTION2chain A and resid -100:-5
3X-RAY DIFFRACTION3chain C and resid -100:-5
4X-RAY DIFFRACTION4chain C and resid -4:100
5X-RAY DIFFRACTION5chain B and resid 500:651
6X-RAY DIFFRACTION6chain B and resid 652:683
7X-RAY DIFFRACTION7chain B and resid 684:779
8X-RAY DIFFRACTION8chain B and resid 799:845
9X-RAY DIFFRACTION9chain B and resid 846:887
10X-RAY DIFFRACTION10chain B and resid 888:960
11X-RAY DIFFRACTION11chain D and resid 500:651
12X-RAY DIFFRACTION12chain D and resid 652:683
13X-RAY DIFFRACTION13chain D and resid 684:779
14X-RAY DIFFRACTION14chain D and resid 799:845
15X-RAY DIFFRACTION15chain D and resid 846:887
16X-RAY DIFFRACTION16chain D and resid 888:960

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