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- PDB-4at9: Crystal structure of the NF90-NF45 dimerisation domain complex wi... -

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Basic information

Entry
Database: PDB / ID: 4at9
TitleCrystal structure of the NF90-NF45 dimerisation domain complex with UTP
Components
  • INTERLEUKIN ENHANCER-BINDING FACTOR 2
  • INTERLEUKIN ENHANCER-BINDING FACTOR 3
KeywordsIMMUNE SYSTEM / DRPB76 / NFAR / ILF3 / ILF2 / TEMPLATE-FREE NUCLEOTIDYLTRANSFERASE FOLD
Function / homology
Function and homology information


Regulation of CDH11 gene transcription / spliceosome-depend formation of circular RNA / PKR-mediated signaling / mRNA 3'-UTR AU-rich region binding / negative regulation of viral genome replication / Neutrophil degranulation / double-stranded RNA binding / virus receptor activity / defense response to virus / protein phosphorylation ...Regulation of CDH11 gene transcription / spliceosome-depend formation of circular RNA / PKR-mediated signaling / mRNA 3'-UTR AU-rich region binding / negative regulation of viral genome replication / Neutrophil degranulation / double-stranded RNA binding / virus receptor activity / defense response to virus / protein phosphorylation / negative regulation of translation / ribonucleoprotein complex / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleolus / mitochondrion / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Interleukin enhancer-binding factor 3 / DZF domain / : / : / DZF N-terminal domain / DZF C-terminal domain / DZF domain profile. / domain in DSRM or ZnF_C2H2 domain containing proteins / Poly(a)-polymerase, middle domain - #40 ...: / Interleukin enhancer-binding factor 3 / DZF domain / : / : / DZF N-terminal domain / DZF C-terminal domain / DZF domain profile. / domain in DSRM or ZnF_C2H2 domain containing proteins / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / Interleukin enhancer-binding factor 2 / Interleukin enhancer-binding factor 3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsWolkowicz, U.M. / Cook, A.G.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: NF45 Dimerizes with NF90, Zfr and Spnr Via a Conserved Domain that Has a Nucleotidyltransferase Fold.
Authors: Wolkowicz, U.M. / Cook, A.G.
History
DepositionMay 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Jun 20, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN ENHANCER-BINDING FACTOR 2
B: INTERLEUKIN ENHANCER-BINDING FACTOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3954
Polymers82,8872
Non-polymers5082
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-28.6 kcal/mol
Surface area27360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.849, 133.516, 177.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein INTERLEUKIN ENHANCER-BINDING FACTOR 2 / NUCLEAR FACTOR OF ACTIVATED T-CELLS 45 KDA


Mass: 40359.840 Da / Num. of mol.: 1 / Fragment: DZF DOMAIN, RESIDUES 29-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX-6-P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9CXY6
#2: Protein INTERLEUKIN ENHANCER-BINDING FACTOR 3


Mass: 42526.727 Da / Num. of mol.: 1 / Fragment: DZF DOMAIN, RESIDUES 1-381
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETMCN-HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Z1X4
#3: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Sequence detailsTWO RESIDUES ADDED AT N-TERMINUS DERIVED FROM PRESCISSION CLEAVAGE OF THE EXPRESSION TAG TWO ...TWO RESIDUES ADDED AT N-TERMINUS DERIVED FROM PRESCISSION CLEAVAGE OF THE EXPRESSION TAG TWO RESIDUES AT N-TERMINUS DERIVED FROM TEV CLEAVAGE OF THE EXPRESSION TAG

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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: 2.99 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 6.5
Details: 12-14% PEG 3350, 200 MM MGCL2, 100 MM MES PH 6.5 AND 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 30, 2011 / Details: TOROIDAL MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→67 Å / Num. obs: 23950 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.1
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.4 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AT7

4at7


Resolution: 2.803→55.504 Å / SU ML: 0.39 / σ(F): 1.37 / Phase error: 27.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 1237 5.2 %
Rwork0.2357 --
obs0.2372 23928 95.92 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.339 Å2 / ksol: 0.323 e/Å3
Refinement stepCycle: LAST / Resolution: 2.803→55.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4740 0 30 0 4770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014853
X-RAY DIFFRACTIONf_angle_d0.9996626
X-RAY DIFFRACTIONf_dihedral_angle_d15.0261722
X-RAY DIFFRACTIONf_chiral_restr0.058804
X-RAY DIFFRACTIONf_plane_restr0.006850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8031-2.91540.3461240.32952434X-RAY DIFFRACTION94
2.9154-3.0480.36841260.31672555X-RAY DIFFRACTION98
3.048-3.20870.3121340.2742524X-RAY DIFFRACTION97
3.2087-3.40970.27741520.25772508X-RAY DIFFRACTION97
3.4097-3.67290.25331390.23442516X-RAY DIFFRACTION97
3.6729-4.04250.26941410.21572527X-RAY DIFFRACTION96
4.0425-4.62720.21191520.19322512X-RAY DIFFRACTION96
4.6272-5.82870.23791350.21222527X-RAY DIFFRACTION95
5.8287-55.51490.24671340.22372588X-RAY DIFFRACTION93

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