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- PDB-7zhr: Complex structure of drosophila Unr CSD789 and pAbp RRM3 -

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Basic information

Entry
Database: PDB / ID: 7zhr
TitleComplex structure of drosophila Unr CSD789 and pAbp RRM3
Components
  • Polyadenylate-binding protein
  • Upstream of N-ras, isoform A
KeywordsRNA BINDING PROTEIN / drosophila Unr / CSD / cold-shock domain / protein complex / PPI / drosophila pAbp / RRM / Unr / pAbp
Function / homology
Function and homology information


regulation of compound eye photoreceptor development / male meiosis cytokinesis / dosage compensation complex assembly / spermatid nucleus differentiation / protein-RNA adaptor activity / RISC complex binding / male meiotic nuclear division / sex differentiation / poly(A) binding / oocyte development ...regulation of compound eye photoreceptor development / male meiosis cytokinesis / dosage compensation complex assembly / spermatid nucleus differentiation / protein-RNA adaptor activity / RISC complex binding / male meiotic nuclear division / sex differentiation / poly(A) binding / oocyte development / dorsal/ventral pattern formation / poly(U) RNA binding / precatalytic spliceosome / oogenesis / lncRNA binding / negative regulation of translational initiation / catalytic step 2 spliceosome / mRNA regulatory element binding translation repressor activity / positive regulation of translation / mRNA 3'-UTR binding / mRNA splicing, via spliceosome / cytoplasmic stress granule / spermatogenesis / chemical synaptic transmission / cell differentiation / ribonucleoprotein complex / mRNA binding / synapse / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Cold shock domain-containing protein E1 CSD domain / : / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / MLLE domain ...: / Cold shock domain-containing protein E1 CSD domain / : / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / MLLE domain / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotide-binding alpha-beta plait domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Polyadenylate-binding protein / RNA-binding protein Unr
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsHollmann, N.M. / Jagtap, P.K.A. / Hennig, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
Citation
Journal: Nucleic Acids Res. / Year: 2023
Title: Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein.
Authors: Hollmann, N.M. / Jagtap, P.K.A. / Linse, J.B. / Ullmann, P. / Payr, M. / Murciano, B. / Simon, B. / Hub, J.S. / Hennig, J.
#1: Journal: Nucleic Acids Res. / Year: 2023
Title: Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein.
Authors: Hollmann, N.M. / Jagtap, P.K.A. / Linse, J.B. / Ullmann, P. / Payr, M. / Murciano, B. / Simon, B. / Hub, J.S. / Hennig, J.
#2: Journal: Biorxiv / Year: 2022
Title: Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein during translation regulation
Authors: Hollmann, N.M. / Jagtap, P.K.A. / Linse, J.B. / Ullmann, P. / Payr, M. / Murciano, B. / Simon, B. / Hub, J.S. / Hennig, J.
History
DepositionApr 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: 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: Upstream of N-ras, isoform A
B: Polyadenylate-binding protein


Theoretical massNumber of molelcules
Total (without water)36,1152
Polymers36,1152
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-9 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.600, 52.020, 73.500
Angle α, β, γ (deg.)90.000, 96.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Upstream of N-ras, isoform A


Mass: 26166.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Unr, BcDNA:LD13080, CR32028, Dmel\CG7015, dUNR, dUnr, dunr, MRE30, UNR, unr, CG7015, Dmel_CG7015
Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9VSK3
#2: Protein Polyadenylate-binding protein / PABP / Poly(A)-binding protein


Mass: 9948.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: pAbp, CG5119 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21187
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium formate 0.1 M bis-tris propane 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.99→42.36 Å / Num. obs: 7836 / % possible obs: 98.1 % / Redundancy: 6.262 % / Biso Wilson estimate: 44.16 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.26 / Rrim(I) all: 0.283 / Χ2: 0.853 / Net I/σ(I): 6.61 / Num. measured all: 49067
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.99-3.074.7510.6782.174780.6960.7681.4
3.07-3.165.1650.6342.525380.7210.70796.2
3.16-3.255.7940.5393.165730.8640.59499.7
3.25-3.356.3360.5133.845330.8710.5699.8
3.35-3.466.6450.4194.695270.9220.454100
3.46-3.586.7180.395.194790.9260.42399.8
3.58-3.716.5980.3475.625130.9590.376100
3.71-3.876.7940.3266.34670.960.354100
3.87-4.046.7440.2517.684420.9770.272100
4.04-4.236.6880.2318.554260.9750.251100
4.23-4.466.5830.19110.074240.980.20899.5
4.46-4.736.5990.17610.963890.980.191100
4.73-5.066.5260.17810.043590.9870.193100
5.06-5.476.4480.2198.33370.980.238100
5.47-5.996.4720.247.553260.9660.261100
5.99-6.696.4680.2367.522990.9750.25799.7
6.69-7.736.3670.1948.862480.9820.211100
7.73-9.475.7280.13211.42170.990.14599.5
9.47-13.395.8340.11213.551750.990.12299.4
13.39-42.365.2440.11312.13860.9840.12686

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZHH

7zhh


Resolution: 2.99→42.36 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3154 392 5 %
Rwork0.2531 7443 -
obs0.256 7835 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.52 Å2 / Biso mean: 40.3117 Å2 / Biso min: 26.1 Å2
Refinement stepCycle: final / Resolution: 2.99→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 0 0 17 2296
Biso mean---35.31 -
Num. residues----288
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.99-3.430.31941250.29732379250495
3.43-4.320.34951330.256925302663100
4.32-42.360.28651340.22842534266899
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)
12.0815-0.7198-1.1130.2490.37670.92320.1463-0.17350.4513-0.19550.1475-0.0727-0.00550.1052-0.21330.38050.02440.05160.5087-0.03950.4766-1.551534.097522.3897
21.0223-0.5382-0.01031.6597-0.06070.1431-0.07430.0287-0.1154-0.25080.13210.2280.156-0.3894-0.00410.5741-0.13610.08680.71340.01250.40392.681931.788320.8358
30.29970.4631-0.6771.1874-0.27762.7816-0.1886-0.0321-0.0554-0.9644-0.0178-0.5370.23670.42460.08040.703-0.10340.19880.2736-0.0110.541831.513526.5333-4.1362
42.0552-1.1082-0.4793.57071.51343.21550.03180.2260.3892-0.7699-0.2188-0.22460.0183-0.20050.18110.4401-0.020.10980.35630.04970.393127.746127.7135-8.1257
51.48490.64380.68180.93930.09531.0440.0355-0.17750.00840.1293-0.0614-0.072-0.065-0.12890.04710.34240.05070.03730.35190.00250.312325.32932.368122.4799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 163 through 219 )A163 - 219
2X-RAY DIFFRACTION2chain 'A' and (resid 220 through 235 )A220 - 235
3X-RAY DIFFRACTION3chain 'B' and (resid 9 through 22 )B9 - 22
4X-RAY DIFFRACTION4chain 'B' and (resid 23 through 88 )B23 - 88
5X-RAY DIFFRACTION5chain 'A' and (resid 8 through 162 )A8 - 162

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