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- PDB-4zka: High Resolution Crystal Structure of Fox1 RRM -

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Basic information

Entry
Database: PDB / ID: 4zka
TitleHigh Resolution Crystal Structure of Fox1 RRM
ComponentsRNA binding protein fox-1 homolog 1
KeywordsRNA BINDING PROTEIN / RRM RNA Binding
Function / homology
Function and homology information


regulation of skeletal muscle cell differentiation / RNA transport / nuclear stress granule / MECP2 regulates transcription factors / regulation of alternative mRNA splicing, via spliceosome / neuromuscular process controlling balance / RNA splicing / mRNA 3'-UTR binding / trans-Golgi network / mRNA processing ...regulation of skeletal muscle cell differentiation / RNA transport / nuclear stress granule / MECP2 regulates transcription factors / regulation of alternative mRNA splicing, via spliceosome / neuromuscular process controlling balance / RNA splicing / mRNA 3'-UTR binding / trans-Golgi network / mRNA processing / cytoplasmic stress granule / nervous system development / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
: / RNA binding protein Fox-1 / Fox-1 C-terminal domain / Calcitonin gene-related peptide regulator C terminal / FOX1, 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 protein Fox-1 / Fox-1 C-terminal domain / Calcitonin gene-related peptide regulator C terminal / FOX1, 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
RNA binding protein fox-1 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBlatter, M. / Allain, F.H.-T.
CitationJournal: To Be Published
Title: High Resolution Crystal Structure of Fox1 RRM
Authors: Blatter, M. / Allain, F.H.-T.
History
DepositionApr 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA binding protein fox-1 homolog 1
B: RNA binding protein fox-1 homolog 1
C: RNA binding protein fox-1 homolog 1
D: RNA binding protein fox-1 homolog 1
E: RNA binding protein fox-1 homolog 1
F: RNA binding protein fox-1 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,15518
Polymers68,5076
Non-polymers1,64812
Water5,963331
1
A: RNA binding protein fox-1 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7093
Polymers11,4181
Non-polymers2912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA binding protein fox-1 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7064
Polymers11,4181
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA binding protein fox-1 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6132
Polymers11,4181
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA binding protein fox-1 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7083
Polymers11,4181
Non-polymers2902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: RNA binding protein fox-1 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7093
Polymers11,4181
Non-polymers2912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: RNA binding protein fox-1 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7093
Polymers11,4181
Non-polymers2912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.980, 77.617, 106.386
Angle α, β, γ (deg.)90.00, 93.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
RNA binding protein fox-1 homolog 1 / Ataxin-2-binding protein 1 / Fox-1 homolog A / Hexaribonucleotide-binding protein 1


Mass: 11417.867 Da / Num. of mol.: 6 / Fragment: UNP residues 109-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBFOX1, A2BP, A2BP1, FOX1, HRNBP1 / Plasmid: pTYB11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NWB1
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350 12.5%w/v PEG 1000 12.5%w/v NPS 6.6% MPD 12.5%w/v MES 0.1M, pH 6.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987 Å / Relative weight: 1
ReflectionResolution: 1.8→45.41 Å / Num. obs: 50898 / % possible obs: 98 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.4
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 4.02 / Num. measured obs: 26029 / Num. unique all: 7510 / CC1/2: 0.876 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XSCALEdata scaling
XDSdata reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.407 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.92 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 3735 3.9 %
Rwork0.1938 --
obs0.1951 50885 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 96 331 4335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084102
X-RAY DIFFRACTIONf_angle_d1.1125492
X-RAY DIFFRACTIONf_dihedral_angle_d14.3481581
X-RAY DIFFRACTIONf_chiral_restr0.065553
X-RAY DIFFRACTIONf_plane_restr0.004731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82280.30131380.28213277X-RAY DIFFRACTION92
1.8228-1.84680.30281170.2813398X-RAY DIFFRACTION91
1.8468-1.87210.32791610.25483354X-RAY DIFFRACTION94
1.8721-1.89880.29741120.24953443X-RAY DIFFRACTION95
1.8988-1.92720.27271460.23463543X-RAY DIFFRACTION95
1.9272-1.95730.31211420.22133367X-RAY DIFFRACTION96
1.9573-1.98940.29511400.22273487X-RAY DIFFRACTION94
1.9894-2.02370.26771370.21073422X-RAY DIFFRACTION96
2.0237-2.06050.23561400.20733494X-RAY DIFFRACTION95
2.0605-2.10010.27971110.19913413X-RAY DIFFRACTION94
2.1001-2.1430.23421850.19433408X-RAY DIFFRACTION95
2.143-2.18960.25441220.19013474X-RAY DIFFRACTION94
2.1896-2.24050.2661350.1943374X-RAY DIFFRACTION93
2.2405-2.29650.23011480.1783449X-RAY DIFFRACTION95
2.2965-2.35860.21541250.17653540X-RAY DIFFRACTION96
2.3586-2.4280.22671560.18223368X-RAY DIFFRACTION95
2.428-2.50640.23931400.18453448X-RAY DIFFRACTION95
2.5064-2.59590.26181430.18613463X-RAY DIFFRACTION94
2.5959-2.69990.21441500.19233355X-RAY DIFFRACTION94
2.6999-2.82270.221210.19713351X-RAY DIFFRACTION93
2.8227-2.97150.23531530.19853358X-RAY DIFFRACTION92
2.9715-3.15770.24611320.19063375X-RAY DIFFRACTION93
3.1577-3.40140.20561360.19163325X-RAY DIFFRACTION92
3.4014-3.74350.20031250.17473382X-RAY DIFFRACTION92
3.7435-4.28490.20061350.17033276X-RAY DIFFRACTION90
4.2849-5.39710.15491490.16963365X-RAY DIFFRACTION94
5.3971-45.42160.22571360.2193456X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 49.3479 Å / Origin y: 7.0787 Å / Origin z: 26.6213 Å
111213212223313233
T0.171 Å20.0074 Å2-0.0292 Å2-0.0938 Å20.0059 Å2--0.1531 Å2
L0.1281 °20.0075 °20.2197 °2--0.0295 °20.0793 °2--0.4711 °2
S0.0133 Å °0.0176 Å °-0.0016 Å °0.0262 Å °0.0009 Å °-0.0109 Å °0.0027 Å °0.0311 Å °-0.0154 Å °
Refinement TLS groupSelection details: all

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