[English] 日本語
Yorodumi
- PDB-3d2s: Crystal structure of MBNL1 tandem zinc finger 3 and 4 domain in c... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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-Tris11
3H2O11
4PEG 335012
5Bis-Tris12
6H2O12

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more