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- PDB-4qu7: Crystal structure of a G-rich RNA sequence binding factor 1 (GRSF... -

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Basic information

Entry
Database: PDB / ID: 4qu7
TitleCrystal structure of a G-rich RNA sequence binding factor 1 (GRSF1) from Homo sapiens at 2.50 A resolution
Components
  • G-rich sequence factor 1
  • RNA 5'-(*AP*GP*GP*GP*AP*UP)-3'
KeywordsRNA Binding Protein/RNA / Canonical RNA binding domain / RRM_6 / PF14259 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / RNA-BINDING PROTEIN / RNA Binding Protein-RNA complex / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


positive regulation of mitochondrial RNA catabolic process / mitochondrial RNA catabolic process / Mitochondrial RNA degradation / ribonucleoprotein granule / morphogenesis of embryonic epithelium / tRNA processing / anterior/posterior pattern specification / : / mitochondrial nucleoid / regulation of RNA splicing ...positive regulation of mitochondrial RNA catabolic process / mitochondrial RNA catabolic process / Mitochondrial RNA degradation / ribonucleoprotein granule / morphogenesis of embryonic epithelium / tRNA processing / anterior/posterior pattern specification / : / mitochondrial nucleoid / regulation of RNA splicing / Viral mRNA Translation / G-quadruplex RNA binding / mitochondrial matrix / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
GRSF-1, RNA recognition motif 2 / GRSF-1, RNA recognition motif 1 / GRSF-1, RNA recognition motif 3 / 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 ...GRSF-1, RNA recognition motif 2 / GRSF-1, RNA recognition motif 1 / GRSF-1, RNA recognition motif 3 / 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 / G-rich sequence factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a G-rich RNA sequence binding factor 1 (GRSF1) from Homo sapiens at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G-rich sequence factor 1
B: G-rich sequence factor 1
C: G-rich sequence factor 1
D: G-rich sequence factor 1
U: RNA 5'-(*AP*GP*GP*GP*AP*UP)-3'
V: RNA 5'-(*AP*GP*GP*GP*AP*UP)-3'
X: RNA 5'-(*AP*GP*GP*GP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)42,8247
Polymers42,8247
Non-polymers00
Water3,279182
1
A: G-rich sequence factor 1
U: RNA 5'-(*AP*GP*GP*GP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)11,1952
Polymers11,1952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: G-rich sequence factor 1
V: RNA 5'-(*AP*GP*GP*GP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)11,1952
Polymers11,1952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: G-rich sequence factor 1


Theoretical massNumber of molelcules
Total (without water)9,2401
Polymers9,2401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: G-rich sequence factor 1
X: RNA 5'-(*AP*GP*GP*GP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)11,1952
Polymers11,1952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.540, 72.320, 103.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
G-rich sequence factor 1 / GRSF-1


Mass: 9239.583 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRSF1, NM_002092 / Plasmid: pET22bNoHis / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21Gold(DE3) / References: UniProt: Q12849
#2: RNA chain RNA 5'-(*AP*GP*GP*GP*AP*UP)-3'


Mass: 1955.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE EXPRESSION OF THE CONSTRUCT (RESIDUES 400-480) REQUIRED THE MUTATION OF THE N-TERMINAL ...SEQUENCE EXPRESSION OF THE CONSTRUCT (RESIDUES 400-480) REQUIRED THE MUTATION OF THE N-TERMINAL LEU400 TO METHIONINE (L400M).

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20.0% polyethylene glycol 6000, 0.1M TRIS pH 8.5, 1mM AGGGAU, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→42.507 Å / Num. obs: 14045 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 50.312 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.5-2.570.5460.8791.6316810079821.05297.5
2.57-2.640.6550.72723391103110220.86499.1
2.64-2.710.7540.5872.531039649520.70198.8
2.71-2.80.8260.463330929709490.55397.8
2.8-2.890.8540.3723.526779168890.45297.1
2.89-2.990.90.3134.328958898820.37399.2
2.99-3.10.9290.273529408888820.32599.3
3.1-3.230.9630.196.927128208130.22699.1
3.23-3.370.9710.1428.826017987940.1799.5
3.37-3.540.9870.09512.225397867790.11499.1
3.54-3.730.9880.08912.721727407140.10796.5
3.73-3.950.9920.07614.621826936780.09197.8
3.95-4.230.9960.0641621956666590.07698.9
4.23-4.560.9960.05120.319846126040.06198.7
4.56-50.9960.05618.918185725680.06799.3
5-5.590.9960.05916.914985295130.07297
5.59-6.460.9950.06116.814904694670.07499.6
6.46-7.910.9970.04820.512424033940.05797.8
7.91-11.180.9980.03127.48693243090.03895.4
11.1810.02137.25502051950.02695.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WEZ

1wez


Resolution: 2.5→42.507 Å / Cor.coef. Fo:Fc: 0.9292 / Cor.coef. Fo:Fc free: 0.8934 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). 3. LEU400 WAS MUTATED TO MET (START CODON) FOR EXPRESSION OF THE CONSTRUCT 400-480.
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 704 5.03 %RANDOM
Rwork0.1917 ---
obs0.1948 14006 98.4 %-
Displacement parametersBiso max: 124.23 Å2 / Biso mean: 44.378 Å2 / Biso min: 15.91 Å2
Baniso -1Baniso -2Baniso -3
1--9.8663 Å20 Å20 Å2
2--1.2026 Å20 Å2
3---8.6636 Å2
Refine analyzeLuzzati coordinate error obs: 0.358 Å
Refinement stepCycle: LAST / Resolution: 2.5→42.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 229 0 182 2941
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1244SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes405HARMONIC5
X-RAY DIFFRACTIONt_it2881HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion374SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion100SINUSOIDAL1
X-RAY DIFFRACTIONt_ideal_dist_contact3126SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2881HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3945HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion3.05
LS refinement shellResolution: 2.5→2.7 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2909 152 5.38 %
Rwork0.2381 2671 -
all0.2409 2823 -
obs--98.4 %
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)
10.5948-0.87140.47912.4883-1.45092.33610.0750.14090.0837-0.1153-0.01140.0577-0.1931-0.1075-0.06360.01720.0458-0.00590.02620.0041-0.0720.5081-12.3002-13.1006
21.17820.0916-1.08190.4148-1.265800.00060.00590.0964-0.01640.0242-0.0715-0.05310.1061-0.0248-0.11030.15160.00920.11490.152-0.018829.347-7.6129-25.8486
33.87592.3082-0.25884.46062.58122.99830.2353-0.51620.2465-0.3467-0.21980.2466-0.54420.1767-0.01560.10050.0064-0.0646-0.1046-0.0175-0.1619.11639.1908-7.3462
40-0.7972-1.26730.9512.35272.24510.0044-0.1218-0.17750.06610.0108-0.04430.0241-0.0441-0.01520.0130.15020.04820.0423-0.152-0.06736.82175.60161.3713
52.40440.62320.39823.4161.01072.0832-0.0753-0.21630.1740.26750.08540.04150.0642-0.0533-0.0101-0.0457-0.00340.007-0.0379-0.0082-0.104512.3136-10.772414.6278
63.89180.9981-0.05270.80630.37345.828-0.1043-0.09550.09370.06870.2938-0.1032-0.03230.5423-0.1894-0.1124-0.0115-0.0090.0281-0.0989-0.109226.27935.258721.0099
72.2648-0.6822.76320.9032-0.81160-0.0077-0.0342-0.12260.04280.0262-0.0010.19040.1048-0.0186-0.03680.152-0.1520.1988-0.0376-0.165632.0475-3.284832.8837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|400 - 480}A400 - 480
2X-RAY DIFFRACTION2{U|802 - 804}U802 - 804
3X-RAY DIFFRACTION3{B|400 - 478}B400 - 478
4X-RAY DIFFRACTION4{V|802 - 805}V802 - 805
5X-RAY DIFFRACTION5{C|400 - 478}C400 - 478
6X-RAY DIFFRACTION6{D|400 - 476}D400 - 476
7X-RAY DIFFRACTION7{X|802 - 804}X802 - 804

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