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- PDB-1xmk: The Crystal structure of the Zb domain from the RNA editing enzym... -

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Basic information

Entry
Database: PDB / ID: 1xmk
TitleThe Crystal structure of the Zb domain from the RNA editing enzyme ADAR1
ComponentsDouble-stranded RNA-specific adenosine deaminase
KeywordsHYDROLASE / winged Helix-Turn-Helix / RNA editing / Interferon / ADAR1
Function / homology
Function and homology information


somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / supraspliceosomal complex / adenosine to inosine editing / tRNA-specific adenosine deaminase activity / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation ...somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / supraspliceosomal complex / adenosine to inosine editing / tRNA-specific adenosine deaminase activity / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing / response to interferon-alpha / hematopoietic stem cell homeostasis / RISC complex assembly / pre-miRNA processing / negative regulation of hepatocyte apoptotic process / definitive hemopoiesis / negative regulation of type I interferon-mediated signaling pathway / hepatocyte apoptotic process / hematopoietic progenitor cell differentiation / positive regulation of viral genome replication / RNA processing / protein export from nucleus / erythrocyte differentiation / response to virus / PKR-mediated signaling / cellular response to virus / mRNA processing / osteoblast differentiation / protein import into nucleus / double-stranded RNA binding / Interferon alpha/beta signaling / defense response to virus / innate immune response / nucleolus / DNA binding / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
ADAR1, first double-stranded RNA binding domain / ADAR1, third double-stranded RNA binding domain / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain / Adenosine deaminase z-alpha domain / Z-binding domain profile. / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) ...ADAR1, first double-stranded RNA binding domain / ADAR1, third double-stranded RNA binding domain / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain / Adenosine deaminase z-alpha domain / Z-binding domain profile. / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / NICKEL (II) ION / Double-stranded RNA-specific adenosine deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 0.97 Å
AuthorsAthanasiadis, A. / Placido, D. / Maas, S. / Brown II, B.A. / Lowenhaupt, K. / Rich, A.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: The Crystal Structure of the Z[beta] Domain of the RNA-editing Enzyme ADAR1 Reveals Distinct Conserved Surfaces Among Z-domains.
Authors: Athanasiadis, A. / Placido, D. / Maas, S. / Brown II, B.A. / Lowenhaupt, K. / Rich, A.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2001
Title: Structure of the DLM-1-Z-DNA complex reveals a conserved family of Z-DNA-binding proteins
Authors: Schwartz, T. / Behlke, J. / Lowenhaupt, K. / Heinemann, U. / Rich, A.
#2: Journal: Science / Year: 1999
Title: Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA
Authors: Schwartz, T. / Rould, M.A. / Lowenhaupt, K. / Herbert, A. / Rich, A.
History
DepositionOct 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Double-stranded RNA-specific adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3606
Polymers9,0051
Non-polymers3545
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.557, 43.526, 45.471
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 Double-stranded RNA-specific adenosine deaminase / DRADA / 136 kDa double-stranded RNA binding protein / P136 / K88DSRBP / Interferon-inducible ...DRADA / 136 kDa double-stranded RNA binding protein / P136 / K88DSRBP / Interferon-inducible protein 4 / IFI-4 protein / ADAR1


Mass: 9005.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAR, ADAR1, DSRAD, IFI4 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P55265, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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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: 1.7 Å3/Da / Density % sol: 27.5 %
Crystal growTemperature: 312 K / pH: 9
Details: PEG1000, Cadmium Chloride, Nickel Chloride, Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 312K, pH 9.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 22, 2002
RadiationMonochromator: MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.97→27.92 Å / Num. obs: 41638 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 6.5 Å2 / Rsym value: 0.075 / Net I/σ(I): 5.2
Reflection shellResolution: 0.97→1.02 Å / % possible all: 94.7

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
SHELXLrefinement
RefinementMethod to determine structure: MIR / Resolution: 0.97→10 Å
Cross valid method: THROUGHOUT WITH THE EXCEPTION OF THE LAST TWO REFINEMENT CYCLES
σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: CNS WAS USED IN EARLY REFINEMENT stages
RfactorNum. reflection% reflectionSelection details
Rfree0.183 4051 10 %RANDOM
all0.145 42408 --
obs0.145 40681 95.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.mol.biol.91(1973)201-228
Refine analyzeNum. disordered residues: 4
Refinement stepCycle: LAST / Resolution: 0.97→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms663 0 5 125 793
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0.062
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.111
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps0.104

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