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- PDB-2qfj: Crystal Structure of First Two RRM Domains of FIR Bound to ssDNA ... -

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Basic information

Entry
Database: PDB / ID: 2qfj
TitleCrystal Structure of First Two RRM Domains of FIR Bound to ssDNA from a Portion of FUSE
Components
  • DNA (5'-D(*DTP*DCP*DGP*DGP*DGP*DAP*DTP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DTP*DTP*DGP*DTP*DGP*DTP*DTP*DAP*DTP*DT)-3')
  • FBP-interacting repressor
KeywordsTranscription repressor/DNA / protein-DNA complex / RRM domains / Transcription repressor-DNA COMPLEX
Function / homology
Function and homology information


alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding ...alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding / RNA binding / nucleoplasm / identical protein binding
Similarity search - Function
Poly-U binding splicing factor, PUF60-like / PUF60, RNA recognition motif 1 / PUF60, RNA recognition motif 2 / PUF60, RNA recognition motif 3 / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...Poly-U binding splicing factor, PUF60-like / PUF60, RNA recognition motif 1 / PUF60, RNA recognition motif 2 / PUF60, RNA recognition motif 3 / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Poly(U)-binding-splicing factor PUF60 / Poly(U)-binding-splicing factor PUF60
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsCrichlow, G.V. / Yang, Y. / Fan, C. / Lolis, E. / Braddock, D.
CitationJournal: EMBO J. / Year: 2007
Title: Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition
Authors: Crichlow, G.V. / Zhou, H. / Hsiao, H.-H. / Frederick, K.B. / Debrosse, M. / Yang, Y. / Folta-Stogniew, E.J. / Chung, H.-J. / Fan, C. / De La Cruz, E.M. / Levens, D. / Lolis, E. / Braddock, D.
History
DepositionJun 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE THE SEQUENCE REPORTED FOR the DNA IN CHAIN C IS COMPLIMENTARY TO THAT IN THE SEQUENCE ...SEQUENCE THE SEQUENCE REPORTED FOR the DNA IN CHAIN C IS COMPLIMENTARY TO THAT IN THE SEQUENCE DATABASE REFERENCE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*DTP*DCP*DGP*DGP*DGP*DAP*DTP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DTP*DTP*DGP*DTP*DGP*DTP*DTP*DAP*DTP*DT)-3')
A: FBP-interacting repressor
B: FBP-interacting repressor


Theoretical massNumber of molelcules
Total (without water)54,5143
Polymers54,5143
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.135, 63.135, 82.589
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.5001, 0.866), (0.866, 0.5001, -0.0001), (-0.0001, -0.0001, -1)31.5613, -18.2303, -72.3741
DetailsAuthors propose that the biological unit is the same as the asymmetric unit

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Components

#1: DNA chain DNA (5'-D(*DTP*DCP*DGP*DGP*DGP*DAP*DTP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DTP*DTP*DGP*DTP*DGP*DTP*DTP*DAP*DTP*DT)-3')


Mass: 7696.959 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence naturally occurs in humans in an enchancer of the c-myc gene known as the Far Up Stream Element (FUSE)
References: GenBank: 188913
#2: Protein FBP-interacting repressor / Fuse-binding protein-interacting repressor


Mass: 23408.537 Da / Num. of mol.: 2 / Mutation: R106G, C112S, C238A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FIR, SIAHBP1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZA0, UniProt: Q9UHX1*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 1.52 Å3/Da / Density % sol: 27.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: Reservoir: 0.1 M Tris-HCl, 32% PEG 4000, pH 8.5 mixed 1:1 with protein/DNA complex in 20 mM Tris-HCl (pH 8.0), 100 mM NaCl, vapor diffusion, hanging drop
Components of the solutions
IDNameCrystal-IDSol-ID
120 mM Tris-HCl11
2NaClSodium chloride11
30.1 M Tris-HCl12
4PEG 400012

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONNSLS X2520.9794, 0.9798, 0.9600
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 1, 2005
ADSC QUANTUM 3152CCDAug 1, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97941
30.97981
40.961
Reflection

D res high: 2.6 Å / D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
5.6118.91266750.0681.062262598.4
5.7219.21283300.0691.042269299.4
5.6318.11283210.0671.062290899.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.65093.810.0421.0915.5
4.455.69510.0541.0155.3
3.884.4596.810.0641.0735.5
3.533.8899.610.071.0525.7
3.283.5399.610.0831.0545.7
3.083.2810010.1071.0155.8
2.933.0810010.1411.0715.8
2.82.9310010.1871.0845.8
2.692.810010.2391.0655.7
2.62.6999.610.2841.0955.2
5.6509720.0470.9845.6
4.455.698.920.0581.0015.4
3.884.4598.920.0691.0755.6
3.533.8899.820.0771.115.7
3.283.5399.920.0851.0255.7
3.083.2810020.1081.0525.8
2.933.0810020.1341.0465.8
2.82.9310020.1671.0275.7
2.692.810020.2211.025.7
2.62.6910020.2721.0835.4
5.65098.130.0391.2435.6
4.455.698.730.0470.9955.2
3.884.4599.230.0615.4
3.533.8899.830.0691.0185.6
3.283.5399.930.0841.0495.7
3.083.2810030.12215.7
2.933.0810030.1711.0045.7
2.82.9310030.2371.0365.7
2.692.810030.3221.0855.7
2.62.6910030.411.1625.7
ReflectionResolution: 2.1→50 Å / Num. obs: 20889 / % possible obs: 97.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.1-2.182.90.3792.2
2.18-2.263.60.28799.1
2.26-2.375.30.322100
2.37-2.495.70.235100
2.49-2.655.70.17100
2.65-2.855.70.101100
2.85-3.145.70.069100
3.14-3.595.70.05199
3.59-4.525.40.04494.1
4.52-505.20.03890.3

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Phasing

Phasing MRRfactor: 0.395 / Cor.coef. Fo:Fc: 0.566 / Cor.coef. Io to Ic: 0.568
Highest resolutionLowest resolution
Rotation3.5 Å15 Å
Translation3.5 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.2refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→45.59 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 761627.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.295 953 4.9 %RANDOM
Rwork0.258 ---
obs0.258 19562 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.7695 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 54.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.1→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 41 0 22 3010
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.472.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.408 96 5.4 %
Rwork0.389 1693 -
obs--82.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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