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- PDB-8j25: Crystal structure of PML B-box2 mutant -

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Basic information

Entry
Database: PDB / ID: 8j25
TitleCrystal structure of PML B-box2 mutant
ComponentsMaltose/maltodextrin-binding periplasmic protein,Protein PML
KeywordsLIGASE / PML / TRIM19 / B-Box2
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 / maintenance of protein location in nucleus / protein-containing complex localization / endoplasmic reticulum calcium ion homeostasis / regulation of double-strand break repair / 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 / detection of maltose stimulus / SMAD binding / maltose transport complex / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / carbohydrate transport / 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 / carbohydrate transmembrane transporter activity / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / maltose binding / cell fate commitment / maltose transport / maltodextrin transmembrane transport / protein targeting / regulation of cell adhesion / SUMOylation of DNA damage response and repair proteins / response to UV / retinoic acid receptor signaling pathway / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / ATP-binding cassette (ABC) transporter complex / transforming growth factor beta receptor signaling pathway / Regulation of PTEN localization / negative regulation of angiogenesis / cellular response to leukemia inhibitory factor / response to gamma radiation / cell chemotaxis / DNA damage response, signal transduction by p53 class mediator / circadian regulation of gene expression / negative regulation of cell growth / regulation of circadian rhythm / PML body / nuclear matrix / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / Interferon gamma signaling / HCMV Early Events / protein import into nucleus / cellular senescence / outer membrane-bounded periplasmic space / protein-containing complex assembly / early endosome membrane / nuclear membrane / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / periplasmic space / transcription coactivator activity / chromosome, telomeric region / response to hypoxia / 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 / DNA damage response / regulation of DNA-templated transcription / endoplasmic reticulum membrane / nucleolus / protein homodimerization activity / DNA binding / zinc ion binding
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) / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Bacterial extracellular solute-binding protein / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Protein PML
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhou, C. / Zang, N. / Zhang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cancer Discov / Year: 2023
Title: Structural Basis of PML-RARA Oncoprotein Targeting by Arsenic Unravels a Cysteine Rheostat Controlling PML Body Assembly and Function.
Authors: Bercier, P. / Wang, Q.Q. / Zang, N. / Zhang, J. / Yang, C. / Maimaitiyiming, Y. / Abou-Ghali, M. / Berthier, C. / Wu, C. / Niwa-Kawakita, M. / Dirami, T. / Geoffroy, M.C. / Ferhi, O. / ...Authors: Bercier, P. / Wang, Q.Q. / Zang, N. / Zhang, J. / Yang, C. / Maimaitiyiming, Y. / Abou-Ghali, M. / Berthier, C. / Wu, C. / Niwa-Kawakita, M. / Dirami, T. / Geoffroy, M.C. / Ferhi, O. / Quentin, S. / Benhenda, S. / Ogra, Y. / Gueroui, Z. / Zhou, C. / Naranmandura, H. / de The, H. / Lallemand-Breitenbach, V.
History
DepositionApr 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4924
Polymers47,0191
Non-polymers4733
Water75742
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.568, 121.568, 161.332
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Protein PML / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / E3 SUMO-protein ligase PML / ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / 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: 47019.188 Da / Num. of mol.: 1 / Mutation: C213A,A216V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, PML, MYL, PP8675, RNF71, TRIM19 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEX9, UniProt: P29590, Transferases; Acyltransferases; Aminoacyltransferases
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→44.08 Å / Num. obs: 27057 / % possible obs: 99.6 % / Redundancy: 5 % / CC1/2: 0.988 / Rpim(I) all: 0.092 / Rsym value: 0.184 / Net I/σ(I): 7.24
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 2853 / CC1/2: 0.393

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4924: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.08 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 1255 4.64 %
Rwork0.2042 --
obs0.2063 27057 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3181 0 25 42 3248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043285
X-RAY DIFFRACTIONf_angle_d0.634464
X-RAY DIFFRACTIONf_dihedral_angle_d17.9861199
X-RAY DIFFRACTIONf_chiral_restr0.042494
X-RAY DIFFRACTIONf_plane_restr0.004576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70.37171350.35042853X-RAY DIFFRACTION98
2.7-2.830.40811310.31382866X-RAY DIFFRACTION99
2.83-2.980.36721050.30482954X-RAY DIFFRACTION99
2.98-3.160.32591450.27892866X-RAY DIFFRACTION99
3.16-3.410.29211610.25442839X-RAY DIFFRACTION99
3.41-3.750.27461390.19652860X-RAY DIFFRACTION99
3.75-4.290.21731230.16722902X-RAY DIFFRACTION99
4.29-5.40.17191340.15282855X-RAY DIFFRACTION99
5.41-44.080.20551820.15592807X-RAY DIFFRACTION98
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)
12.3136-0.19850.1851.70230.13882.0629-0.24240.20060.5249-0.0110.2545-0.0168-0.4734-0.2629-0.04060.50570.0035-0.01790.48720.03010.5005-8.1984-31.7373-13.7408
22.925-0.282-0.57211.5702-0.43251.7978-0.1903-0.37570.11310.2560.2758-0.26130.2381-0.1215-0.0670.34450.0727-0.00350.2723-0.12950.38620.9703-47.2505-0.0426
32.1767-0.34640.55111.27630.3521.5851-0.1431-0.21220.31020.36770.1917-0.2278-0.1066-0.0089-0.04530.37680.0783-0.01960.3514-0.12840.42470.9265-42.05940.8808
41.232-0.18520.56220.9210.22410.3791-0.2013-0.05560.13410.31150.19910.0723-0.0133-0.2255-0.05320.4030.04620.04110.3858-0.00480.3617-8.2104-49.3853-1.5156
50.31650.8560.0462.3633-0.2640.2534-0.19150.0367-0.6888-0.2544-0.1395-1.58630.35631.11880.0250.5808-0.00360.10550.64420.08470.6886-13.6722-64.4999-12.5702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -188 through -118 )
2X-RAY DIFFRACTION2chain 'A' and (resid -117 through -16 )
3X-RAY DIFFRACTION3chain 'A' and (resid -15 through 104 )
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 204 )
5X-RAY DIFFRACTION5chain 'A' and (resid 205 through 227 )

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