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- PDB-4a4i: Crystal structure of the human Lin28b cold shock domain -

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Basic information

Entry
Database: PDB / ID: 4a4i
TitleCrystal structure of the human Lin28b cold shock domain
ComponentsPROTEIN LIN-28 HOMOLOG B
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of pre-miRNA processing / positive regulation of miRNA catabolic process / negative regulation of primary miRNA processing / RNA destabilization / miRNA catabolic process / RNA 3'-end processing / pre-miRNA processing / sequence-specific double-stranded DNA binding / mRNA binding / nucleolus ...negative regulation of pre-miRNA processing / positive regulation of miRNA catabolic process / negative regulation of primary miRNA processing / RNA destabilization / miRNA catabolic process / RNA 3'-end processing / pre-miRNA processing / sequence-specific double-stranded DNA binding / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Lin-28A-like, second zinc knuckle / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / zinc finger ...: / : / Lin-28A-like, second zinc knuckle / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / 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
Protein lin-28 homolog B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionOct 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2May 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN LIN-28 HOMOLOG B
B: PROTEIN LIN-28 HOMOLOG B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9494
Polymers19,7612
Non-polymers1882
Water3,747208
1
A: PROTEIN LIN-28 HOMOLOG B


Theoretical massNumber of molelcules
Total (without water)9,8801
Polymers9,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN LIN-28 HOMOLOG B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0683
Polymers9,8801
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.181, 62.477, 77.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN LIN-28 HOMOLOG B / LIN28B / LIN-28B


Mass: 9880.287 Da / Num. of mol.: 2 / Fragment: COLD SHOCK DOMAIN, RESIDUES 24-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQLINKH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PHAGE-RESISTANT / References: UniProt: Q6ZN17
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.88 Å3/Da / Density % sol: 57.3 % / Description: NONE
Crystal growpH: 6.5 / Details: 2 M AMMONIUM SULFATE, 0.2 M NACL, 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.95→48.59 Å / Num. obs: 16277 / % possible obs: 96.6 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.5
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.1 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48.59 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.037 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23464 828 5.1 %RANDOM
Rwork0.18096 ---
obs0.18367 15419 96.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.592 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å20 Å20 Å2
2---1.51 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 11 208 1527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191375
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9721845
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7275175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77521.9357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35415246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0431512
X-RAY DIFFRACTIONr_chiral_restr0.1430.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211036
X-RAY DIFFRACTIONr_gen_planes_other
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: 1.953→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 50 -
Rwork0.226 1005 -
obs--93.86 %
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)
10.5106-0.40880.24180.5761-0.10031.32240.0782-0.01760.0262-0.055-0.05130.030.078-0.0073-0.02690.0629-0.0055-0.01580.0181-0.01480.022533.612232.20876.2335
20.44430.05790.38961.14490.20030.39950.04440.0013-0.01680.0256-0.0335-0.05360.008-0.0284-0.01090.06240.00720.00910.0229-0.01230.016645.269353.221417.0022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 110
2X-RAY DIFFRACTION2B27 - 111

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