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- PDB-8ytf: Crystal structures of human IRF2BP2 RING domain in complex with V... -

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Basic information

Entry
Database: PDB / ID: 8ytf
TitleCrystal structures of human IRF2BP2 RING domain in complex with VGLL4 peptide
Components
  • Interferon regulatory factor 2-binding protein 2
  • Transcription cofactor vestigial-like protein 4
KeywordsTRANSCRIPTION / IRF2BP2 / RING domain / VGLL4
Function / homology
Function and homology information


negative regulation of cardiac muscle cell proliferation / immature B cell differentiation / negative regulation of Wnt signaling pathway / negative regulation of hippo signaling / transcription coactivator binding / negative regulation of cell growth / positive regulation of protein catabolic process / transcription corepressor activity / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...negative regulation of cardiac muscle cell proliferation / immature B cell differentiation / negative regulation of Wnt signaling pathway / negative regulation of hippo signaling / transcription coactivator binding / negative regulation of cell growth / positive regulation of protein catabolic process / transcription corepressor activity / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription cofactor vestigial-like protein 4 / Transcription cofactor vestigial-like protein 4 / TDU repeat / 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 / Short repeats in human TONDU, fly vestigial and other proteins.
Similarity search - Domain/homology
Transcription cofactor vestigial-like protein 4 / Interferon regulatory factor 2-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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: Transcription cofactor vestigial-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9105
Polymers9,7142
Non-polymers1963
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-32 kcal/mol
Surface area5450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.372, 43.209, 55.761
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 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 Transcription cofactor vestigial-like protein 4 / Vgl-4


Mass: 847.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14135
#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.: 128 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% 2-proponal, 0.1 M MES (pH 6.0) and 20% (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: 0.9752 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9752 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 11169 / % possible obs: 98.9 % / Redundancy: 12.6 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.024 / Rrim(I) all: 0.088 / Χ2: 0.695 / Net I/σ(I): 5.2 / Num. measured all: 141058
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.59-1.6212.30.3274830.9750.9940.0940.3410.56792.9
1.62-1.6512.80.2825260.9810.9950.0790.2930.54795.1
1.65-1.6812.70.2745390.9840.9960.0780.2850.53696.8
1.68-1.7112.80.2425330.9880.9970.0690.2520.56398.3
1.71-1.7513.20.2085580.9920.9980.0590.2160.59498.2
1.75-1.7912.90.1895450.9910.9980.0530.1960.62599.8
1.79-1.84130.185480.9920.9980.0510.1870.61499.6
1.84-1.8912.70.1575560.9940.9980.0450.1640.63899.6
1.89-1.94120.1385650.9940.9980.0410.1440.66499.8
1.94-211.50.1355520.9950.9990.0410.1410.68999.8
2-2.0713.30.1255640.9960.9990.0350.130.725100
2.07-2.1613.40.125590.9960.9990.0330.1240.732100
2.16-2.2613.30.15550.9970.9990.0280.1040.73499.8
2.26-2.3813.10.0945700.9970.9990.0270.0980.75699.8
2.38-2.5212.80.0795620.9980.9990.0220.0820.758100
2.52-2.7212.10.0745750.9980.9990.0220.0770.756100
2.72-2.9911.90.0715650.9970.9990.0210.0740.82199.1
2.99-3.4313.20.065820.99910.0170.0620.821100
3.43-4.3212.60.0545950.99810.0160.0570.879100
4.32-5011.30.0516370.99910.0150.0530.8398.8

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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: 1.59→23.43 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 15.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1727 519 4.7 %
Rwork0.1527 --
obs0.1536 11054 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→23.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms646 0 3 128 777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007662
X-RAY DIFFRACTIONf_angle_d1.064900
X-RAY DIFFRACTIONf_dihedral_angle_d6.29189
X-RAY DIFFRACTIONf_chiral_restr0.057102
X-RAY DIFFRACTIONf_plane_restr0.011117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.750.17951370.13982448X-RAY DIFFRACTION95
1.75-2.010.1631270.13322620X-RAY DIFFRACTION99
2.01-2.530.17671350.15072661X-RAY DIFFRACTION100
2.53-23.430.17181200.1642806X-RAY DIFFRACTION99

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