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- PDB-8wq5: Crystal structure of the C-terminal RRM domain of an RBP in compl... -

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Basic information

Entry
Database: PDB / ID: 8wq5
TitleCrystal structure of the C-terminal RRM domain of an RBP in complex with ssDNA
Components
  • DNA (5'-D(*GP*AP*CP*GP*CP*AP*G)-3')
  • RNA-binding protein 45
KeywordsRNA BINDING PROTEIN/DNA / RBM45 / RRM / ALS / FTLD / RNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


nervous system development / cell differentiation / ribonucleoprotein complex / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
RBM45, RNA recognition motif 1 / RBM45, RNA recognition motif 2 / RBM45, RNA recognition motif 3 / RBM45, RNA recognition motif 4 / 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
Similarity search - Domain/homology
DNA / RNA-binding protein 45
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsChen, X. / Yang, Z. / Chen, X. / Wei, Q. / Guo, S. / Jiang, M. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2108085MC75 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural basis for RNA recognition by the C-terminal RRM domain of human RBM45.
Authors: Chen, X. / Wei, Q. / Yang, Z. / Chen, X. / Guo, S. / Jiang, M. / Wang, M.
History
DepositionOct 11, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein 45
B: RNA-binding protein 45
C: RNA-binding protein 45
D: RNA-binding protein 45
E: DNA (5'-D(*GP*AP*CP*GP*CP*AP*G)-3')
F: DNA (5'-D(*GP*AP*CP*GP*CP*AP*G)-3')
G: DNA (5'-D(*GP*AP*CP*GP*CP*AP*G)-3')
H: DNA (5'-D(*GP*AP*CP*GP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,87110
Polymers61,6878
Non-polymers1842
Water11,458636
1
A: RNA-binding protein 45
E: DNA (5'-D(*GP*AP*CP*GP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)15,4222
Polymers15,4222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-1 kcal/mol
Surface area6660 Å2
MethodPISA
2
B: RNA-binding protein 45
F: DNA (5'-D(*GP*AP*CP*GP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5143
Polymers15,4222
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-0 kcal/mol
Surface area6470 Å2
MethodPISA
3
C: RNA-binding protein 45
G: DNA (5'-D(*GP*AP*CP*GP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)15,4222
Polymers15,4222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-0 kcal/mol
Surface area6680 Å2
MethodPISA
4
D: RNA-binding protein 45
H: DNA (5'-D(*GP*AP*CP*GP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5143
Polymers15,4222
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-1 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.403, 83.767, 77.762
Angle α, β, γ (deg.)90.00, 96.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RNA-binding protein 45 / Developmentally-regulated RNA-binding protein 1 / RB-1 / RNA-binding motif protein 45


Mass: 13274.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM45, DRB1, DRBP1 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IUH3
#2: DNA chain
DNA (5'-D(*GP*AP*CP*GP*CP*AP*G)-3')


Mass: 2147.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: 8% PEG 2000 and 0.1M succinic acid, pH 5.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 64857 / % possible obs: 99.8 % / Redundancy: 5 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.06 / Rrim(I) all: 0.136 / Χ2: 1.065 / Net I/σ(I): 7.5 / Num. measured all: 327484
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.65-1.715.10.97464600.8410.9560.4681.0841.02699.8
1.71-1.784.90.69664370.8680.9640.3410.7781.09899.7
1.78-1.865.10.48364620.9230.980.2350.5391.09799.7
1.86-1.965.10.33264570.9540.9880.1630.3721.11799.8
1.96-2.085.10.22864630.9730.9930.1130.2561.084100
2.08-2.2450.16764990.980.9950.0840.1881.06199.8
2.24-2.465.10.12864680.9880.9970.0640.1431.06599.9
2.46-2.825.10.165060.9910.9980.0510.1131.07799.9
2.82-3.555.10.07565020.9950.9990.0380.0841.04999.9
3.55-504.80.06666030.9950.9990.0340.0750.97899.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→38.97 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 3187 4.93 %
Rwork0.1584 --
obs0.1608 64589 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 450 12 636 4194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.741
X-RAY DIFFRACTIONf_dihedral_angle_d16.2141533
X-RAY DIFFRACTIONf_chiral_restr0.052621
X-RAY DIFFRACTIONf_plane_restr0.008608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.27091260.22822559X-RAY DIFFRACTION96
1.67-1.70.22681310.19282668X-RAY DIFFRACTION99
1.7-1.730.24041170.18632635X-RAY DIFFRACTION99
1.73-1.760.27411420.18132670X-RAY DIFFRACTION99
1.76-1.790.24321390.1762650X-RAY DIFFRACTION99
1.79-1.820.2251460.17092646X-RAY DIFFRACTION99
1.82-1.860.22411530.16172656X-RAY DIFFRACTION99
1.86-1.90.20961590.15892617X-RAY DIFFRACTION99
1.9-1.950.19441530.16542660X-RAY DIFFRACTION99
1.95-1.990.22291730.15492629X-RAY DIFFRACTION100
1.99-2.050.19481440.14522676X-RAY DIFFRACTION100
2.05-2.110.21391210.14592687X-RAY DIFFRACTION100
2.11-2.180.23431360.15122661X-RAY DIFFRACTION100
2.18-2.250.2221090.14642724X-RAY DIFFRACTION100
2.25-2.340.19231350.14782691X-RAY DIFFRACTION100
2.34-2.450.18761400.15112643X-RAY DIFFRACTION100
2.45-2.580.20341320.15492703X-RAY DIFFRACTION100
2.58-2.740.22141230.16562692X-RAY DIFFRACTION100
2.74-2.950.20681470.17272687X-RAY DIFFRACTION100
2.95-3.250.20691450.16792695X-RAY DIFFRACTION100
3.25-3.720.22161330.14872700X-RAY DIFFRACTION100
3.72-4.690.16751550.13062712X-RAY DIFFRACTION100
4.69-38.970.19291280.17412741X-RAY DIFFRACTION99

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