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- PDB-3d2q: Crystal structure of MBNL1 tandem zinc finger 3 and 4 domain -

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Basic information

Entry
Database: PDB / ID: 3d2q
TitleCrystal structure of MBNL1 tandem zinc finger 3 and 4 domain
ComponentsMuscleblind-like protein 1
KeywordsMETAL BINDING / RNA BINDING PROTEIN / tandem zinc finger domain / Alternative splicing / Metal-binding / Nucleus / RNA-binding / Zinc / Zinc-finger
Function / homology
Function and homology information


regulatory region RNA binding / myoblast differentiation / embryonic limb morphogenesis / regulation of RNA splicing / RNA splicing / cytoplasmic stress granule / mRNA processing / double-stranded RNA binding / nervous system development / in utero embryonic development ...regulatory region RNA binding / myoblast differentiation / embryonic limb morphogenesis / regulation of RNA splicing / RNA splicing / cytoplasmic stress granule / mRNA processing / double-stranded RNA binding / nervous system development / in utero embryonic development / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #210 / : / ZAP-like CCCH zinc finger / RNA-binding, Nab2-type zinc finger / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Muscleblind-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsTeplova, M. / Patel, D.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1.
Authors: Teplova, M. / Patel, D.J.
History
DepositionMay 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Muscleblind-like protein 1
B: Muscleblind-like protein 1
C: Muscleblind-like protein 1
D: Muscleblind-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,20012
Polymers32,6774
Non-polymers5238
Water5,441302
1
A: Muscleblind-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3003
Polymers8,1691
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Muscleblind-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3003
Polymers8,1691
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Muscleblind-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3003
Polymers8,1691
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Muscleblind-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3003
Polymers8,1691
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.166, 80.459, 55.357
Angle α, β, γ (deg.)90.00, 101.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Muscleblind-like protein 1 / Triplet-expansion RNA-binding protein


Mass: 8169.182 Da / Num. of mol.: 4
Fragment: tandem zinc finger 3 and 4 domains (UNP residues 178-246)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBNL1, EXP, KIAA0428, MBNL / Plasmid: Pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9NR56
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 1.95 Å3/Da / Density % sol: 36.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.8
Details: 18% PEG 3350, 0.1M Mg acetate, 0.2 M sodium fluoride, pH 6.8, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2827 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 38947 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rsym value: 0.089
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 3.4 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.381 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21748 1979 5.1 %RANDOM
Rwork0.19716 ---
obs0.19822 36934 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.674 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å2-0.02 Å2
2---0.17 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 8 302 2476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212205
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9322962
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86922.868129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35615384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5111530
X-RAY DIFFRACTIONr_chiral_restr0.0810.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021742
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2960
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21474
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2221
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9061.51389
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45722152
X-RAY DIFFRACTIONr_scbond_it2.2313915
X-RAY DIFFRACTIONr_scangle_it3.2994.5810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 131 -
Rwork0.266 2615 -
obs--93.27 %

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