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

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Basic information

Entry
Database: PDB / ID: 4atb
TitleCrystal structure of the NF90-NF45 dimerisation domain complex with CTP
Components
  • INTERLEUKIN ENHANCER-BINDING FACTOR 2
  • INTERLEUKIN ENHANCER-BINDING FACTOR 3
KeywordsIMMUNE SYSTEM / TEMPLATE-FREE NUCLEOTIDYL TRANSFERASE 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
CYTIDINE-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: 3.1 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: Atomic model / Database references / Other
Revision 1.2Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
C: INTERLEUKIN ENHANCER-BINDING FACTOR 2
D: INTERLEUKIN ENHANCER-BINDING FACTOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,7888
Polymers165,7734
Non-polymers1,0154
Water00
1
A: INTERLEUKIN ENHANCER-BINDING FACTOR 2
B: INTERLEUKIN ENHANCER-BINDING FACTOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3944
Polymers82,8872
Non-polymers5072
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-25.3 kcal/mol
Surface area28510 Å2
MethodPISA
2
C: INTERLEUKIN ENHANCER-BINDING FACTOR 2
D: INTERLEUKIN ENHANCER-BINDING FACTOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3944
Polymers82,8872
Non-polymers5072
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-26.2 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.158, 83.967, 159.679
Angle α, β, γ (deg.)90.00, 93.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.58491, -0.00013, 0.8111), (-1.0E-5, -1, -0.00016), (0.8111, 9.0E-5, -0.58491)
Vector: 25.59116, 1.51806, -51.02044)

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Components

#1: Protein INTERLEUKIN ENHANCER-BINDING FACTOR 2 / NUCLEAR FACTOR OF ACTIVATED T-CELLS 45 KDA / NF45


Mass: 40359.840 Da / Num. of mol.: 2 / 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 / NF90


Mass: 42526.727 Da / Num. of mol.: 2 / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
Sequence detailsTWO RESIDUES ADDED AT N-TERMINUS DERIVED FROM PRESCISSION CLEAVAGE SITE TWO RESIDUES AT N-TERMINUS ...TWO RESIDUES ADDED AT N-TERMINUS DERIVED FROM PRESCISSION CLEAVAGE SITE TWO RESIDUES AT N-TERMINUS ADDED FROM TEV CLEAVAGE SEQUENCE

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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: 2.8 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 6.5
Details: 12-14 % PEG3350, 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: I04-1 / Wavelength: 0.9173
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2011 / Details: TOROIDAL MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 3.1→66 Å / Num. obs: 33184 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 40.31 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6
Reflection shellResolution: 3.1→3.27 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.8 / % possible all: 98.7

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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: 3.1→66.427 Å / SU ML: 0.38 / σ(F): 1.36 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 1718 5.2 %
Rwork0.2142 --
obs0.2162 33174 96.49 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.336 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1-15.8279 Å20 Å216.4201 Å2
2---18.0185 Å20 Å2
3---2.1905 Å2
Refinement stepCycle: LAST / Resolution: 3.1→66.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9664 0 60 0 9724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129923
X-RAY DIFFRACTIONf_angle_d0.87313542
X-RAY DIFFRACTIONf_dihedral_angle_d14.973590
X-RAY DIFFRACTIONf_chiral_restr0.0581653
X-RAY DIFFRACTIONf_plane_restr0.0061722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.19130.32911480.31182633X-RAY DIFFRACTION98
3.1913-3.29430.37451430.29312632X-RAY DIFFRACTION99
3.2943-3.4120.30251540.26122686X-RAY DIFFRACTION99
3.412-3.54860.27331510.23392666X-RAY DIFFRACTION98
3.5486-3.71010.24891530.21092637X-RAY DIFFRACTION99
3.7101-3.90570.2621460.2082649X-RAY DIFFRACTION98
3.9057-4.15030.20581620.19092625X-RAY DIFFRACTION98
4.1503-4.47070.21711320.17662617X-RAY DIFFRACTION96
4.4707-4.92050.21651380.16982557X-RAY DIFFRACTION95
4.9205-5.63220.22491400.19652608X-RAY DIFFRACTION95
5.6322-7.09470.21751200.23392573X-RAY DIFFRACTION93
7.0947-66.44190.26281310.19242573X-RAY DIFFRACTION91

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