[English] 日本語
Yorodumi
- PDB-3ulj: Crystal structure of apo Lin28B cold shock domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ulj
TitleCrystal structure of apo Lin28B cold shock domain
ComponentsLin28b, DNA-binding protein
KeywordsDNA BINDING PROTEIN / beta barrel / cold shock domain fold / nucleic acid binding
Function / homology
Function and homology information


RNA-mediated gene silencing / nucleic acid binding / nucleolus / zinc ion binding
Similarity search - Function
Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / Zinc knuckle / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger CCHC-type profile. ...Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / Zinc knuckle / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger CCHC-type profile. / Zinc finger, CCHC-type / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Lin-28 homolog B
Similarity search - Component
Biological speciesXenopus tropicalis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsMayr, F. / Schuetz, A. / Doege, N. / Heinemann, U.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The Lin28 cold-shock domain remodels pre-let-7 microRNA.
Authors: Mayr, F. / Schutz, A. / Doge, N. / Heinemann, U.
History
DepositionNov 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lin28b, DNA-binding protein
B: Lin28b, DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,44911
Polymers19,8842
Non-polymers5649
Water4,900272
1
A: Lin28b, DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3898
Polymers9,9421
Non-polymers4467
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lin28b, DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0603
Polymers9,9421
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Lin28b, DNA-binding protein
B: Lin28b, DNA-binding protein
hetero molecules

A: Lin28b, DNA-binding protein
B: Lin28b, DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,89822
Polymers39,7694
Non-polymers1,12918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2650 Å2
ΔGint-11 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.620, 52.620, 137.336
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Lin28b, DNA-binding protein


Mass: 9942.231 Da / Num. of mol.: 2 / Fragment: unp residues 27-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus (Silurana) tropicalis (tropical clawed frog)
Gene: lin28b / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: B4F6I0
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.76 Å3/Da / Density % sol: 55.29 %
Crystal growMethod: evaporation / pH: 7
Details: 2.5 M sodium acetate, 0.1 M HEPES , pH 7.0, EVAPORATION

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98141 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98141 Å / Relative weight: 1
ReflectionResolution: 1.06→32.3 Å / Num. all: 100674 / Num. obs: 100170 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 17.8
Reflection shellResolution: 1.06→1.087 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.61 / % possible all: 98.3

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 312Z
Resolution: 1.06→32.3 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / Occupancy max: 1 / Occupancy min: 0.12 / SU B: 0.56 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1391 5027 5 %RANDOM
Rwork0.1196 ---
obs0.1206 100170 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 66.98 Å2 / Biso mean: 15.9469 Å2 / Biso min: 3.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.06→32.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 38 272 1688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221613
X-RAY DIFFRACTIONr_bond_other_d0.0010.021199
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9882193
X-RAY DIFFRACTIONr_angle_other_deg0.87832921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4535225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3622.39471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27215283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1211515
X-RAY DIFFRACTIONr_chiral_restr0.0920.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211857
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02356
X-RAY DIFFRACTIONr_mcbond_it2.9135992
X-RAY DIFFRACTIONr_mcbond_other0.9645399
X-RAY DIFFRACTIONr_mcangle_it4.25971599
X-RAY DIFFRACTIONr_scbond_it5.0649621
X-RAY DIFFRACTIONr_scangle_it6.78311570
X-RAY DIFFRACTIONr_rigid_bond_restr1.72232812
LS refinement shellResolution: 1.06→1.087 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 363 -
Rwork0.226 6894 -
all-7257 -
obs--100 %

+
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