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- PDB-4u8t: Crystal structure of YTH domain of Zygosaccharomyces rouxii MRB1 ... -

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Basic information

Entry
Database: PDB / ID: 4u8t
TitleCrystal structure of YTH domain of Zygosaccharomyces rouxii MRB1 protein in complex with N6-Methyladenosine RNA
Components
  • RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')
  • ZYRO0G01672p
KeywordsRNA Binding Protein/RNA / N6-Methyladenosine RNA / YTH RNA binding domain / RNA Binding Protein-RNA complex
Function / homology
Function and homology information


N6-methyladenosine-containing RNA reader activity / mRNA destabilization / mRNA binding / cytoplasm
Similarity search - Function
ph1033 like fold / ph1033 like domains / YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesZygosaccharomyces rouxii (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsLuo, S. / Tong, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain.
Authors: Luo, S. / Tong, L.
History
DepositionAug 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Jul 20, 2016Group: Data collection
Revision 1.4Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ZYRO0G01672p
B: ZYRO0G01672p
C: ZYRO0G01672p
D: ZYRO0G01672p
E: ZYRO0G01672p
F: ZYRO0G01672p
O: RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')
P: RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')
Q: RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')
R: RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')
S: RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')
T: RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)136,81912
Polymers136,81912
Non-polymers00
Water2,000111
1
A: ZYRO0G01672p
O: RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)22,8032
Polymers22,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-2 kcal/mol
Surface area9060 Å2
MethodPISA
2
B: ZYRO0G01672p
P: RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)22,8032
Polymers22,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-4 kcal/mol
Surface area9120 Å2
MethodPISA
3
C: ZYRO0G01672p
Q: RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)22,8032
Polymers22,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-5 kcal/mol
Surface area9130 Å2
MethodPISA
4
D: ZYRO0G01672p
T: RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)22,8032
Polymers22,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-4 kcal/mol
Surface area10390 Å2
MethodPISA
5
E: ZYRO0G01672p
S: RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)22,8032
Polymers22,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-3 kcal/mol
Surface area9090 Å2
MethodPISA
6
F: ZYRO0G01672p
R: RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)22,8032
Polymers22,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-4 kcal/mol
Surface area9020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.390, 117.390, 380.928
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
12chain O
22chain P
32chain Q
42chain R
52chain S
62chain T

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASPASPchain AAA165 - 32713 - 175
21GLYGLYASPASPchain BBB165 - 32613 - 174
31GLYGLYASPASPchain CCC165 - 32513 - 173
41GLYGLYASPASPchain DDD165 - 32513 - 173
51GLYGLYASPASPchain EEE165 - 32513 - 173
61GLYGLYASPASPchain FFF165 - 32513 - 173
12AAUUchain OOG-3 - 31 - 7
22AAUUchain PPH-3 - 31 - 7
32AAUUchain QQI-3 - 31 - 7
42AAUUchain RRJ-3 - 31 - 7
52AAUUchain SSK-3 - 31 - 7
62AAUUchain TTL-3 - 31 - 7

NCS ensembles :
ID
1
2
DetailsThe biological unit is a heterodimer of YTH domain and RNA. There are six YTH/RNA complexes in the asymmetric unit( AO, BP, CQ, DT, ES, FR

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Components

#1: Protein
ZYRO0G01672p


Mass: 20544.639 Da / Num. of mol.: 6 / Fragment: YTH domain, UNP residues 166-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zygosaccharomyces rouxii (yeast)
Strain: ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229
Gene: ZYRO0G01672g / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5E1V0
#2: RNA chain
RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')


Mass: 2258.446 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: N6-Methyladenosine 7-mer RNA / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 277 K / Method: microbatch / Details: 0.8 M ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 41339 / % possible obs: 94.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 42.55 Å2 / Rmerge(I) obs: 0.137 / Χ2: 1.082 / Net I/av σ(I): 10.906 / Net I/σ(I): 6.6 / Num. measured all: 186118
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.84.60.49841231.00696.1
2.8-2.914.50.36441031.04595.9
2.91-3.044.40.25140921.12495.3
3.04-3.24.50.20641061.14495.4
3.2-3.44.50.16841051.15294.9
3.4-3.664.60.13841361.10894.7
3.66-4.034.50.12341081.10894.2
4.03-4.614.50.10941011.01993.1
4.61-5.84.50.10841681.04492.8
5.8-254.40.10542971.07489.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SHARPphasing
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.9_1675)refinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→24.921 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 1758 4.49 %
Rwork0.1988 --
obs0.2009 37767 94.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.06 Å2 / Biso mean: 34.672 Å2 / Biso min: 8.12 Å2
Refinement stepCycle: final / Resolution: 2.7→24.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7561 900 0 111 8572
Biso mean---28.6 -
Num. residues----971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158768
X-RAY DIFFRACTIONf_angle_d1.33612040
X-RAY DIFFRACTIONf_chiral_restr0.0721325
X-RAY DIFFRACTIONf_plane_restr0.0071352
X-RAY DIFFRACTIONf_dihedral_angle_d14.9433304
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4350X-RAY DIFFRACTION7.781TORSIONAL
12B4350X-RAY DIFFRACTION7.781TORSIONAL
13C4350X-RAY DIFFRACTION7.781TORSIONAL
14D4350X-RAY DIFFRACTION7.781TORSIONAL
15E4350X-RAY DIFFRACTION7.781TORSIONAL
16F4350X-RAY DIFFRACTION7.781TORSIONAL
21O390X-RAY DIFFRACTION7.781TORSIONAL
22P390X-RAY DIFFRACTION7.781TORSIONAL
23Q390X-RAY DIFFRACTION7.781TORSIONAL
24R390X-RAY DIFFRACTION7.781TORSIONAL
25S390X-RAY DIFFRACTION7.781TORSIONAL
26T390X-RAY DIFFRACTION7.781TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.73550.33641360.27363057319394
2.7355-2.77630.39571430.2763052319596
2.7763-2.81960.33721460.28283079322595
2.8196-2.86580.32661420.25973104324696
2.8658-2.91510.27451470.26293017316495
2.9151-2.96810.26811440.25063059320395
2.9681-3.02510.31311440.24263110325495
3.0251-3.08670.31821420.24223089323196
3.0867-3.15370.30871510.23693037318895
3.1537-3.22690.32821450.22273040318595
3.2269-3.30740.29881420.22842951309393
3.3074-3.39660.24251470.21553064321195
3.3966-3.49630.2581460.20613038318495
3.4963-3.60890.22111490.19263050319995
3.6089-3.73740.26431520.18923001315394
3.7374-3.88650.26261470.17893061320895
3.8865-4.06270.22021360.18033061319795
4.0627-4.27590.21161450.16193000314594
4.2759-4.54230.19851320.15322936306891
4.5423-4.89060.1891380.15093025316394
4.8906-5.37820.18461320.16522969310193
5.3782-6.14630.23461410.18593001314293
6.1463-7.70550.19711410.19842937307892
7.7055-24.9210.21171300.18962946307691

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