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- PDB-4qu6: Crystal structure of a G-rich RNA sequence binding factor 1 (GRSF... -

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Basic information

Entry
Database: PDB / ID: 4qu6
TitleCrystal structure of a G-rich RNA sequence binding factor 1 (GRSF1) from Homo sapiens at 1.75 A resolution
Components
  • G-rich sequence factor 1
  • RNA 5'-(*AP*GP*GP*GP*UP*GP)-3'
KeywordsRNA Binding Protein/RNA / RNA binding domain / RRM_6 / PF14259 family / 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: 1.75 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 1.75 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 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: RNA 5'-(*AP*GP*GP*GP*UP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6858
Polymers14,4142
Non-polymers2716
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: G-rich sequence factor 1
B: RNA 5'-(*AP*GP*GP*GP*UP*GP)-3'
hetero molecules

A: G-rich sequence factor 1
B: RNA 5'-(*AP*GP*GP*GP*UP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,37016
Polymers28,8284
Non-polymers54112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3600 Å2
ΔGint-79 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.480, 60.480, 59.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-1003-

HOH

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

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


Mass: 12443.009 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC040485, GRSF1 / Plasmid: SpeedE6T / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12849
#2: RNA chain RNA 5'-(*AP*GP*GP*GP*UP*GP)-3'


Mass: 1971.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 91 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 140-245 OF THE TARGET SEQUENCE.

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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: 1.88 Å3/Da / Density % sol: 34.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M calcium chloride 20.0% polyethylene glycol 3350, 1 mM AGGGUG, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

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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: Jun 6, 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: 1.75→42.766 Å / Num. obs: 11466 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.802 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 17.73
Reflection shell

Rmerge(I) obs: 0.014 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.75-1.80.6641.658658387381.45188.1
1.8-1.840.8122.474458217871.06795.9
1.84-1.90.893.295597997900.94798.9
1.9-1.960.9384.8101367697690.675100
1.96-2.020.9736.297597537520.50299.9
2.02-2.090.9787.792727297280.40499.9
2.09-2.170.9758.584927057040.34799.9
2.17-2.260.98711.188626726710.27699.9
2.26-2.360.99512.686276616610.234100
2.36-2.480.99213.679526206200.219100
2.48-2.610.99416.772516046040.168100
2.61-2.770.99719.172785645640.147100
2.77-2.960.99824.470265395390.109100
2.96-3.20.99932.963935045040.073100
3.2-3.50.99940.354684634620.05699.8
3.5-3.91151.655604314310.042100
3.91-4.520.99954.847893843840.038100
4.52-5.530.99951.837193303280.04199.4
5.53-7.830.99951.631572682670.04499.6
7.83163.215941651630.0398.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
MOLREPphasing
XSCALEJuly 4, 2012data scaling
REFMAC5.7.0032refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DB1

2db1


Resolution: 1.75→42.766 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.126 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. EDO, CALCIUM AND CL MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 5. RNA MOLECULE SITS ON 2-FOLD AXIS WITH HALF OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 546 4.8 %RANDOM
Rwork0.1826 ---
obs0.1855 11465 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.21 Å2 / Biso mean: 28.5744 Å2 / Biso min: 14.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0 Å2-0 Å2
2---1.19 Å20 Å2
3---2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms805 69 12 85 971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019932
X-RAY DIFFRACTIONr_bond_other_d0.0020.02844
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.8871271
X-RAY DIFFRACTIONr_angle_other_deg0.84631942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9465108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8924.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0215162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.984159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021038
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02227
X-RAY DIFFRACTIONr_mcbond_it1.5011.88405
X-RAY DIFFRACTIONr_mcbond_other1.5021.875404
X-RAY DIFFRACTIONr_mcangle_it2.3812.805507
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 29 -
Rwork0.306 704 -
all-733 -
obs--87.89 %
Refinement TLS params.Method: refined / Origin x: 18.2816 Å / Origin y: 3.3933 Å / Origin z: 19.1628 Å
111213212223313233
T0.0177 Å2-0.0004 Å20.0112 Å2-0.0134 Å20.0087 Å2--0.0426 Å2
L2.2869 °2-0.371 °20.0487 °2-0.4009 °20.0413 °2--0.6509 °2
S0.0231 Å °0.0644 Å °0.1278 Å °-0.0415 Å °-0.0316 Å °-0.0289 Å °-0.0277 Å °0.0339 Å °0.0085 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A147 - 245
2X-RAY DIFFRACTION1B802 - 804

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