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- PDB-8j2p: Crystal structure of PML B-box2 -

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Basic information

Entry
Database: PDB / ID: 8j2p
TitleCrystal structure of PML B-box2
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 / 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 / detection of maltose stimulus / entrainment of circadian clock by photoperiod / SMAD binding / maltose transport complex / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / carbohydrate transport / 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 / carbohydrate transmembrane transporter activity / cell fate commitment / maltose binding / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / maltose transport / maltodextrin transmembrane transport / 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 / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / extrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation / positive regulation of defense response to virus by host / response to cytokine / ATP-binding cassette (ABC) transporter complex / transforming growth factor beta receptor signaling pathway / cellular response to interleukin-4 / negative regulation of angiogenesis / cellular response to leukemia inhibitory factor / cell chemotaxis / 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 / outer membrane-bounded periplasmic space / protein-containing complex assembly / early endosome membrane / molecular adaptor activity / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / response to hypoxia / periplasmic space / 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 / DNA damage response / endoplasmic reticulum membrane / regulation of DNA-templated transcription / 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: 2.09 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 15, 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
E: Maltose/maltodextrin-binding periplasmic protein,Protein PML
A: Maltose/maltodextrin-binding periplasmic protein,Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9938
Polymers94,0462
Non-polymers9466
Water5,729318
1
E: Maltose/maltodextrin-binding periplasmic protein,Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4964
Polymers47,0231
Non-polymers4733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Maltose/maltodextrin-binding periplasmic protein,Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4964
Polymers47,0231
Non-polymers4733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.550, 122.550, 163.224
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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: 47023.199 Da / Num. of mol.: 2
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.: 2 / 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.: 4 / 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.: 318 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.09→35.4 Å / Num. obs: 53556 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rpim(I) all: 0.03 / Rsym value: 0.072 / Net I/σ(I): 33.9
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 3559 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4924: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→35.38 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 1979 3.7 %
Rwork0.1912 --
obs0.1927 53520 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→35.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6368 0 50 318 6736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046568
X-RAY DIFFRACTIONf_angle_d0.6888924
X-RAY DIFFRACTIONf_dihedral_angle_d17.4132398
X-RAY DIFFRACTIONf_chiral_restr0.044986
X-RAY DIFFRACTIONf_plane_restr0.0041152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.34811430.26543553X-RAY DIFFRACTION96
2.15-2.20.29361640.23753677X-RAY DIFFRACTION100
2.2-2.270.29391300.23333727X-RAY DIFFRACTION100
2.27-2.340.25611370.2273687X-RAY DIFFRACTION100
2.34-2.430.24851390.21843680X-RAY DIFFRACTION100
2.43-2.520.31111330.2033706X-RAY DIFFRACTION100
2.52-2.640.24771330.21743712X-RAY DIFFRACTION100
2.64-2.780.26251470.20433698X-RAY DIFFRACTION100
2.78-2.950.28491470.22053683X-RAY DIFFRACTION100
2.95-3.180.2451440.19663694X-RAY DIFFRACTION100
3.18-3.50.24611450.20043690X-RAY DIFFRACTION100
3.5-40.20711420.173708X-RAY DIFFRACTION100
4.01-5.040.18581480.16323698X-RAY DIFFRACTION100
5.04-35.380.22091270.17853628X-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)
15.31140.48730.67813.6530.12534.3535-0.02970.06530.11410.1968-0.0467-0.28660.13330.40120.00090.3420.0329-0.00430.3131-0.00670.2368-28.8374-25.46513.5356
22.2631-0.58050.61461.43920.05773.53830.14880.41480.425-0.2266-0.0851-0.1247-0.05660.0574-0.03360.22660.01670.07510.32070.06420.366-39.4-20.7828-4.511
32.26581.77-1.31942.9377-3.65685.34030.22990.0074-0.33890.0469-0.4828-0.2275-0.04910.32940.30160.51360.0074-0.07330.3474-0.03310.4127-41.3138-45.40691.3802
44.7578-0.89070.39094.9245-0.64754.1178-0.17540.12630.3690.00850.0649-0.0372-0.2323-0.30870.09240.29090.008-0.00260.34670.00930.2123-7.6214-37.7137-17.7694
52.1457-0.74590.22671.5966-0.60093.613-0.1188-0.38630.30430.27580.1796-0.3049-0.10050.0256-0.0470.2890.0422-0.02840.2636-0.09910.37111.6866-44.5080.2789
62.10821.54523.63013.77634.14197.9764-0.3642-0.60180.0822-0.1873-0.13780.6686-0.5203-0.82080.46940.39520.0006-0.00250.48810.07270.4219-21.107-54.9893-1.0538
71.1322.21750.67584.93530.98261.7158-0.31220.0716-0.3768-0.53250.1016-0.8774-0.34240.82620.14890.536-0.1673-0.02090.5630.09810.4572-14.0516-65.0274-14.1845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid -188 through -85 )
2X-RAY DIFFRACTION2chain 'E' and (resid -84 through 161 )
3X-RAY DIFFRACTION3chain 'E' and (resid 162 through 227 )
4X-RAY DIFFRACTION4chain 'A' and (resid -188 through -85 )
5X-RAY DIFFRACTION5chain 'A' and (resid -84 through 161 )
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 204 )
7X-RAY DIFFRACTION7chain 'A' and (resid 205 through 227 )

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