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- PDB-5uaz: Crystal structure of the yeast nucleoporin -

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Basic information

Entry
Database: PDB / ID: 5uaz
TitleCrystal structure of the yeast nucleoporin
ComponentsNucleoporin NUP53
KeywordsPROTEIN TRANSPORT / nucleoporin / Nuclear Pore Complex / nucleocytoplasmic transport / dimerization domain
Function / homology
Function and homology information


response to spindle checkpoint signaling / regulation of protein desumoylation / nuclear pore central transport channel / nuclear pore organization / nuclear pore nuclear basket / protein localization to kinetochore / NLS-bearing protein import into nucleus / structural constituent of nuclear pore / nucleocytoplasmic transport / regulation of mitotic nuclear division ...response to spindle checkpoint signaling / regulation of protein desumoylation / nuclear pore central transport channel / nuclear pore organization / nuclear pore nuclear basket / protein localization to kinetochore / NLS-bearing protein import into nucleus / structural constituent of nuclear pore / nucleocytoplasmic transport / regulation of mitotic nuclear division / mRNA transport / nuclear pore / phospholipid binding / protein import into nucleus / nuclear envelope / single-stranded DNA binding / nuclear membrane / cell division / positive regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
RNA-recognition motif (RRM) Nup35-type domain / Nup53/35/40-type RNA recognition motif / RNA-recognition motif (RRM) Nup35-type domain profile. / RRM (RNA recognition motif) domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.753 Å
AuthorsBlus, B.J. / Blobel, G.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Crystal structure of the yeast nucleoporin
Authors: Blus, B.J. / Blobel, G.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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: Nucleoporin NUP53
B: Nucleoporin NUP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9634
Polymers24,8392
Non-polymers1242
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-11 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.497, 100.487, 85.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-508-

HOH

21B-533-

HOH

31B-561-

HOH

41B-566-

HOH

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Components

#1: Protein Nucleoporin NUP53 / Nuclear pore protein NUP53


Mass: 12419.255 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NUP53, YMR153W, YM8520.02 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03790
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.79 Å3/Da / Density % sol: 31.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% (wt/vol) PEG 3350 0.2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen cryo-stream
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2016
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.753→43.282 Å / Num. obs: 18275 / % possible obs: 99.85 % / Redundancy: 13.3 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 21.66
Reflection shellResolution: 1.753→1.816 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 2.55 / CC1/2: 0.832 / % possible all: 98.72

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P3D

3p3d


Resolution: 1.753→43.282 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.4
Details: Phenix RESTRAINTS LIBRARY GEOSTD + MON.LIB. + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1988 895 4.9 %
Rwork0.1564 --
obs0.1585 18275 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.753→43.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 8 135 1611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131555
X-RAY DIFFRACTIONf_angle_d1.252113
X-RAY DIFFRACTIONf_dihedral_angle_d15.17917
X-RAY DIFFRACTIONf_chiral_restr0.078236
X-RAY DIFFRACTIONf_plane_restr0.009264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7527-1.86250.26431510.20822820X-RAY DIFFRACTION99
1.8625-2.00630.20741640.17312832X-RAY DIFFRACTION100
2.0063-2.20820.20621520.15172870X-RAY DIFFRACTION100
2.2082-2.52770.19491490.15392872X-RAY DIFFRACTION100
2.5277-3.18450.21271240.17022958X-RAY DIFFRACTION100
3.1845-43.29510.18351550.1443029X-RAY DIFFRACTION100
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)
12.58931.80040.74492.0598-0.70152.04270.05070.0369-0.17580.0413-0.2547-0.20670.03060.247-0.04170.1570.00080.02180.1965-0.05180.185522.072812.1608-8.7506
21.0917-0.49190.65321.1459-0.10910.9504-0.19390.36830.4506-0.4896-0.2429-0.6149-0.57780.1105-0.0310.3442-0.01110.0250.35160.03340.340128.416613.8207-14.3079
31.10561.12370.50341.29420.38382.4783-0.1775-0.20360.1711-0.01970.1929-0.0820.31730.17850.00110.27420.07040.02360.2333-0.0330.212722.71459.4931-17.76
41.02350.72440.32170.99130.4821.03690.1964-0.2513-0.23960.2681-0.2536-0.21050.3115-0.0078-0.07180.2312-0.0432-0.01680.23090.01870.210424.13418.3492-4.0663
51.32040.1257-0.43581.1999-0.13570.42330.0603-0.20070.145-0.239-0.03910.1007-0.08990.0637-0.00470.2117-0.04060.02460.2578-0.07760.219713.680510.732-6.4174
62.480.1543-1.57522.86010.00891.01110.1363-0.1708-0.04570.23380.11630.07730.01890.12530.04240.1569-0.0232-0.01290.1649-0.01620.13961.393712.10296.078
70.07010.28320.15831.12110.45821.23610.1333-0.46460.278-0.04940.02110.54560.0989-0.7488-0.0140.2106-0.00370.03790.3541-0.02250.2711-7.249913.78699.4559
82.6842-0.4852-0.17373.47240.26552.8605-0.089-0.22110.08490.15660.21290.02680.0184-0.0170.00170.16250.0208-0.00450.1619-0.03650.14180.936712.26159.5715
90.7658-0.0566-1.02620.9242-0.55411.81990.128-0.1620.068-0.00790.0543-0.0457-0.51390.00750.00560.2929-0.04730.03920.2229-0.04720.21958.307614.88652.1192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -1:273 )A-1 - 273
2X-RAY DIFFRACTION2( CHAIN A AND RESID 274:283 )A274 - 283
3X-RAY DIFFRACTION3( CHAIN A AND RESID 284:312 )A284 - 312
4X-RAY DIFFRACTION4( CHAIN A AND RESID 313:330 )A313 - 330
5X-RAY DIFFRACTION5( CHAIN A AND RESID 331:355 )A331 - 355
6X-RAY DIFFRACTION6( CHAIN B AND RESID -1:273 )B-1 - 273
7X-RAY DIFFRACTION7( CHAIN B AND RESID 274:283 )B274 - 283
8X-RAY DIFFRACTION8( CHAIN B AND RESID 284:330 )B284 - 330
9X-RAY DIFFRACTION9( CHAIN B AND RESID 331:355 )B331 - 355

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