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- PDB-4alp: The Lin28b Cold shock domain in complex with hexauridine -

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Basic information

Entry
Database: PDB / ID: 4alp
TitleThe Lin28b Cold shock domain in complex with hexauridine
Components
  • HEXA URIDINE
  • LIN28 ISOFORM B
KeywordsCHAPERONE/RNA / CHAPERONE-RNA COMPLEX / TRANSCRIPTION / LIN-28 / RNA / LET-7 / MIRNA
Function / homology
Function and homology information


pre-miRNA processing / mRNA binding / nucleolus / zinc ion binding / cytoplasm
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 finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type ...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 finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA / Lin-28 homolog B
Similarity search - Component
Biological speciesXENOPUS TROPICALIS (tropical clawed frog)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.48 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
DepositionMar 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Derived calculations
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIN28 ISOFORM B
B: LIN28 ISOFORM B
C: LIN28 ISOFORM B
D: LIN28 ISOFORM B
E: HEXA URIDINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7457
Polymers41,5615
Non-polymers1842
Water11,818656
1
B: LIN28 ISOFORM B
C: LIN28 ISOFORM B
hetero molecules

B: LIN28 ISOFORM B
C: LIN28 ISOFORM B
hetero molecules

A: LIN28 ISOFORM B
D: LIN28 ISOFORM B
E: HEXA URIDINE
hetero molecules

A: LIN28 ISOFORM B
D: LIN28 ISOFORM B
E: HEXA URIDINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,49014
Polymers83,12210
Non-polymers3684
Water18010
TypeNameSymmetry operationNumber
crystal symmetry operation4_444x-1/2,-y-1/2,-z-11
crystal symmetry operation3_554-x+1/2,y+1/2,-z-11
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area11430 Å2
ΔGint-69.3 kcal/mol
Surface area35590 Å2
MethodPISA
2
B: LIN28 ISOFORM B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0342
Polymers9,9421
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LIN28 ISOFORM B


Theoretical massNumber of molelcules
Total (without water)9,9421
Polymers9,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.982, 61.166, 63.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-2010-

HOH

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Components

#1: Protein
LIN28 ISOFORM B


Mass: 9942.231 Da / Num. of mol.: 4 / Fragment: COLD SHOCK DOMAIN, RESIDUES 27-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS TROPICALIS (tropical clawed frog)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B4F6I0
#2: RNA chain HEXA URIDINE


Mass: 1792.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.91 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: BL14-1 / Type: BESSY / Wavelength: 0.91841
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.48→32.4 Å / Num. obs: 60327 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 1

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.48→32.42 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.123 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18768 3023 5 %RANDOM
Rwork0.1693 ---
obs0.17023 57423 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.918 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.48→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2676 115 12 656 3459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193006
X-RAY DIFFRACTIONr_bond_other_d0.0010.022196
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9414069
X-RAY DIFFRACTIONr_angle_other_deg0.88235318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9445374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99822.687134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71215512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4251525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213309
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02674
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.519 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 205 -
Rwork0.202 3863 -
obs--93.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7520.04310.3390.3736-0.36620.58990.01710.04180.01820.0118-0.00040.02130.03320.045-0.01670.03860.0229-0.00190.0208-0.00760.009911.8561-16.9259-21.3675
21.3928-0.1243-0.05240.25450.27240.30590.0058-0.0375-0.0407-0.0028-0.02260.0098-0.0177-0.03240.01680.03360.0017-0.00730.0197-0.00060.013336.2539-12.9261-14.1948
30.4427-0.18570.10341.1878-0.08410.3081-0.007-0.0226-0.0159-0.08970.06180.0316-0.0274-0.0141-0.05480.0341-0.0064-0.00770.00480.00790.033337.0299-16.2834-46.3952
41.544-0.21240.00960.34540.31660.37620.03120.19610.02010.00850.008-0.0234-0.03420.0529-0.03920.0423-0.00480.01290.0414-0.00950.010111.3687-14.0986-51.7769
50.0429-0.08030.06360.1564-0.12030.0953-0.01680.00190.03370.0271-0.0273-0.0651-0.00970.00690.0440.0817-0.0141-0.00070.05030.00910.04876.08871.0597-34.7094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 113
2X-RAY DIFFRACTION2B29 - 114
3X-RAY DIFFRACTION3C29 - 114
4X-RAY DIFFRACTION4D30 - 113
5X-RAY DIFFRACTION5E1 - 6

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