[English] 日本語
Yorodumi
- PDB-9pll: TRIM21-NUP98 Molecular Glue Complex (MAN-056) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9pll
TitleTRIM21-NUP98 Molecular Glue Complex (MAN-056)
Components
  • E3 ubiquitin-protein ligase TRIM21
  • Isoform 2 of Nuclear pore complex protein Nup98-Nup96
KeywordsLIGASE / Molecular glue / ubiquitin ligase / targeted protein degradation / nuclear pore / TRIM21
Function / homology
Function and homology information


telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore outer ring / negative regulation of protein deubiquitination / nuclear pore organization / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / regulation of type I interferon production ...telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore outer ring / negative regulation of protein deubiquitination / nuclear pore organization / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / regulation of type I interferon production / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / suppression of viral release by host / nuclear inclusion body / Transport of Ribonucleoproteins into the Host Nucleus / nuclear pore nuclear basket / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / STING mediated induction of host immune responses / structural constituent of nuclear pore / positive regulation of mRNA splicing, via spliceosome / Transport of Mature mRNA Derived from an Intronless Transcript / negative regulation of viral transcription / cellular response to chemical stress / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / protein K6-linked ubiquitination / Postmitotic nuclear pore complex (NPC) reformation / : / positive regulation of protein binding / nuclear localization sequence binding / protein K27-linked ubiquitination / Viral Messenger RNA Synthesis / nucleocytoplasmic transport / stress granule disassembly / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / pyroptotic inflammatory response / response to type II interferon / nuclear pore / mRNA transport / protein K63-linked ubiquitination / protein monoubiquitination / SUMOylation of DNA damage response and repair proteins / protein autoubiquitination / positive regulation of cell cycle / protein K48-linked ubiquitination / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / proteasomal protein catabolic process / nuclear periphery / positive regulation of autophagy / Mitotic Prometaphase / negative regulation of innate immune response / EML4 and NUDC in mitotic spindle formation / autophagosome / serine-type peptidase activity / antiviral innate immune response / Resolution of Sister Chromatid Cohesion / Regulation of innate immune responses to cytosolic DNA / SUMOylation of chromatin organization proteins / HCMV Late Events / molecular condensate scaffold activity / promoter-specific chromatin binding / P-body / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / RING-type E3 ubiquitin transferase / protein destabilization / ISG15 antiviral mechanism / Interferon gamma signaling / cytoplasmic stress granule / HCMV Early Events / protein import into nucleus / protein polyubiquitination / ubiquitin-protein transferase activity / Separation of Sister Chromatids / ubiquitin protein ligase activity / nuclear envelope / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / regulation of gene expression / cytoplasmic vesicle / snRNP Assembly / nuclear membrane / positive regulation of viral entry into host cell / transcription coactivator activity / nuclear body / protein ubiquitination / ribonucleoprotein complex / innate immune response
Similarity search - Function
Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata ...Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / 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) / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / E3 ubiquitin-protein ligase TRIM21 / Nuclear pore complex protein Nup98-Nup96
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHinshaw, S.M. / Martinez, M. / Fernandez, D. / Gray, N.S. / Yuan, L. / Noman, M.A. / Corsello, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: TRIM21-NUP98 Molecular Glue Complex (MAN-056)
Authors: Hinshaw, S.M. / Martinez, M. / Fernandez, D. / Gray, N.S. / Yuan, L. / Noman, M.A. / Corsello, S.M.
History
DepositionJul 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: E3 ubiquitin-protein ligase TRIM21
C: Isoform 2 of Nuclear pore complex protein Nup98-Nup96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7804
Polymers40,2712
Non-polymers5092
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.481, 71.307, 97.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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: 20736.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cys 285 mutated to Ser / 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 Isoform 2 of Nuclear pore complex protein Nup98-Nup96


Mass: 19535.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal 6his-tev tag remains / Source: (gene. exp.) Homo sapiens (human) / Gene: NUP98, ADAR2 / Production host: Escherichia coli (E. coli)
References: UniProt: P52948, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Chemical ChemComp-A1BLD / (3P)-3-(4-chloro-2-ethoxyphenyl)-6-fluoro-2-[(piperazin-1-yl)methyl]quinazolin-4(3H)-one


Mass: 416.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22ClFN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 100 mM NaCl, 100 mM HEPES, pH 7.5, 12 % polyethylene glycol 20,000

-
Data collection

DiffractionMean temperature: 99.5 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 24, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.56→49.51 Å / Num. obs: 57407 / % possible obs: 99.4 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 7.4
Reflection shellResolution: 1.56→1.6 Å / Num. unique obs: 2696 / CC1/2: 0.344

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
xia20.6.477data reduction
Aimlessdata scaling
PHENIXAutoMR (1.21.2)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→49.51 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.341 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2137 2608 4.985 %
Rwork0.1748 49707 -
all0.177 --
obs-52315 97.617 %
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: 22.846 Å2
Baniso -1Baniso -2Baniso -3
1-2.205 Å2-0 Å20 Å2
2---0.844 Å2-0 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 35 320 3026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122782
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162547
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.8133779
X-RAY DIFFRACTIONr_angle_other_deg0.5941.7675880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9755333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.0585.52619
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87210445
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.9410130
X-RAY DIFFRACTIONr_chiral_restr0.090.2396
X-RAY DIFFRACTIONr_chiral_restr_other0.0330.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023283
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02654
X-RAY DIFFRACTIONr_nbd_refined0.2120.2442
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.22257
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21347
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21383
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0170.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2550.215
X-RAY DIFFRACTIONr_nbd_other0.2280.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3530.214
X-RAY DIFFRACTIONr_mcbond_it1.6931.6491338
X-RAY DIFFRACTIONr_mcbond_other1.6921.6491338
X-RAY DIFFRACTIONr_mcangle_it2.5042.9551669
X-RAY DIFFRACTIONr_mcangle_other2.512.9551670
X-RAY DIFFRACTIONr_scbond_it3.1391.9941444
X-RAY DIFFRACTIONr_scbond_other3.1381.9951445
X-RAY DIFFRACTIONr_scangle_it4.8943.4762110
X-RAY DIFFRACTIONr_scangle_other4.8933.4772111
X-RAY DIFFRACTIONr_lrange_it7.34721.4173180
X-RAY DIFFRACTIONr_lrange_other7.34821.4193181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.352200.3283479X-RAY DIFFRACTION94.9192
1.642-1.6860.3231720.3013494X-RAY DIFFRACTION95.8431
1.686-1.7350.2931570.2883410X-RAY DIFFRACTION96.1196
1.735-1.7890.2761910.2643249X-RAY DIFFRACTION96.1969
1.789-1.8470.2131620.2143205X-RAY DIFFRACTION96.3928
1.847-1.9120.2481630.2113165X-RAY DIFFRACTION97.6812
1.912-1.9840.1981700.1783061X-RAY DIFFRACTION98.2963
1.984-2.0650.1871580.1652905X-RAY DIFFRACTION98.2991
2.065-2.1570.1971510.1552838X-RAY DIFFRACTION98.4195
2.157-2.2620.1711300.1472702X-RAY DIFFRACTION97.9592
2.262-2.3840.2051410.152585X-RAY DIFFRACTION98.0223
2.384-2.5280.1961240.1512427X-RAY DIFFRACTION97.7769
2.528-2.7020.1711160.1412337X-RAY DIFFRACTION99.1913
2.702-2.9180.1931110.1512173X-RAY DIFFRACTION99.2181
2.918-3.1950.2051010.1522037X-RAY DIFFRACTION99.3956
3.195-3.570.219780.1561855X-RAY DIFFRACTION99.5878
3.57-4.1190.191850.1491628X-RAY DIFFRACTION99.709
4.119-5.0360.189700.1561375X-RAY DIFFRACTION97.372
5.036-7.0860.27680.1891109X-RAY DIFFRACTION100
7.086-49.510.185390.177665X-RAY DIFFRACTION99.8582
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)
11.03010.0246-0.03891.2997-0.07451.3250.0132-0.01550.01540.02490.063-0.059-0.039-0.0485-0.07620.01370.00510.01660.00790.00280.027237.882412.594319.354
20.97060.121-0.06620.7208-0.05870.80080.0288-0.0090.035-0.0824-0.0283-0.15390.05520.0949-0.00050.01720.01050.01750.01540.0090.051155.1324-0.832141.6005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLB283 - 465
2X-RAY DIFFRACTION1ALLC712 - 863

+
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