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- PDB-5zuu: Crystal structure of AtCPSF30 YTH domain in complex with 10mer m6... -

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Basic information

Entry
Database: PDB / ID: 5zuu
TitleCrystal structure of AtCPSF30 YTH domain in complex with 10mer m6A-modified RNA
Components
  • 30-kDa cleavage and polyadenylation specificity factor 30
  • RNA (5'-R(*(6MZ)P*CP*UP*AP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / mRNA processing / Arabidopsis / CPSF / modification / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


positive regulation of plant-type hypersensitive response / regulation of salicylic acid mediated signaling pathway / plant-type hypersensitive response / mRNA cleavage and polyadenylation specificity factor complex / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / mRNA 3'-end processing / positive regulation of programmed cell death / RNA processing / RNA endonuclease activity / endonuclease activity ...positive regulation of plant-type hypersensitive response / regulation of salicylic acid mediated signaling pathway / plant-type hypersensitive response / mRNA cleavage and polyadenylation specificity factor complex / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / mRNA 3'-end processing / positive regulation of programmed cell death / RNA processing / RNA endonuclease activity / endonuclease activity / response to oxidative stress / calmodulin binding / mRNA binding / apoptotic process / DNA binding / RNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
ph1033 like fold / ph1033 like domains / YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile. / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. ...ph1033 like fold / ph1033 like domains / YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile. / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Roll / Alpha Beta
Similarity search - Domain/homology
RNA / 30-kDa cleavage and polyadenylation specificity factor 30
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWu, B. / Nie, H. / Li, S. / Patel, D.J.
CitationJournal: Mol Plant / Year: 2021
Title: CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis.
Authors: Hou, Y. / Sun, J. / Wu, B. / Gao, Y. / Nie, H. / Nie, Z. / Quan, S. / Wang, Y. / Cao, X. / Li, S.
History
DepositionMay 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
C: 30-kDa cleavage and polyadenylation specificity factor 30
A: 30-kDa cleavage and polyadenylation specificity factor 30
B: 30-kDa cleavage and polyadenylation specificity factor 30
D: 30-kDa cleavage and polyadenylation specificity factor 30
E: RNA (5'-R(*(6MZ)P*CP*UP*AP*G)-3')
F: RNA (5'-R(*(6MZ)P*CP*UP*AP*G)-3')
G: RNA (5'-R(*(6MZ)P*CP*UP*AP*G)-3')
I: RNA (5'-R(*(6MZ)P*CP*UP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,76210
Polymers94,4328
Non-polymers3302
Water3,909217
1
C: 30-kDa cleavage and polyadenylation specificity factor 30
F: RNA (5'-R(*(6MZ)P*CP*UP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)23,6082
Polymers23,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area10070 Å2
MethodPISA
2
A: 30-kDa cleavage and polyadenylation specificity factor 30
E: RNA (5'-R(*(6MZ)P*CP*UP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7003
Polymers23,6082
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-8 kcal/mol
Surface area8720 Å2
MethodPISA
3
B: 30-kDa cleavage and polyadenylation specificity factor 30
I: RNA (5'-R(*(6MZ)P*CP*UP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8463
Polymers23,6082
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-10 kcal/mol
Surface area7870 Å2
MethodPISA
4
D: 30-kDa cleavage and polyadenylation specificity factor 30
G: RNA (5'-R(*(6MZ)P*CP*UP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)23,6082
Polymers23,6082
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-9 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.108, 74.293, 151.139
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
30-kDa cleavage and polyadenylation specificity factor 30 / AtCPSF30


Mass: 20449.918 Da / Num. of mol.: 4 / Fragment: UNP residues 221-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli)
References: UniProt: A9LNK9, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: RNA chain
RNA (5'-R(*(6MZ)P*CP*UP*AP*G)-3')


Mass: 3158.059 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5, 20% PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 57240 / % possible obs: 99.6 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 15.25
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 5582

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WQN

4wqn


Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.889 / SU B: 5.229 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25577 2513 5.1 %RANDOM
Rwork0.19942 ---
obs0.20223 47044 86.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.742 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.51 Å20 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5080 374 21 217 5692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195622
X-RAY DIFFRACTIONr_bond_other_d0.0020.024904
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.9197652
X-RAY DIFFRACTIONr_angle_other_deg1.083311422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4925626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56924.255275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59215914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.381543
X-RAY DIFFRACTIONr_chiral_restr0.1090.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026015
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021168
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6773.0052525
X-RAY DIFFRACTIONr_mcbond_other2.6653.0032524
X-RAY DIFFRACTIONr_mcangle_it4.2954.4793144
X-RAY DIFFRACTIONr_mcangle_other4.2964.4823145
X-RAY DIFFRACTIONr_scbond_it3.0023.3533097
X-RAY DIFFRACTIONr_scbond_other2.9993.3533097
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7634.9424509
X-RAY DIFFRACTIONr_long_range_B_refined734.4776399
X-RAY DIFFRACTIONr_long_range_B_other734.4816400
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 43 -
Rwork0.285 860 -
obs--21.62 %

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