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- PDB-5yuf: Crystal Structure of PML RING tetramer -

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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 / negative regulation of mitotic cell cycle / 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 / 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 / protein targeting / regulation of cell adhesion / SUMOylation of DNA damage response and repair proteins / response to UV / retinoic acid receptor signaling pathway / 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 / cellular response to interleukin-4 / transforming growth factor beta receptor signaling pathway / 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 / positive regulation of fibroblast proliferation / HCMV Early Events / 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 / nuclear membrane / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / response to hypoxia / 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 / ubiquitin protein ligase binding / apoptotic process / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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Sample preparation

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

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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

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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 )

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