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- PDB-8yth: Crystal structures of human IRF2BP2 RING domain in complex with Z... -

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Basic information

Entry
Database: PDB / ID: 8yth
TitleCrystal structures of human IRF2BP2 RING domain in complex with ZBTB16 peptide
Components
  • Interferon regulatory factor 2-binding protein 2
  • Zinc finger and BTB domain-containing protein 16
KeywordsTRANSCRIPTION / IRF2BP2 / RING domain / ZBTB16
Function / homology
Function and homology information


male germ-line stem cell asymmetric division / type 2 angiotensin receptor binding / forelimb morphogenesis / positive regulation of cartilage development / positive regulation of chondrocyte differentiation / mesonephros development / negative regulation of myeloid cell differentiation / positive regulation of NK T cell differentiation / immature B cell differentiation / embryonic pattern specification ...male germ-line stem cell asymmetric division / type 2 angiotensin receptor binding / forelimb morphogenesis / positive regulation of cartilage development / positive regulation of chondrocyte differentiation / mesonephros development / negative regulation of myeloid cell differentiation / positive regulation of NK T cell differentiation / immature B cell differentiation / embryonic pattern specification / myeloid cell differentiation / positive regulation of ossification / embryonic hindlimb morphogenesis / anterior/posterior pattern specification / cartilage development / ossification involved in bone maturation / embryonic digit morphogenesis / hemopoiesis / protein localization to nucleus / positive regulation of fat cell differentiation / transcription repressor complex / male germ cell nucleus / central nervous system development / transcription corepressor binding / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / DNA-binding transcription activator activity, RNA polymerase II-specific / cell population proliferation / nuclear speck / protein ubiquitination / nuclear body / positive regulation of apoptotic process / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / apoptotic process / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Interferon regulatory factor 2-binding protein 1 & 2, zinc finger / Interferon regulatory factor 2-binding protein 1/2, C3HC4-type RING finger superfamily / Interferon regulatory factor 2-binding protein zinc finger / C2H2-type zinc finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger ...Interferon regulatory factor 2-binding protein 1 & 2, zinc finger / Interferon regulatory factor 2-binding protein 1/2, C3HC4-type RING finger superfamily / Interferon regulatory factor 2-binding protein zinc finger / C2H2-type zinc finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger and BTB domain-containing protein 16 / Interferon regulatory factor 2-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, G.C. / Ding, J.P.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030305 China
CitationJournal: Nat Commun / Year: 2024
Title: IRF2BP2 binds to a conserved RxSVI motif of protein partners and regulates megakaryocytic differentiation.
Authors: Wang, G. / Lu, T. / Zhang, L. / Ding, J.
History
DepositionMar 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon regulatory factor 2-binding protein 2
B: Zinc finger and BTB domain-containing protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8845
Polymers9,6882
Non-polymers1963
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-32 kcal/mol
Surface area4520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.315, 47.315, 57.489
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Interferon regulatory factor 2-binding protein 2 / IRF-2-binding protein 2 / IRF-2BP2


Mass: 8867.110 Da / Num. of mol.: 1 / Fragment: RING domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF2BP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z5L9
#2: Protein/peptide Zinc finger and BTB domain-containing protein 16 / Promyelocytic leukemia zinc finger protein / Zinc finger protein 145 / Zinc finger protein PLZF


Mass: 820.913 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q05516
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.92 Å3/Da / Density % sol: 35.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M potassium thiocyanate and 30% (w/v) PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 2903 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.912 / CC star: 0.977 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.038 / Rrim(I) all: 0.165 / Χ2: 1.851 / Net I/σ(I): 5.1 / Num. measured all: 58179
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.4420.60.4551230.970.9920.1030.4660.929100
2.44-2.4920.60.4181620.9750.9940.0940.4290.934100
2.49-2.5320.70.3611290.9780.9950.0820.371.012100
2.53-2.5920.10.3531480.9810.9950.0810.3620.958100
2.59-2.6419.40.3221570.9750.9940.0750.3311.045100
2.64-2.720.30.2921350.9820.9950.0670.31.15100
2.7-2.7720.30.261520.9840.9960.060.2671.187100
2.77-2.8519.80.2361400.9790.9950.0540.2431.364100
2.85-2.9320.60.2131450.9910.9980.0490.2191.44100
2.93-3.0221.30.2011400.9840.9960.0450.2061.533100
3.02-3.1320.90.1961520.9910.9980.0440.2011.469100
3.13-3.2620.50.1671340.9930.9980.0380.1711.75100
3.26-3.4119.30.1631490.9950.9990.0370.1671.98100
3.41-3.5820.70.1461420.9960.9990.0330.152.243100
3.58-3.8119.90.1511500.9950.9990.0340.1542.242100
3.81-4.120.70.1451420.9960.9990.0330.1492.619100
4.1-4.5220.50.1381430.9960.9990.0320.1422.744100
4.52-5.1719.20.1451540.9950.9990.0350.1493.019100
5.17-6.5119.40.1571440.9790.9950.0370.1613.419100
6.51-5016.80.1591620.9960.9990.0420.1654.22399.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→33.37 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2807 112 3.89 %
Rwork0.243 --
obs0.2447 2879 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms557 0 3 1 561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004569
X-RAY DIFFRACTIONf_angle_d0.752771
X-RAY DIFFRACTIONf_dihedral_angle_d17.175198
X-RAY DIFFRACTIONf_chiral_restr0.04991
X-RAY DIFFRACTIONf_plane_restr0.00897
LS refinement shellResolution: 2.4→33.37 Å
RfactorNum. reflection% reflection
Rfree0.2807 112 -
Rwork0.243 2767 -
obs--100 %

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