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- PDB-6imq: Crystal structure of PML B1-box multimers -

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Basic information

Entry
Database: PDB / ID: 6imq
TitleCrystal structure of PML B1-box multimers
ComponentsProtein PML
KeywordsONCOPROTEIN / TRIM19 / PML / nuclear body / B1-box / PML-RARA / APL / leukemia
Function / homology
Function and homology information


regulation of calcium ion transport into cytosol / negative regulation of translation in response to oxidative stress / ubiquitin-like protein ligase activity / SUMO-modified protein reader activity / positive regulation of protein localization to chromosome, telomeric region / positive regulation of peptidyl-lysine acetylation / PML body organization / suppression of viral release by host / : / SUMO binding ...regulation of calcium ion transport into cytosol / negative regulation of translation in response to oxidative stress / ubiquitin-like protein ligase activity / SUMO-modified protein reader activity / positive regulation of protein localization to chromosome, telomeric region / positive regulation of peptidyl-lysine acetylation / PML body organization / suppression of viral release by host / : / SUMO binding / fibroblast migration / negative regulation of telomerase activity / positive regulation of apoptotic process involved in mammary gland involution / regulation of double-strand break repair / positive regulation of telomere maintenance / myeloid cell differentiation / SMAD protein signal transduction / maintenance of protein location in nucleus / protein-containing complex localization / Transferases; Acyltransferases; Aminoacyltransferases / endoplasmic reticulum calcium ion homeostasis / oncogene-induced cell senescence / positive regulation of extrinsic apoptotic signaling pathway / Regulation of RUNX1 Expression and Activity / branching involved in mammary gland duct morphogenesis / SUMO transferase activity / positive regulation of signal transduction by p53 class mediator / negative regulation of interleukin-1 beta production / cobalt ion binding / intrinsic apoptotic signaling pathway in response to oxidative stress / SUMOylation of ubiquitinylation proteins / entrainment of circadian clock by photoperiod / SMAD binding / negative regulation of telomere maintenance via telomerase / protein sumoylation / negative regulation of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / protein targeting / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / cell fate commitment / cellular response to interleukin-4 / heterochromatin / SUMOylation of DNA damage response and repair proteins / regulation of cell adhesion / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / response to UV / extrinsic apoptotic signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of defense response to virus by host / Regulation of TP53 Activity through Acetylation / Regulation of PTEN localization / cellular response to leukemia inhibitory factor / negative regulation of angiogenesis / transforming growth factor beta receptor signaling pathway / response to cytokine / response to gamma radiation / circadian regulation of gene expression / regulation of circadian rhythm / negative regulation of cell growth / PML body / nuclear matrix / HCMV Early Events / protein import into nucleus / Transcriptional regulation of granulopoiesis / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of fibroblast proliferation / Interferon gamma signaling / cellular senescence / early endosome membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / nuclear membrane / chromosome, telomeric region / transcription coactivator activity / protein stabilization / molecular adaptor activity / response to hypoxia / regulation of cell cycle / 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 / nucleolus / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein of unknown function DUF3583 / Protein of unknown function (DUF3583) / : / B-box zinc finger / 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 ...Protein of unknown function DUF3583 / Protein of unknown function (DUF3583) / : / B-box zinc finger / 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: 2.06 Å
AuthorsLi, Y. / Ma, X. / Chen, Z. / Wu, H. / Wang, P. / Wu, W. / Cheng, N. / Zeng, L. / Zhang, H. / Cai, X. ...Li, Y. / Ma, X. / Chen, Z. / Wu, H. / Wang, P. / Wu, W. / Cheng, N. / Zeng, L. / Zhang, H. / Cai, X. / Chen, S.J. / Chen, Z. / Meng, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81770142, 81370620, 81570120, 31070645 China
CitationJournal: Nat Commun / Year: 2019
Title: B1 oligomerization regulates PML nuclear body biogenesis and leukemogenesis.
Authors: Li, Y. / Ma, X. / Chen, Z. / Wu, H. / Wang, P. / Wu, W. / Cheng, N. / Zeng, L. / Zhang, H. / Cai, X. / Chen, S.J. / Chen, Z. / Meng, G.
History
DepositionOct 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)24,32613
Polymers23,7674
Non-polymers5599
Water1,47782
1
A: Protein PML
B: Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1817
Polymers11,8842
Non-polymers2975
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-20 kcal/mol
Surface area6800 Å2
MethodPISA
2
C: Protein PML
D: Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1456
Polymers11,8842
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-7 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.670, 50.460, 51.430
Angle α, β, γ (deg.)90.00, 101.35, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe PML B1 can form three types of dimer via W157-interface, F158-interface, and N-terminal augmentation. Through combinations of these dimeric interfaces, PML B1 can polymerize into an remarkable B1-network. Via self-self interaction, PML B1 box can form polymer (i.e. N-mer).

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Components

#1: Protein
Protein PML / Promyelocytic leukemia protein


Mass: 5941.795 Da / Num. of mol.: 4 / Fragment: UNP residues 12-=168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PML / Production host: Escherichia coli (E. coli) / References: UniProt: P29590
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE 5 ISOFORM FOUND IN UNP P29590.

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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: 1.96 Å3/Da / Density % sol: 37.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG6K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.282 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.06→50.4 Å / Num. obs: 11287 / % possible obs: 98 % / Redundancy: 4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.5
Reflection shellResolution: 2.06→2.17 Å / Rmerge(I) obs: 0.69 / Num. unique all: 6697 / Num. unique obs: 1650 / CC1/2: 0.61 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.06→25.23 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.41
RfactorNum. reflection% reflection
Rfree0.2265 557 4.94 %
Rwork0.1863 --
obs0.1883 11270 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.06→25.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 9 82 1700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061649
X-RAY DIFFRACTIONf_angle_d0.9932220
X-RAY DIFFRACTIONf_dihedral_angle_d19.088982
X-RAY DIFFRACTIONf_chiral_restr0.042229
X-RAY DIFFRACTIONf_plane_restr0.005286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.26720.27731230.24562696X-RAY DIFFRACTION99
2.2672-2.5950.25711630.2232687X-RAY DIFFRACTION99
2.595-3.26830.24691280.1932724X-RAY DIFFRACTION99
3.2683-25.23190.19521430.15562606X-RAY DIFFRACTION94
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)
10.0230.03390.00620.4635-0.49630.9740.2710.34670.08460.672-0.53650.06080.25260.9228-0.06260.4172-0.03730.07080.3151-0.09650.34813.81327.647.0359
21.0115-0.0791-0.5641.8732-0.1330.5860.37411.03110.1528-0.644-0.56250.1083-0.0045-1.701-0.02380.28830.093-0.08030.61640.03530.392312.0144.5117-8.0486
32.1547-0.9769-1.47551.2739-0.80932.5508-0.43890.1822-0.17580.3349-0.0270.0520.2785-0.3852-0.73260.2418-0.03180.01430.2146-0.07670.176219.5159-3.2797-3.8012
40.79450.4261-0.30081.6581.87662.7805-1.1926-0.2665-0.97341.93990.48560.34021.78440.40030.20730.580.15330.17420.34070.12380.172518.0609-5.11451.7619
51.41521.2456-1.4612.19850.01940.2079-0.21540.1138-0.170.0030.1222-0.0679-0.02810.0829-0.00640.19870.0103-0.0070.1740.03120.20724.95389.957417.2106
61.48650.6527-0.19561.1868-0.73080.5156-0.1695-0.14070.44510.33710.27480.2924-0.3203-0.12450.00880.24140.00730.01290.15540.01340.21725.421121.477515.032
70.095-0.0632-0.04640.0894-0.0450.0371-0.8675-0.18810.8867-0.2577-0.43640.3952-0.24-0.9157-0.00070.31610.08140.03040.3952-0.07510.37831.8028-2.828319.8949
80.3589-0.2411-0.00130.23020.10010.25810.23440.7197-0.13910.0774-0.2179-0.22190.4983-0.9972-0.00060.2849-0.0053-0.03820.3783-0.03450.2452-13.25660.42419.7068
90.3194-0.1106-0.16490.53410.70410.52250.3180.0447-0.0310.14650.07-0.2290.2064-0.07250.02520.21290.0451-0.04330.2337-0.00420.242-4.95344.534425.632
102.4072-2.4228-1.36423.11922.72234.19560.57940.19330.8121-0.55090.0268-0.9765-0.0864-0.04181.02440.18130.05310.07420.15770.02170.2307-12.61511.898528.2371
110.2606-0.5302-0.31541.69480.03240.73970.4137-0.28440.5404-0.8007-0.1102-0.8023-1.1476-0.4601-0.04570.16740.020.00190.2813-0.10640.472-3.51999.816423.282
120.2209-0.14330.0561.7605-0.80211.72230.4767-0.30660.76010.85-0.867-0.2039-0.1917-0.0699-0.190.18140.05570.09970.074-0.04070.311212.1162.83957.6569
131.8331.5115-1.07163.1378-1.34670.88140.5966-0.8767-0.58360.362-1.0554-0.1342-0.58020.5863-0.15970.193-0.0556-0.04050.33440.04390.268313.7032-7.134316.2772
140.52471.042-0.23621.21250.00730.2307-0.16250.25580.2012-0.43130.11720.09030.2312-0.0520.01410.2147-0.0173-0.04570.23770.01590.16227.9832-9.58867.9072
15-0.0536-0.0589-0.22560.8064-0.5870.6080.227-0.1003-0.12650.0163-0.3543-0.43140.4296-0.02-0.03020.2436-0.01610.03580.1437-0.00030.23198.2946-17.906215.4886
160.196-0.16920.38120.2058-0.27820.55050.12670.0025-0.976-0.7317-0.0255-0.23720.75050.00460.02130.5269-0.0728-0.03830.3258-0.06860.35389.0301-15.13515.0664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 119 through 123 )
2X-RAY DIFFRACTION2chain 'D' and (resid 124 through 137 )
3X-RAY DIFFRACTION3chain 'D' and (resid 138 through 158 )
4X-RAY DIFFRACTION4chain 'D' and (resid 159 through 167 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 148 )
6X-RAY DIFFRACTION6chain 'A' and (resid 149 through 167 )
7X-RAY DIFFRACTION7chain 'B' and (resid 119 through 123 )
8X-RAY DIFFRACTION8chain 'B' and (resid 124 through 137 )
9X-RAY DIFFRACTION9chain 'B' and (resid 138 through 148 )
10X-RAY DIFFRACTION10chain 'B' and (resid 149 through 158 )
11X-RAY DIFFRACTION11chain 'B' and (resid 159 through 168 )
12X-RAY DIFFRACTION12chain 'C' and (resid 119 through 128 )
13X-RAY DIFFRACTION13chain 'C' and (resid 129 through 137 )
14X-RAY DIFFRACTION14chain 'C' and (resid 138 through 148 )
15X-RAY DIFFRACTION15chain 'C' and (resid 149 through 158 )
16X-RAY DIFFRACTION16chain 'C' and (resid 159 through 167 )

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