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- PDB-3p1x: Crystal structure of DRBM 2 domain of Interleukin enhancer-bindin... -

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Basic information

Entry
Database: PDB / ID: 3p1x
TitleCrystal structure of DRBM 2 domain of Interleukin enhancer-binding factor 3 from Homo sapiens, Northeast Structural Genomics Consortium Target HR4527E
ComponentsInterleukin enhancer-binding factor 3
KeywordsTranscription regulator / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


spliceosome-depend formation of circular RNA / Regulation of CDH11 gene transcription / mRNA 3'-UTR AU-rich region binding / negative regulation of viral genome replication / PKR-mediated signaling / double-stranded RNA binding / virus receptor activity / defense response to virus / negative regulation of translation / single-stranded RNA binding ...spliceosome-depend formation of circular RNA / Regulation of CDH11 gene transcription / mRNA 3'-UTR AU-rich region binding / negative regulation of viral genome replication / PKR-mediated signaling / double-stranded RNA binding / virus receptor activity / defense response to virus / negative regulation of translation / single-stranded RNA binding / ribonucleoprotein complex / protein phosphorylation / negative regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / DNA binding / RNA binding / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
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 / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif ...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 / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Interleukin enhancer-binding factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSeetharaman, J. / Neely, H. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Seetharaman, J. / Neely, H. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of DRBM 2 domain of Interleukin enhancer-binding factor 3 from Homo sapiens, Northeast Structural Genomics Consortium Target HR4527E
Authors: Seetharaman, J. / Neely, H. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin enhancer-binding factor 3
B: Interleukin enhancer-binding factor 3


Theoretical massNumber of molelcules
Total (without water)16,8192
Polymers16,8192
Non-polymers00
Water3,585199
1
A: Interleukin enhancer-binding factor 3


Theoretical massNumber of molelcules
Total (without water)8,4091
Polymers8,4091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Interleukin enhancer-binding factor 3


Theoretical massNumber of molelcules
Total (without water)8,4091
Polymers8,4091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.572, 24.384, 71.626
Angle α, β, γ (deg.)90.00, 124.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Interleukin enhancer-binding factor 3 / Nuclear factor of activated T-cells 90 kDa / NF-AT-90 / Double-stranded RNA-binding protein 76 / ...Nuclear factor of activated T-cells 90 kDa / NF-AT-90 / Double-stranded RNA-binding protein 76 / DRBP76 / Translational control protein 80 / TCP80 / Nuclear factor associated with dsRNA / NFAR / M-phase phosphoprotein 4 / MPP4


Mass: 8409.390 Da / Num. of mol.: 2 / Fragment: DRBM 2 domain residues 520-594 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12906
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 277 K / pH: 8
Details: 0.1M Sodium chloride, 0.1 M Tris, pH (8, 24% (w/v) PEG 20K, microbatch under oil method, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Sep 2, 2010
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 12584 / Num. obs: 12584 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.039 / Net I/σ(I): 33.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2 % / Rmerge(I) obs: 0.064 / % possible all: 92.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.39 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 241974.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1091 4.9 %RANDOM
Rwork0.213 ---
obs0.213 22466 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.0575 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1--6.23 Å20 Å2-0.45 Å2
2--11.33 Å20 Å2
3----5.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 0 199 1197
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 165 4.8 %
Rwork0.234 3299 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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