[English] 日本語
Yorodumi
- PDB-3tix: Crystal structure of the Chp1-Tas3 complex core -

+
Open data


ID or keywords:

Loading...

-
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 / heterochromatin island / subtelomeric heterochromatin / 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 / heterochromatin island / subtelomeric heterochromatin / 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 / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / siRNA-mediated pericentric heterochromatin formation / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / condensed chromosome, centromeric region / pericentric heterochromatin formation / siRNA binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / spindle pole body / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / ubiquitin-like protein ligase binding / protein sumoylation / subtelomeric heterochromatin formation / pericentric heterochromatin / : / histone reader activity / condensed nuclear chromosome / chromosome segregation / protein tag activity / heterochromatin formation / 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 ...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 / Chp1 domain II / Ku70; Chain: A; Domain 2 / : / Cobalt-precorrin-4 Transmethylase; domain 1 / Chromo domain, conserved site / 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 / Special / RNA-binding domain superfamily / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more