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- PDB-1un6: THE CRYSTAL STRUCTURE OF A ZINC FINGER - RNA COMPLEX REVEALS TWO ... -

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Basic information

Entry
Database: PDB / ID: 1un6
TitleTHE CRYSTAL STRUCTURE OF A ZINC FINGER - RNA COMPLEX REVEALS TWO MODES OF MOLECULAR RECOGNITION
Components
  • 5S RIBOSOMAL RNA
  • TRANSCRIPTION FACTOR IIIA
KeywordsRNA-BINDING PROTEIN/RNA / COMPLEX(ZINC FINGER-RNA) / TFIIIA / 5S RIBOSOMAL RNA / ZINC FINGER / RNA-PROTEIN COMPLEX / X. LAEVIS / TRANSCRIPTION REGULATION / RNA-BINDING / DNA-BINDING / NUCLEAR PROTEIN / RNA-BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


ribosomal large subunit biogenesis / DNA binding / RNA binding / nucleus / metal ion binding
Similarity search - Function
Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Transcription factor IIIA
Similarity search - Component
Biological speciesXENOPUS LAEVIS (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsLu, D. / Searles, M.A. / Klug, A.
Citation
Journal: Nature / Year: 2003
Title: Crystal Structure of a Zinc-Finger-RNA Complex Reveals Two Modes of Molecular Recognition
Authors: Lu, D. / Searles, M.A. / Klug, A.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: The Role of the Central Zinc Fingers of Transcription Factor Iiia in Binding to 5S RNA
Authors: Searles, M.A. / Lu, D. / Klug, A.
History
DepositionSep 4, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: TRANSCRIPTION FACTOR IIIA
C: TRANSCRIPTION FACTOR IIIA
D: TRANSCRIPTION FACTOR IIIA
E: 5S RIBOSOMAL RNA
F: 5S RIBOSOMAL RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,15626
Polymers70,3175
Non-polymers83921
Water28816
1
C: TRANSCRIPTION FACTOR IIIA
E: 5S RIBOSOMAL RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3029
Polymers30,0092
Non-polymers2937
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TRANSCRIPTION FACTOR IIIA
D: TRANSCRIPTION FACTOR IIIA
F: 5S RIBOSOMAL RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,85417
Polymers40,3083
Non-polymers54614
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.598, 191.593, 79.770
Angle α, β, γ (deg.)90.00, 101.51, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE ENTRY CONTAINS TWO COPIES OF THE RNA- PROTEIN COMPLEXAND AN EXTRA PROTEIN WITH CHAIN IDENTIFIER D. THE TWOCOPIES OF RNA ARE IN CHAIN IDENTIFIERS E AND F, AND THE TWOCOPIES OF THE PROTEIN IN THE COMPLEXES ARE IN THE CHAINIDENTIFIERS B AND C.THE DIMER DESCRIBED IN REMARK 350 DOES NOT REFLECTA BIOLOGICALLY FUNCTIONAL DIMER.

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Components

#1: Protein TRANSCRIPTION FACTOR IIIA / TFIIIA / FACTOR A / S-TFIIIA/O-TFIIIA


Mass: 10299.835 Da / Num. of mol.: 3
Fragment: FINGERS 4,5 AND 6, RESIDUES 127 - 212 UNDER SWISSPROT NUMBERING FOR SOMATIC TFIIIA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Cell: OOCYTE / Organ: OVARY / Plasmid: PET13A3F / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03001
#2: RNA chain 5S RIBOSOMAL RNA


Mass: 19708.777 Da / Num. of mol.: 2
Fragment: CENTRAL REGION, NUCLEOTIDES 4 - 15,64 -82,94-115, PLUS TWO TETRALOOPS JOINING 15 - 64 AND 82 -94 RESPECTIVELY
Source method: isolated from a natural source / Details: IN VITRO TRANSCRIPTION TO PRODUCE THE RNA / Source: (natural) XENOPUS LAEVIS (African clawed frog) / Cell: OOCYTE / Organ: OVARY
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTS BOTH AS A POSITIVE TRANSCRIPTION FACTOR FOR 5S RNA GENES AND A SPECIFIC RNA BINDING PROTEIN ...ACTS BOTH AS A POSITIVE TRANSCRIPTION FACTOR FOR 5S RNA GENES AND A SPECIFIC RNA BINDING PROTEIN THAT COMPLEXES WITH 5S RNA IN OOCYTES TO FORM THE 7S RIBONUCLEOPROTEIN STORAGE PARTICLE. COULD PLAY AN ESSENTIAL ROLE IN THE DEVELOPMENTAL CHANGE IN 5S RNA GENE EXPRESSION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.6
Details: 20% PEG 8000, 200MM KCL, 5MM MGCL2, 50MM MES, PH 5.6, 3MM DTT, 0.3MM ZNSO4
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 %PEG80001reservoir
2200 mM1reservoirKCl
35 mM1reservoirMgCl2
450 mMMES1reservoirpH5.6
53 mMdithiothreitol1reservoir
60.3 mM1reservoirZnSO4
75 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)Wavelength
SYNCHROTRONESRF BM30A11.28200, 1.28347, 1.0426
SYNCHROTRONSRS PX14.220.979
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDOct 15, 2002MIRRORS
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111)MADMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.2821
21.283471
31.04261
40.9791
ReflectionResolution: 3.1→35.2 Å / Num. obs: 15267 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 7.9
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2 / % possible all: 97.5
Reflection
*PLUS
Highest resolution: 3.1 Å / Rmerge(I) obs: 0.051

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Processing

Software
NameVersionClassification
CNSmodel building
SCALAdata scaling
CCP4phasing
SHELXphasing
SHARPphasing
CNSphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 3.1→35.19 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2782617.75 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFMAC5 WAS USED TO REACH R=0.2 AND RFREE=0.3, THEN THE MODEL WAS REFINED IN CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 754 4.9 %RANDOM
Rwork0.216 ---
obs0.216 15266 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.8942 Å2 / ksol: 0.272189 e/Å3
Displacement parametersBiso mean: 92 Å2
Baniso -1Baniso -2Baniso -3
1-5.94 Å20 Å24.94 Å2
2--0.1 Å20 Å2
3----6.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3.1→35.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 2608 21 16 4554
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.38
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.591.5
X-RAY DIFFRACTIONc_mcangle_it2.882
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 139 5.5 %
Rwork0.322 2385 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 3.1 Å / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.38

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