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- PDB-7qhy: Structure of a Kluyveromyces lactis protein involved in RNA decay -

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Basic information

Entry
Database: PDB / ID: 7qhy
TitleStructure of a Kluyveromyces lactis protein involved in RNA decay
ComponentsNonsense-mediated decay protein 4,Nonsense-mediated decay protein 4,Nonsense mediated mRNA decay protein 4 (Nmd4)
KeywordsRNA BINDING PROTEIN / RNA decay / PIN domain / AlphaFold model / RoseTTAFold model
Function / homologynuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cytoplasm / Nonsense-mediated decay protein 4
Function and homology information
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsBarbarin-Bocahu, I. / Graille, M.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0003-04 France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study report.
Authors: Barbarin-Bocahu, I. / Graille, M.
History
DepositionDec 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nonsense-mediated decay protein 4,Nonsense-mediated decay protein 4,Nonsense mediated mRNA decay protein 4 (Nmd4)
B: Nonsense-mediated decay protein 4,Nonsense-mediated decay protein 4,Nonsense mediated mRNA decay protein 4 (Nmd4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0509
Polymers57,3932
Non-polymers6577
Water59433
1
A: Nonsense-mediated decay protein 4,Nonsense-mediated decay protein 4,Nonsense mediated mRNA decay protein 4 (Nmd4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8893
Polymers28,6971
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nonsense-mediated decay protein 4,Nonsense-mediated decay protein 4,Nonsense mediated mRNA decay protein 4 (Nmd4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1616
Polymers28,6971
Non-polymers4645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.82, 76.82, 174.31
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Nonsense-mediated decay protein 4,Nonsense-mediated decay protein 4,Nonsense mediated mRNA decay protein 4 (Nmd4) /


Mass: 28696.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: NMD4, KLLA0B08107g, KDRO_E07780 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CVZ8
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate pH 5.6, 0.9-1 M Li2SO4 and 0.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.45→43.77 Å / Num. obs: 22619 / % possible obs: 99.8 % / Redundancy: 59.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0115 / Net I/σ(I): 30.8
Reflection shellResolution: 2.45→2.51 Å / Rmerge(I) obs: 3.897 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1648 / CC1/2: 0.605 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model

Resolution: 2.45→43.76 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.301 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.299 / SU Rfree Blow DPI: 0.237 / SU Rfree Cruickshank DPI: 0.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1131 -RANDOM
Rwork0.2295 ---
obs0.2314 22619 99.9 %-
Displacement parametersBiso mean: 94.56 Å2
Baniso -1Baniso -2Baniso -3
1--2.8488 Å20 Å20 Å2
2---2.8488 Å20 Å2
3---5.6975 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.45→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 39 33 3013
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083050HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.974115HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1066SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes493HARMONIC5
X-RAY DIFFRACTIONt_it3050HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion406SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2313SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion18.83
LS refinement shellResolution: 2.45→2.47 Å
RfactorNum. reflection% reflection
Rfree0.4208 22 -
Rwork0.2762 --
obs0.2827 453 99.56 %
Refinement TLS params.

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)
13.8798-0.3852-1.44391.47470.12273.6170.3942-0.1462-0.2954-0.1462-0.398-0.563-0.2954-0.5630.0038-0.09420.2351-0.0130.2556-0.0439-0.138115.42360.619610.542
24.6879-0.99930.48623.08440.22924.32280.2366-0.2334-0.313-0.2334-0.274-0.2082-0.313-0.20820.0374-0.16550.2042-0.0382-0.0328-0.12710.11137.9638-27.1327-4.5071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-1 - 234
2X-RAY DIFFRACTION2{ B|* }B1 - 245
3X-RAY DIFFRACTION2{ B|* }B303 - 306

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