[English] 日本語
Yorodumi
- PDB-32qs: Ternary complex of TRIM21 and BRD4 in complex with PROTAC 1b -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 32qs
TitleTernary complex of TRIM21 and BRD4 in complex with PROTAC 1b
Components
  • Bromodomain-containing protein 4
  • E3 ubiquitin-protein ligase TRIM21
KeywordsLIGASE / TRIM21 / BRD4 / PROTAC / Ternary Complex
Function / homology
Function and homology information


negative regulation of protein deubiquitination / regulation of type I interferon production / suppression of viral release by host / STING mediated induction of host immune responses / negative regulation of viral transcription / cellular response to chemical stress / protein K6-linked ubiquitination / positive regulation of protein binding / protein K27-linked ubiquitination / stress granule disassembly ...negative regulation of protein deubiquitination / regulation of type I interferon production / suppression of viral release by host / STING mediated induction of host immune responses / negative regulation of viral transcription / cellular response to chemical stress / protein K6-linked ubiquitination / positive regulation of protein binding / protein K27-linked ubiquitination / stress granule disassembly / histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / negative regulation of DNA damage checkpoint / P-TEFb complex binding / histone H3K9ac reader activity / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription / histone H4K16ac reader activity / pyroptotic inflammatory response / positive regulation of G2/M transition of mitotic cell cycle / protein monoubiquitination / positive regulation of T-helper 17 cell lineage commitment / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of cell cycle / response to type II interferon / negative regulation of innate immune response / positive regulation of autophagy / autophagosome / Regulation of innate immune responses to cytosolic DNA / antiviral innate immune response / condensed nuclear chromosome / transcription coregulator activity / proteasomal protein catabolic process / positive regulation of transcription elongation by RNA polymerase II / P-body / protein destabilization / positive regulation of non-canonical NF-kappaB signal transduction / RING-type E3 ubiquitin transferase / Interferon gamma signaling / protein polyubiquitination / cytoplasmic stress granule / ubiquitin-protein transferase activity / p53 binding / Regulation of PD-L1(CD274) transcription / regulation of gene expression / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / regulation of inflammatory response / chromosome / cytoplasmic vesicle / histone binding / Potential therapeutics for SARS / positive regulation of viral entry into host cell / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / transcription cis-regulatory region binding / protein ubiquitination / chromatin remodeling / ribonucleoprotein complex / innate immune response / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / DNA damage response / positive regulation of DNA-templated transcription / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / Modified RING finger domain / U-box domain / SPRY-associated domain / SPRY-associated / PRY / B-box zinc finger / Butyrophylin-like, SPRY domain ...TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / Modified RING finger domain / U-box domain / SPRY-associated domain / SPRY-associated / PRY / B-box zinc finger / Butyrophylin-like, SPRY domain / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Bromodomain-containing protein 4 / E3 ubiquitin-protein ligase TRIM21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKim, Y. / Sokolenko, Y. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Ternary complex of TRIM21 and BRD4 in complex with PROTAC 1a
Authors: Kim, Y. / Sokolenko, Y. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
History
DepositionJul 21, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM21
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6904
Polymers35,6512
Non-polymers1,0392
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-3 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.515, 41.984, 112.945
Angle α, β, γ (deg.)90.000, 101.648, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

-
Components

#1: Protein E3 ubiquitin-protein ligase TRIM21 / 52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / RING finger protein 81 / Ro(SS-A) ...52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / RING finger protein 81 / Ro(SS-A) / Sjoegren syndrome type A antigen / SS-A / Tripartite motif-containing protein 21


Mass: 20551.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM21, RNF81, RO52, SSA1 / Production host: Escherichia coli (E. coli)
References: UniProt: P19474, RING-type E3 ubiquitin transferase
#2: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 15099.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-A1KEC / ~{N}-[(3-chloranylpyridin-4-yl)methyl]-~{N}-[6-[2-[(9~{S})-7-(4-chlorophenyl)-4,5-dimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]hexyl]-4-(4-fluoranyl-2-methylsulfanyl-phenyl)-2-methylsulfonyl-benzamide


Mass: 932.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H44Cl2FN7O4S3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 6, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.7→34.469 Å / Num. obs: 7966 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.987 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.093 / Rrim(I) all: 0.248 / Χ2: 0.97 / Net I/σ(I): 6.8
Reflection shellResolution: 2.7→2.83 Å / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.82 / Num. measured all: 7693 / Num. unique obs: 1049 / CC1/2: 0.85 / Rpim(I) all: 0.324 / Rrim(I) all: 0.882 / Χ2: 1.11 / Net I/σ(I) obs: 2.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→34.469 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.902 / SU B: 14.837 / SU ML: 0.297 / Cross valid method: FREE R-VALUE / ESU R Free: 0.402
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2601 349 4.382 %
Rwork0.216 7615 -
all0.218 --
obs-7964 99.912 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.691 Å2
Baniso -1Baniso -2Baniso -3
1--2.916 Å2-0 Å22.224 Å2
2--0.269 Å20 Å2
3---1.594 Å2
Refinement stepCycle: LAST / Resolution: 2.7→34.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 69 4 2419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122496
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162214
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.7943413
X-RAY DIFFRACTIONr_angle_other_deg0.4371.7635089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4465289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.578510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82310349
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.74510117
X-RAY DIFFRACTIONr_chiral_restr0.0540.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
X-RAY DIFFRACTIONr_nbd_refined0.1980.2518
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22016
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21192
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21185
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.270
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1160.215
X-RAY DIFFRACTIONr_nbd_other0.2140.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.25
X-RAY DIFFRACTIONr_mcbond_it1.823.6411168
X-RAY DIFFRACTIONr_mcbond_other1.8143.6421168
X-RAY DIFFRACTIONr_mcangle_it3.0666.5351453
X-RAY DIFFRACTIONr_mcangle_other3.0686.5381454
X-RAY DIFFRACTIONr_scbond_it1.6143.6611328
X-RAY DIFFRACTIONr_scbond_other1.6143.6611329
X-RAY DIFFRACTIONr_scangle_it2.836.6871960
X-RAY DIFFRACTIONr_scangle_other2.8296.6861961
X-RAY DIFFRACTIONr_lrange_it4.72135.532737
X-RAY DIFFRACTIONr_lrange_other4.72135.5252738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.315280.297556X-RAY DIFFRACTION100
2.77-2.8450.441280.281525X-RAY DIFFRACTION100
2.845-2.9270.449180.276533X-RAY DIFFRACTION100
2.927-3.0160.312250.28498X-RAY DIFFRACTION100
3.016-3.1150.26240.26507X-RAY DIFFRACTION99.812
3.115-3.2230.34230.256480X-RAY DIFFRACTION100
3.223-3.3430.419180.229454X-RAY DIFFRACTION100
3.343-3.4790.215200.215456X-RAY DIFFRACTION100
3.479-3.6320.212200.212427X-RAY DIFFRACTION100
3.632-3.8070.314170.191413X-RAY DIFFRACTION100
3.807-4.010.22200.201384X-RAY DIFFRACTION100
4.01-4.250.188220.186374X-RAY DIFFRACTION100
4.25-4.5380.192180.152351X-RAY DIFFRACTION100
4.538-4.8950.18480.156327X-RAY DIFFRACTION100
4.895-5.3510.217160.183310X-RAY DIFFRACTION100
5.351-5.9650.199100.199274X-RAY DIFFRACTION100
5.965-6.8530.293110.22253X-RAY DIFFRACTION100
6.853-8.3120.242150.203205X-RAY DIFFRACTION100

+
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