[English] 日本語
Yorodumi
- PDB-5yuf: Crystal Structure of PML RING tetramer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yuf
TitleCrystal Structure of PML RING tetramer
ComponentsProtein PML
KeywordsONCOPROTEIN / PML nuclear body biogenesis / sumoylation / RING tetramerization / PML-RARA / targeted therapy
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 / suppression of viral release by host / PML body organization / SUMO binding / fibroblast migration / positive regulation of apoptotic process involved in mammary gland involution / SMAD protein signal transduction ...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 / suppression of viral release by host / PML body organization / SUMO binding / fibroblast migration / positive regulation of apoptotic process involved in mammary gland involution / SMAD protein signal transduction / myeloid cell differentiation / protein-containing complex localization / maintenance of protein location in nucleus / regulation of double-strand break repair / endoplasmic reticulum calcium ion homeostasis / branching involved in mammary gland duct morphogenesis / oncogene-induced cell senescence / Regulation of RUNX1 Expression and Activity / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / positive regulation of extrinsic apoptotic signaling pathway / cobalt ion binding / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of interleukin-1 beta production / SUMOylation of ubiquitinylation proteins / entrainment of circadian clock by photoperiod / SMAD binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / negative regulation of mitotic cell cycle / protein sumoylation / negative regulation of ubiquitin-dependent protein catabolic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of signal transduction by p53 class mediator / cell fate commitment / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein targeting / SUMOylation of DNA damage response and repair proteins / regulation of cell adhesion / response to UV / retinoic acid receptor signaling pathway / Regulation of PTEN localization / extrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation / positive regulation of defense response to virus by host / response to cytokine / transforming growth factor beta receptor signaling pathway / cellular response to interleukin-4 / negative regulation of angiogenesis / cellular response to leukemia inhibitory factor / response to gamma radiation / DNA damage response, signal transduction by p53 class mediator / circadian regulation of gene expression / regulation of circadian rhythm / negative regulation of cell growth / PML body / nuclear matrix / Transcriptional regulation of granulopoiesis / HCMV Early Events / positive regulation of fibroblast proliferation / Interferon gamma signaling / intrinsic apoptotic signaling pathway in response to DNA damage / protein import into nucleus / cellular senescence / protein-containing complex assembly / early endosome membrane / molecular adaptor activity / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / response to hypoxia / transcription coactivator activity / chromosome, telomeric region / regulation of cell cycle / protein stabilization / chromatin remodeling / protein heterodimerization activity / negative regulation of cell population proliferation / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / endoplasmic reticulum membrane / regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein of unknown function DUF3583 / PML-like, coiled-coil / PML, C-terminal domain / : / ANCHR-like B-box zinc-binding 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) ...Protein of unknown function DUF3583 / PML-like, coiled-coil / PML, C-terminal domain / : / ANCHR-like B-box zinc-binding 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) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsWang, P. / Benhend, S. / Wu, H. / Breitenbach, V. / Zhen, T. / Jollivet, F. / Peres, L. / Li, Y. / Chen, S. / Chen, Z. ...Wang, P. / Benhend, S. / Wu, H. / Breitenbach, V. / Zhen, T. / Jollivet, F. / Peres, L. / Li, Y. / Chen, S. / Chen, Z. / de THE, H. / Meng, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Scientific Foundation of China81770142, 81370620, 81570120, 31070645 China
CitationJournal: Nat Commun / Year: 2018
Title: RING tetramerization is required for nuclear body biogenesis and PML sumoylation.
Authors: Wang, P. / Benhenda, S. / Wu, H. / Lallemand-Breitenbach, V. / Zhen, T. / Jollivet, F. / Peres, L. / Li, Y. / Chen, S.J. / Chen, Z. / de The, H. / Meng, G.
History
DepositionNov 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein PML
B: Protein PML
C: Protein PML
D: Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,98612
Polymers22,4624
Non-polymers5238
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-65 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.510, 84.690, 86.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Protein PML / Promyelocytic leukemia protein / RING finger protein 71 / Tripartite motif-containing protein 19


Mass: 5615.592 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PML, MYL, PP8675, RNF71, TRIM19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29590
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.2824 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 12, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 1.6→60.4 Å / Num. obs: 37754 / % possible obs: 99.4 % / Redundancy: 2.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 1.33 / Num. measured obs: 64239 / CC1/2: 0.848

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: v1.0)refinement
iMOSFLMdata reduction
SCALAdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→26.825 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.18
RfactorNum. reflection% reflection
Rfree0.2168 1910 5.09 %
Rwork0.2028 --
obs0.2035 37545 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→26.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 8 224 1635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051441
X-RAY DIFFRACTIONf_angle_d0.9541954
X-RAY DIFFRACTIONf_dihedral_angle_d19.016902
X-RAY DIFFRACTIONf_chiral_restr0.053213
X-RAY DIFFRACTIONf_plane_restr0.007254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.36611380.34982495X-RAY DIFFRACTION99
1.64-1.68430.29871490.27672543X-RAY DIFFRACTION100
1.6843-1.73390.26821170.25562533X-RAY DIFFRACTION100
1.7339-1.78990.21631420.24792525X-RAY DIFFRACTION100
1.7899-1.85380.2231180.22762541X-RAY DIFFRACTION100
1.8538-1.9280.30821210.28172573X-RAY DIFFRACTION100
1.928-2.01570.23271500.2252534X-RAY DIFFRACTION100
2.0157-2.1220.26171610.21582515X-RAY DIFFRACTION100
2.122-2.25490.24281460.22982521X-RAY DIFFRACTION99
2.2549-2.42880.21691510.21222507X-RAY DIFFRACTION99
2.4288-2.67310.20131560.18752546X-RAY DIFFRACTION99
2.6731-3.05940.18551070.2032631X-RAY DIFFRACTION100
3.0594-3.85270.20471190.18112655X-RAY DIFFRACTION99
3.8527-26.8290.19041350.17132516X-RAY DIFFRACTION91
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)
10.28370.0817-0.03870.4221-0.17240.3625-0.03640.29370.0728-0.6503-0.14170.2817-0.096-0.4547-0.02390.5845-0.0503-0.12260.37380.04940.2823-2.310624.28913.1613
20.59250.91930.10231.38730.10550.0642-0.0071-0.0938-0.3467-0.8582-0.0733-0.2632-0.2166-0.754-0.01140.5876-0.028-0.08360.41720.10.2696-0.196227.211311.7085
3-0.00230.15150.03680.2730.31380.1935-0.0745-0.0052-0.0923-0.04520.0383-0.07180.13270.0619-00.35830.0101-0.04580.2970.03090.24953.460827.611522.5087
40.05570.03170.01320.05460.04010.0313-0.228-0.14490.0431-0.5666-0.05540.02330.00340.41350.00070.4512-0.02650.01670.29820.05050.32966.006235.841117.3562
50.14760.1994-0.32270.2743-0.24350.38330.1171-0.21140.0544-0.0452-0.0663-0.468-0.04420.13860.00050.3124-0.009-0.02450.28440.05560.33214.0536.84927.8917
60.11750.095-0.13450.1325-0.11390.1399-0.55-0.34770.3767-0.45340.0843-0.1492-0.35590.2719-0.01260.3346-0.037-0.09050.3968-0.0470.382910.951625.351122.9788
70.049-0.0020.0277-0.00230.04950.02710.3367-0.6399-0.64230.1433-0.2496-0.86440.08920.1580.00110.2360.0086-0.02990.37780.05620.37846.787911.703923.9212
80.02120.0128-0.0020.12230.11320.09970.0238-0.6522-0.7379-0.24240.1733-0.3096-0.17260.23450.00590.25630.01210.01620.38450.02160.351210.835415.692321.2234
90.22450.07190.25950.20680.15940.1761-0.0715-0.01390.2307-0.458-0.02110.1082-0.05850.03030.00010.32120.00780.00170.31190.00890.302-0.271314.761717.7561
100.11470.0230.0790.05050.06230.0717-0.26610.5577-0.18470.11110.3577-0.91380.1850.6049-0.00110.4245-0.04630.08350.3508-0.03810.3916.25568.59913.8154
110.27850.1653-0.08770.5316-0.06280.08310.11310.0159-0.374-0.2816-0.07330.0582-0.0328-0.0371-0.00030.3190.0254-0.00310.266-0.03070.2968-4.02435.160816.2227
120.02230.0138-0.07260.0471-0.01330.05870.19340.17170.4522-0.2306-0.0427-0.059-0.6442-0.1163-0.00040.32530.02310.00710.32540.01610.3402-15.712527.27933.6249
130.02540.01660.0430.28390.59611.22-0.03930.4120.2155-0.417-0.09010.6274-0.3543-0.1319-0.07430.24170.02470.00710.26660.09180.469-18.038319.865423.6962
140.109-0.0575-0.00450.0223-0.0010.0497-0.4654-0.4168-0.15840.2349-0.47310.54020.2668-0.3681-0.00520.34750.11610.0710.49490.04270.5035-19.427421.183533.8891
15-0.0323-0.2544-0.07680.17490.24770.1685-0.1221-0.1075-0.11770.35490.4020.2027-0.05860.18310.01230.29110.07230.04050.29720.0380.3568-11.902513.511429.0936
160.4923-0.2370.38440.669-0.10960.2856-0.2056-0.5009-0.9024-0.07950.14550.53690.1635-0.438-0.09850.30350.01190.12820.38410.14910.9864-21.810710.899228.5875
170.09220.04680.0190.32380.25610.1914-0.1446-0.0945-0.5267-0.2520.27590.76450.2248-0.2688-0.00160.25250.0047-0.01710.29180.04460.5285-14.15735.684423.6327
180.05460.0040.01470.0017-0.00440.00620.151-0.3016-0.74720.07380.2420.504-0.10950.1875-0.00020.6216-0.0431-0.00040.43490.11620.3965-11.135310.161636.5781
190.5762-0.04540.07720.2790.05710.04280.1626-0.1498-0.58830.14980.093-0.6270.2838-0.360.02550.44890.039-0.04590.47740.08820.2666-1.492819.787540.1716
201.3642-0.1895-0.0080.04620.01850.13540.1696-0.2864-0.36060.9394-0.0708-0.38230.3478-0.4213-0.0060.6912-0.0184-0.05010.54210.1340.3438-6.553516.491542.1148
210.08450.138-0.00750.35090.09270.0242-0.2555-0.21640.1104-0.11620.08870.23950.1677-0.2068-0.00040.35520.0032-0.0210.39760.04890.1908-7.595725.922535.3741
220.0866-0.11710.03250.11010.00310.0706-0.08-0.83320.27560.57350.15770.0881-0.8342-0.28830.00020.61060.03660.01010.5558-0.03210.2178-6.299228.277245.0847
231.2053-0.5122-0.25120.46790.00830.23230.2193-0.60960.82530.2755-0.315-0.3494-0.09940.0224-0.01790.4076-0.0489-0.0340.4143-0.07120.2237-1.904934.220137.6467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 51 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 84 )
5X-RAY DIFFRACTION5chain 'A' and (resid 85 through 97 )
6X-RAY DIFFRACTION6chain 'B' and (resid 51 through 55 )
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 60 )
8X-RAY DIFFRACTION8chain 'B' and (resid 61 through 65 )
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 77 )
10X-RAY DIFFRACTION10chain 'B' and (resid 78 through 82 )
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 97 )
12X-RAY DIFFRACTION12chain 'C' and (resid 52 through 56 )
13X-RAY DIFFRACTION13chain 'C' and (resid 57 through 61 )
14X-RAY DIFFRACTION14chain 'C' and (resid 62 through 66 )
15X-RAY DIFFRACTION15chain 'C' and (resid 67 through 77 )
16X-RAY DIFFRACTION16chain 'C' and (resid 78 through 84 )
17X-RAY DIFFRACTION17chain 'C' and (resid 85 through 97 )
18X-RAY DIFFRACTION18chain 'D' and (resid 51 through 55 )
19X-RAY DIFFRACTION19chain 'D' and (resid 56 through 60 )
20X-RAY DIFFRACTION20chain 'D' and (resid 61 through 65 )
21X-RAY DIFFRACTION21chain 'D' and (resid 66 through 77 )
22X-RAY DIFFRACTION22chain 'D' and (resid 78 through 84 )
23X-RAY DIFFRACTION23chain 'D' and (resid 85 through 96 )

+
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