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- PDB-6waj: Crystal structure of the UBL domain of human NLE1 -

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Basic information

Entry
Database: PDB / ID: 6waj
TitleCrystal structure of the UBL domain of human NLE1
ComponentsNLE1
KeywordsPROTEIN BINDING / Crystal structure of the human NLE1-UBD domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


inner cell mass cell differentiation / hematopoietic stem cell homeostasis / skeletal system morphogenesis / negative regulation of mitotic cell cycle / somitogenesis / Notch signaling pathway / ribosomal large subunit biogenesis / kidney development / positive regulation of canonical Wnt signaling pathway / mitotic cell cycle ...inner cell mass cell differentiation / hematopoietic stem cell homeostasis / skeletal system morphogenesis / negative regulation of mitotic cell cycle / somitogenesis / Notch signaling pathway / ribosomal large subunit biogenesis / kidney development / positive regulation of canonical Wnt signaling pathway / mitotic cell cycle / nucleolus / nucleoplasm
Similarity search - Function
NLE / NLE (NUC135) domain / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats ...NLE / NLE (NUC135) domain / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Notchless protein homolog 1 / Notchless protein homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsHalabelian, L. / Zeng, H. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the UBL domain of human NLE1
Authors: Halabelian, L. / Zeng, H. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: NLE1


Theoretical massNumber of molelcules
Total (without water)10,5795
Polymers10,5791
Non-polymers04
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.546, 35.546, 205.994
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-101-

UNX

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Components

#1: Protein NLE1


Mass: 10578.938 Da / Num. of mol.: 1 / Fragment: UBL domain (UNP residues 1-97)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B4E074, UniProt: Q9NVX2*PLUS
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.78 Å3/Da / Density % sol: 30.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.5 M ammonium sulfate, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2020
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→41.2 Å / Num. obs: 6917 / % possible obs: 100 % / Redundancy: 19.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.016 / Rrim(I) all: 0.069 / Net I/σ(I): 21.7 / Num. measured all: 132701
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9420.80.8888934280.930.1960.9033.2100
9.11-41.211.90.0512511050.9990.0130.05141.499.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.19 Å
Translation2.5 Å34.19 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5DTC

5dtc


Resolution: 1.9→34.33 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 510 7.47 %
Rwork0.2485 6321 -
obs0.2491 6831 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.79 Å2 / Biso mean: 40.9211 Å2 / Biso min: 26.22 Å2
Refinement stepCycle: final / Resolution: 1.9→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms594 0 4 13 611
Biso mean--43.56 42.74 -
Num. residues----81
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-2.090.29591360.268515161652
2.09-2.390.27721130.251415221635
2.39-3.020.31241290.282215611690
3.02-34.330.22741320.236217221854

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