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- PDB-4j3h: Ring cycle for dilating and constricting the nuclear pore: struct... -

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Basic information

Entry
Database: PDB / ID: 4j3h
TitleRing cycle for dilating and constricting the nuclear pore: structure of a Nup54 homo-tetramer.
ComponentsNuclear pore complex protein Nup54Nuclear pore
KeywordsTRANSPORT PROTEIN / FG-repeat / mid-plane ring / gating / nup / Helical bundle / four helix bundle / transport channel / Nucleoporin / transport / nucleo-cytoplasmic transport / mRNP export / Nup58 / Nup62 / Karyopherin / Nup45 / Nuclear envelope / nuclear pore complex / nucleus / NPC
Function / homology
Function and homology information


Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins ...Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / Transcriptional regulation by small RNAs / Regulation of Glucokinase by Glucokinase Regulatory Protein / SUMOylation of DNA damage response and repair proteins / regulation of protein import into nucleus / protein localization to nuclear inner membrane / Regulation of HSF1-mediated heat shock response / nuclear pore central transport channel / nuclear pore organization / structural constituent of nuclear pore / nucleocytoplasmic transport / NLS-bearing protein import into nucleus / mRNA transport / protein targeting / nuclear pore / nuclear envelope / nuclear membrane / protein-containing complex binding / protein-containing complex / identical protein binding
Similarity search - Function
Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear pore complex protein Nup54
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5002 Å
AuthorsSolmaz, S.R. / Blobel, G. / Melcak, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Ring cycle for dilating and constricting the nuclear pore.
Authors: Solmaz, S.R. / Blobel, G. / Melcak, I.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear pore complex protein Nup54
B: Nuclear pore complex protein Nup54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3605
Polymers11,2402
Non-polymers1203
Water1,44180
1
A: Nuclear pore complex protein Nup54
B: Nuclear pore complex protein Nup54
hetero molecules

A: Nuclear pore complex protein Nup54
B: Nuclear pore complex protein Nup54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,72010
Polymers22,4804
Non-polymers2406
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+7/61
Buried area6620 Å2
ΔGint-104 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.320, 41.320, 198.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein/peptide Nuclear pore complex protein Nup54 / Nuclear pore / 54 kDa nucleoporin / Nucleoporin Nup54 / nucleoporin p54


Mass: 5619.972 Da / Num. of mol.: 2 / Fragment: UNP Residues 453-494 / Mutation: I458M I481M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nup54 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P70582
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 22-26% PEG 400, 0.1 M Na Hepes buffer pH 7.1 - 8.1, 0.2 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2011
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→35 Å / Num. all: 30293 / Num. obs: 30293 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 24 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.053 / Net I/σ(I): 38.4
Reflection shellResolution: 1.5→1.7 Å / Redundancy: 22 % / Mean I/σ(I) obs: 13.3 / Num. unique all: 9434 / Rsym value: 0.252 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5002→33.661 Å / SU ML: 0.34 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / Phase error: 17.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 3044 10.05 %Random
Rwork0.1919 ---
all0.1949 30293 --
obs0.1949 30293 99.77 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.117 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1764 Å2-0 Å2-0 Å2
2--0.1764 Å2-0 Å2
3----0.3529 Å2
Refinement stepCycle: LAST / Resolution: 1.5002→33.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms675 0 3 80 758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01701
X-RAY DIFFRACTIONf_angle_d1.24937
X-RAY DIFFRACTIONf_dihedral_angle_d13.461286
X-RAY DIFFRACTIONf_chiral_restr0.076101
X-RAY DIFFRACTIONf_plane_restr0.005123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5002-1.52360.2621400.25641264X-RAY DIFFRACTION99
1.5236-1.54860.26581470.24181193X-RAY DIFFRACTION100
1.5486-1.57530.23821390.21631232X-RAY DIFFRACTION99
1.5753-1.60390.27961390.21641236X-RAY DIFFRACTION100
1.6039-1.63480.20981330.20871242X-RAY DIFFRACTION100
1.6348-1.66810.23491350.2061235X-RAY DIFFRACTION100
1.6681-1.70440.19611440.20421257X-RAY DIFFRACTION100
1.7044-1.74410.2121390.19131221X-RAY DIFFRACTION100
1.7441-1.78770.22811400.18121245X-RAY DIFFRACTION100
1.7877-1.8360.19021310.18481221X-RAY DIFFRACTION100
1.836-1.890.24811380.18221252X-RAY DIFFRACTION100
1.89-1.9510.17571390.1781246X-RAY DIFFRACTION100
1.951-2.02080.22451340.17421221X-RAY DIFFRACTION100
2.0208-2.10170.19451340.18271261X-RAY DIFFRACTION100
2.1017-2.19730.19131420.18251233X-RAY DIFFRACTION100
2.1973-2.31310.24761380.17481247X-RAY DIFFRACTION100
2.3131-2.4580.2141360.17311237X-RAY DIFFRACTION100
2.458-2.64770.27551340.19291237X-RAY DIFFRACTION100
2.6477-2.9140.23621420.21611252X-RAY DIFFRACTION100
2.914-3.33540.25341420.20711220X-RAY DIFFRACTION100
3.3354-4.20090.18651390.16841262X-RAY DIFFRACTION100
4.2009-33.66970.22871390.20611235X-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)
10.8671-0.0887-0.19130.38380.55420.71720.0597-0.0657-0.0345-0.15450.02150.3942-0.1204-0.0901-0.00320.16220.00190.03290.12580.02210.17080.06939.4392130.327
25.7128-3.1529-5.43795.5152.7356.7713-0.4254-0.3378-0.56890.3440.4785-0.79210.39320.71010.01750.1587-0.02330.08940.1884-0.08340.241513.081529.4968121.5124
36.5139-1.7496-4.3372.90061.78057.6088-0.079-0.65990.41840.20350.3797-0.1677-0.24750.5067-0.22410.1839-0.01930.06140.2143-0.08340.232722.274724.2793107.6354
47.14955.92410.98465.2560.2021.31650.2548-0.38240.81960.4255-0.20770.1046-0.3379-0.26010.07390.1908-0.00870.08670.1108-0.07920.345933.035726.322298.718
53.43222.70620.29864.02211.74321.30070.0120.1356-0.2777-0.61640.00520.3239-0.01380.05790.03750.20980.0345-0.03250.1933-0.03610.160117.269915.665497.7067
67.1275-3.2376-4.71944.52673.44325.7591-0.3411-0.8104-0.40430.44640.2750.03130.56880.56230.03420.14760.0393-0.00630.18910.02050.099913.926216.9324113.1248
73.07810.5703-4.20751.5680.998.2547-0.0570.19210.0074-0.07590.1269-0.0044-0.1613-0.3777-0.02570.1315-0.00250.00770.1951-0.0190.0792.2724.9233121.5887
89.4295-5.0228-6.37134.09663.4824.32980.22210.8718-0.1382-0.601-0.03631.3166-0.3746-1.2332-0.1990.23890.0263-0.03250.34260.0350.3383-8.236432.39126.1671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and resseq 453:466
2X-RAY DIFFRACTION2chain 'A' and resseq 467:478
3X-RAY DIFFRACTION3chain 'A' and resseq 479:489
4X-RAY DIFFRACTION4chain 'A' and resseq 490:494
5X-RAY DIFFRACTION5chain 'B' and resseq 453:459
6X-RAY DIFFRACTION6chain 'B' and resseq 460:472
7X-RAY DIFFRACTION7chain 'B' and resseq 473:482
8X-RAY DIFFRACTION8chain 'B' and resseq 483:490

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