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- PDB-4ycz: Y-COMPLEX HUB (NUP85-NUP120-NUP145C-SEC13 COMPLEX) FROM M. THERMO... -

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Basic information

Entry
Database: PDB / ID: 4ycz
TitleY-COMPLEX HUB (NUP85-NUP120-NUP145C-SEC13 COMPLEX) FROM M. THERMOPHILA (A.K.A. T. HETEROTHALLICA)
Components
  • Fusion Protein of Sec13 and Nup145C
  • Nup120
  • Nup85
KeywordsSTRUCTURAL PROTEIN / Structural Protein Complex / Nuclear Pore Complex / Macromolecular Assemblies
Function / homology
Function and homology information


COPII-coated vesicle budding / nuclear pore outer ring / COPII vesicle coat / structural constituent of nuclear pore / mRNA transport / nuclear pore / positive regulation of TORC1 signaling / protein transport / nuclear membrane / Golgi membrane ...COPII-coated vesicle budding / nuclear pore outer ring / COPII vesicle coat / structural constituent of nuclear pore / mRNA transport / nuclear pore / positive regulation of TORC1 signaling / protein transport / nuclear membrane / Golgi membrane / structural molecule activity / nucleus
Similarity search - Function
Protein Sec13 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Sec13/Seh1 family / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nucleoporin peptidase S59-like / : / Quinoprotein alcohol dehydrogenase-like superfamily ...Protein Sec13 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Sec13/Seh1 family / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nucleoporin peptidase S59-like / : / Quinoprotein alcohol dehydrogenase-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Uncharacterized protein / Nuclear pore complex protein Nup85 / Protein transport protein SEC13 / Nup96 domain-containing protein
Similarity search - Component
Biological speciesThielavia heterothallica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.1 Å
AuthorsKelley, K. / Knockenhauer, K.E. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM077537 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Atomic structure of the Y complex of the nuclear pore.
Authors: Kelley, K. / Knockenhauer, K.E. / Kabachinski, G. / Schwartz, T.U.
History
DepositionFeb 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2May 27, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion Protein of Sec13 and Nup145C
B: Nup85
C: Nup120


Theoretical massNumber of molelcules
Total (without water)234,4833
Polymers234,4833
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-42 kcal/mol
Surface area77250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.984, 212.022, 170.643
Angle α, β, γ (deg.)90.00, 107.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fusion Protein of Sec13 and Nup145C /


Mass: 96425.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia heterothallica (fungus) / Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2306744, MYCTH_2306912 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-LOBSTR / References: UniProt: G2QES5, UniProt: G2QEZ2
#2: Protein Nup85


Mass: 103380.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia heterothallica (fungus) / Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2059413 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-LOBSTR / References: UniProt: G2Q7J4
#3: Protein Nup120


Mass: 34677.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia heterothallica (fungus) / Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2296711 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-LOBSTR / References: UniProt: G2Q2S2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.23
Details: 50mM Tris-HCL pH 8.23, 0.7M Ammonium Sulfate, 20mM EDTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 4.1→163 Å / Num. obs: 53692 / % possible obs: 98.2 % / Redundancy: 6.1 % / Rsym value: 0.19 / Net I/σ(I): 8.9
Reflection shellResolution: 4.1→4.25 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.9 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1951)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 4.1→163 Å / SU ML: 0.81 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 42.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3583 1975 7.24 %Random selection
Rwork0.3189 ---
obs0.3218 53648 97.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.1→163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10051 0 0 0 10051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210226
X-RAY DIFFRACTIONf_angle_d0.6414023
X-RAY DIFFRACTIONf_dihedral_angle_d9.0033054
X-RAY DIFFRACTIONf_chiral_restr0.0271757
X-RAY DIFFRACTIONf_plane_restr0.0041756

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