[English] 日本語
Yorodumi
- PDB-8dji: Ternary complex of SUMO1 with the SIM of PML and zinc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dji
TitleTernary complex of SUMO1 with the SIM of PML and zinc
Components
  • Protein PML
  • Small ubiquitin-related modifier 1
KeywordsNUCLEAR PROTEIN / SUMO1 / PML Nuclear Bodies / Zinc / auto-inhibition / Daxx
Function / homology
Function and homology information


regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / negative regulation of potassium ion transmembrane transporter activity / suppression of viral release by host / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / negative regulation of delayed rectifier potassium channel activity ...regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / negative regulation of potassium ion transmembrane transporter activity / suppression of viral release by host / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / negative regulation of delayed rectifier potassium channel activity / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / PML body organization / negative regulation of DNA binding / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / nuclear stress granule / SUMO binding / small protein activating enzyme binding / fibroblast migration / positive regulation of apoptotic process involved in mammary gland involution / SMAD protein signal transduction / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / myeloid cell differentiation / XY body / SUMOylation of SUMOylation proteins / protein-containing complex localization / maintenance of protein location in nucleus / regulation of calcium ion transmembrane transport / regulation of double-strand break repair / endoplasmic reticulum calcium ion homeostasis / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / branching involved in mammary gland duct morphogenesis / oncogene-induced cell senescence / Regulation of RUNX1 Expression and Activity / negative regulation of mitotic cell cycle / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cardiac muscle cell contraction / SUMO transferase activity / positive regulation of extrinsic apoptotic signaling pathway / Postmitotic nuclear pore complex (NPC) reformation / cobalt ion binding / Maturation of nucleoprotein / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of interleukin-1 beta production / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / transcription factor binding / ubiquitin-specific protease binding / entrainment of circadian clock by photoperiod / SMAD binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / cellular response to cadmium ion / ubiquitin-like protein ligase binding / roof of mouth development / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of signal transduction by p53 class mediator / negative regulation of ubiquitin-dependent protein catabolic process / cell fate commitment / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / postsynaptic cytosol / potassium channel regulator activity / transporter activator activity / Regulation of IFNG signaling / nuclear pore / protein targeting / negative regulation of DNA-binding transcription factor activity / regulation of cell adhesion / SUMOylation of DNA damage response and repair proteins / response to UV / retinoic acid receptor signaling pathway / presynaptic cytosol / Regulation of PTEN localization / Regulation of TP53 Activity through Acetylation / extrinsic apoptotic signaling pathway / positive regulation of defense response to virus by host / response to cytokine / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to interleukin-4 / transforming growth factor beta receptor signaling pathway / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / negative regulation of angiogenesis / cellular response to leukemia inhibitory factor / response to gamma radiation / DNA damage response, signal transduction by p53 class mediator / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / circadian regulation of gene expression / Formation of Incision Complex in GG-NER / protein tag activity / regulation of circadian rhythm / negative regulation of cell growth
Similarity search - Function
Protein of unknown function DUF3583 / PML-like, coiled-coil / PML, C-terminal domain / : / ANCHR-like B-box zinc-binding domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / B-Box-type zinc finger / B-box-type zinc finger ...Protein of unknown function DUF3583 / PML-like, coiled-coil / PML, C-terminal domain / : / ANCHR-like B-box zinc-binding domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Protein PML / Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsLussier-Price, M. / Wahba, H.M. / Mascle, X.H. / Cappadocia, L. / Bourdeau, V. / Gagnon, C. / Igelmann, S. / Sakaguchi, K. / Ferbeyre, G. / Omichinski, J.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)70439, 130414 and 166104 Canada
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1.
Authors: Lussier-Price, M. / Wahba, H.M. / Mascle, X.H. / Cappadocia, L. / Bourdeau, V. / Gagnon, C. / Igelmann, S. / Sakaguchi, K. / Ferbeyre, G. / Omichinski, J.G.
History
DepositionJun 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Small ubiquitin-related modifier 1
B: Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2175
Polymers14,0202
Non-polymers1963
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-91 kcal/mol
Surface area5460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.995, 47.156, 63.777
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Small ubiquitin-related modifier 1 / SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain ...SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein SMT3C / Smt3C / Ubiquitin-like protein UBL1


Mass: 11043.335 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Production host: Escherichia coli (E. coli) / References: UniProt: P63165
#2: Protein/peptide Protein PML / E3 SUMO-protein ligase PML / Promyelocytic leukemia protein / RING finger protein 71 / RING-type E3 ...E3 SUMO-protein ligase PML / Promyelocytic leukemia protein / RING finger protein 71 / RING-type E3 SUMO transferase PML / Tripartite motif-containing protein 19 / TRIM19


Mass: 2976.985 Da / Num. of mol.: 1 / Fragment: SIM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PML, MYL, PP8675, RNF71, TRIM19 / Production host: Escherichia coli (E. coli)
References: UniProt: P29590, Transferases; Acyltransferases; Aminoacyltransferases
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES pH 7.0, 19 to 31 % (w/v) PEG 3350, and 1-5 mM zinc chloride

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.97→32 Å / Num. obs: 14192 / % possible obs: 96.58 % / Redundancy: 5.5 % / CC1/2: 0.982 / Net I/σ(I): 5.34
Reflection shellResolution: 1.97→2.044 Å / Num. unique obs: 637 / CC1/2: 0.263

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V7P
Resolution: 1.97→32 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 1443 10.17 %
Rwork0.2308 12749 -
obs0.2336 14192 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.06 Å2 / Biso mean: 34.7233 Å2 / Biso min: 16.14 Å2
Refinement stepCycle: final / Resolution: 1.97→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms734 0 3 60 797
Biso mean--44.5 38.04 -
Num. residues----90
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.97-2.040.3614910.347786295362
2.04-2.130.39241290.33151077120681
2.13-2.220.29441440.30051292143695
2.22-2.340.3391550.2751355151099
2.34-2.490.32571540.256613661520100
2.49-2.680.23421560.243113501506100
2.68-2.950.27151540.240913661520100
2.95-3.370.25291500.202213791529100
3.37-4.250.19761490.178113471496100
4.25-320.23611610.218813551516100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0095-0.49310.6731.33160.13710.9263-0.03430.0462-0.07120.04290.0230.03890.03830.1081-0.00010.3143-0.02710.01210.26840.00470.24360.95077.24646.7637
20.24930.12980.15360.3063-0.11030.2789-0.0221-0.0884-0.0149-0.25080.02030.1499-0.05620.1020.00540.283-0.02420.02140.3896-0.01720.3412-7.031318.09049.7802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA19 - 93
2X-RAY DIFFRACTION2chain BB7 - 29

+
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