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- PDB-3d2s: Crystal structure of MBNL1 tandem zinc finger 3 and 4 domain in c... -

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Basic information

Entry
Database: PDB / ID: 3d2s
TitleCrystal structure of MBNL1 tandem zinc finger 3 and 4 domain in complex with CGCUGU RNA
Components
  • 5'-R(*CP*GP*CP*UP*GP*U)-3'
  • Muscleblind-like protein 1
KeywordsMETAL BINDING PROTEIN/RNA / tandem zinc finger domain / RNA / Metal-binding / Nucleus / RNA-binding / Zinc-finger / METAL BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


regulatory region RNA binding / embryonic limb morphogenesis / myoblast differentiation / regulation of RNA splicing / RNA splicing / mRNA processing / cytoplasmic stress granule / double-stranded RNA binding / nervous system development / in utero embryonic development ...regulatory region RNA binding / embryonic limb morphogenesis / myoblast differentiation / regulation of RNA splicing / RNA splicing / mRNA processing / cytoplasmic stress granule / double-stranded RNA binding / nervous system development / in utero embryonic development / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #210 / 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
RNA / Muscleblind-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Advisory / Refinement description / Version format compliance
Revision 1.2Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / struct_ref / struct_ref_seq / 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 / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-R(*CP*GP*CP*UP*GP*U)-3'
F: 5'-R(*CP*GP*CP*UP*GP*U)-3'
G: 5'-R(*CP*GP*CP*UP*GP*U)-3'
H: 5'-R(*CP*GP*CP*UP*GP*U)-3'
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)40,67316
Polymers40,1498
Non-polymers5238
Water7,242402
1
E: 5'-R(*CP*GP*CP*UP*GP*U)-3'

F: 5'-R(*CP*GP*CP*UP*GP*U)-3'

E: 5'-R(*CP*GP*CP*UP*GP*U)-3'
A: Muscleblind-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9046
Polymers13,7744
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_645-x+1,y-1/2,-z1
crystal symmetry operation1_554x,y,z-11
identity operation1_555x,y,z1
2
F: 5'-R(*CP*GP*CP*UP*GP*U)-3'
B: Muscleblind-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1684
Polymers10,0372
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 5'-R(*CP*GP*CP*UP*GP*U)-3'

H: 5'-R(*CP*GP*CP*UP*GP*U)-3'

G: 5'-R(*CP*GP*CP*UP*GP*U)-3'
C: Muscleblind-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9046
Polymers13,7744
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_545-x,y-1/2,-z1
crystal symmetry operation1_554x,y,z-11
identity operation1_555x,y,z1
4
H: 5'-R(*CP*GP*CP*UP*GP*U)-3'
D: Muscleblind-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1684
Polymers10,0372
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.421, 56.899, 58.222
Angle α, β, γ (deg.)90.00, 108.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain
5'-R(*CP*GP*CP*UP*GP*U)-3'


Mass: 1868.149 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesized RNA oligonucleotide / Source: (synth.) Synthetic construct (others)
#2: 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
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG 3350, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2Bis-TrisBis-tris methane11
3H2O11
4PEG 335012
5Bis-TrisBis-tris methane12
6H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 38651 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Rsym value: 0.074 / Net I/σ(I): 17.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 3846 / Rsym value: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MBNL1 ZnF3/4 structure

Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.62 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25984 1935 5 %RANDOM
Rwork0.22448 ---
obs0.2263 36684 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.101 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20.37 Å2
2---0.12 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 364 8 402 2952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212651
X-RAY DIFFRACTIONr_bond_other_d0.0010.021739
X-RAY DIFFRACTIONr_angle_refined_deg1.6312.1193625
X-RAY DIFFRACTIONr_angle_other_deg1.2933.0114155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1085266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67422.923130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93215384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.271530
X-RAY DIFFRACTIONr_chiral_restr0.0840.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022704
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02534
X-RAY DIFFRACTIONr_nbd_refined0.1950.2461
X-RAY DIFFRACTIONr_nbd_other0.2120.22085
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21253
X-RAY DIFFRACTIONr_nbtor_other0.0880.21349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2238
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1881.51397
X-RAY DIFFRACTIONr_mcbond_other0.2331.5536
X-RAY DIFFRACTIONr_mcangle_it1.84522172
X-RAY DIFFRACTIONr_scbond_it2.2731525
X-RAY DIFFRACTIONr_scangle_it3.4544.51453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 136 -
Rwork0.278 2642 -
obs--99.29 %
Refinement TLS params.Method: refined / Origin x: 13.995 Å / Origin y: 3.97 Å / Origin z: 13.604 Å
111213212223313233
T0.0442 Å20.0119 Å20.0021 Å2--0.104 Å20.0025 Å2---0.1119 Å2
L0.9481 °20.0271 °2-0.0555 °2-0.3509 °20.0411 °2--0.9276 °2
S-0.0124 Å °0.0499 Å °0.0141 Å °0.0267 Å °0.0019 Å °-0.021 Å °-0.0669 Å °0.0929 Å °0.0105 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A179 - 245
2X-RAY DIFFRACTION1B178 - 245
3X-RAY DIFFRACTION1C179 - 245
4X-RAY DIFFRACTION1D178 - 245
5X-RAY DIFFRACTION1E1 - 6
6X-RAY DIFFRACTION1F1 - 5
7X-RAY DIFFRACTION1G1 - 6
8X-RAY DIFFRACTION1H1 - 5

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