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- PDB-5c2u: Ferredoxin-like domain of nucleoporin Nup54 bound to a nanobody -

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Basic information

Entry
Database: PDB / ID: 5c2u
TitleFerredoxin-like domain of nucleoporin Nup54 bound to a nanobody
Components
  • Nanobody
  • Nup54
KeywordsTRANSPORT PROTEIN / Nucleoporin Nup54 / Nup54 alpha-beta domain / Ferredoxin-like fold
Function / homology
Function and homology information


protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / structural constituent of nuclear pore / NLS-bearing protein import into nucleus
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nucleoporin 54kDa S homeolog isoform X2
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsChug, H. / Trakhanov, S. / Hulsmann, B.B. / Pleiner, T. / Gorlich, D.
CitationJournal: Science / Year: 2015
Title: Crystal structure of the metazoan Nup62Nup58Nup54 nucleoporin complex.
Authors: Chug, H. / Trakhanov, S. / Hulsmann, B.B. / Pleiner, T. / Gorlich, D.
History
DepositionJun 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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
B: Nanobody
A: Nup54


Theoretical massNumber of molelcules
Total (without water)30,0132
Polymers30,0132
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-9 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.860, 90.860, 57.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-286-

HOH

21B-288-

HOH

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Components

#1: Antibody Nanobody


Mass: 14341.810 Da / Num. of mol.: 1 / Fragment: Nanobody
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Gene: Immunoglobulin G / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Variant (production host): NEB SHuffle
#2: Protein Nup54


Mass: 15671.594 Da / Num. of mol.: 1
Fragment: Nup54 ferredoxin-like domain, UNP residues 212-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Variant (production host): NEB Express / References: UniProt: K9ZTJ6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: PEG 6000, Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2014 / Details: dynamically bendable mirror
RadiationMonochromator: Double crystal fixed-exit monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→46.5 Å / Num. obs: 40071 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.9 % / Biso Wilson estimate: 24.56 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.067 / Χ2: 0.914 / Net I/σ(I): 22.9 / Num. measured all: 672687
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.55-1.5915.90.4342.2121.726843324031032.35299.8
1.54-1.580.6481.6651.5232823313031071.7599.3
1.58-1.630.8051.2992.2542281308030801.349100
1.63-1.680.8741.113.0149328297529751.145100
1.68-1.730.9120.8833.9347710288628860.912100
1.73-1.790.9560.6285.5645778282628260.649100
1.79-1.860.9730.4357.7541680270027000.45100
1.86-1.940.9890.29711.6843896257925780.306100
1.94-2.020.9950.20116.1842755250925090.207100
2.02-2.120.9970.14421.2240219240524050.148100
2.12-2.240.9980.1125.2436037227022700.114100
2.24-2.370.9990.09130.6336809213821380.094100
2.37-2.540.9990.07336.2835444206620660.075100
2.54-2.740.9990.05843.0631443188718870.06100
2.74-30.9990.04650.6428163176017600.048100
3-3.350.9990.04259.5327232160116010.043100
3.35-3.870.9990.0464.3622755140414040.041100
3.87-4.740.9990.04164.218660120912090.042100
4.74-6.710.9990.04363.42151109559550.045100
6.710.9990.04361.1277215495480.04599.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4klm

4klm


Resolution: 1.55→29.741 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 2002 5 %Random selection
Rwork0.1764 38058 --
obs0.1779 40060 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.37 Å2 / Biso mean: 39.5108 Å2 / Biso min: 16.89 Å2
Refinement stepCycle: final / Resolution: 1.55→29.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 0 198 2066
Biso mean---44.89 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081942
X-RAY DIFFRACTIONf_angle_d1.0512637
X-RAY DIFFRACTIONf_chiral_restr0.043287
X-RAY DIFFRACTIONf_plane_restr0.005347
X-RAY DIFFRACTIONf_dihedral_angle_d14.477714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.55-1.58880.31041400.310126622802
1.5888-1.63170.2891420.272726982840
1.6317-1.67970.31181420.261426992841
1.6797-1.7340.29431410.24626852826
1.734-1.79590.26491420.226526962838
1.7959-1.86780.23811420.21226832825
1.8678-1.95280.21521430.190827172860
1.9528-2.05570.19931420.184127082850
2.0557-2.18450.20281430.181527062849
2.1845-2.35310.21561420.179127062848
2.3531-2.58980.20051440.179127272871
2.5898-2.96420.2181440.171727442888
2.9642-3.73350.21721450.164827632908
3.7335-29.74640.16071500.151628643014
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)
11.15410.3185-0.66978.7159-2.75931.67040.2474-0.13430.03810.4385-0.459-0.6903-0.14950.24980.18040.25370.02120.00440.2380.04780.182518.593240.234117.8831
24.2672-1.3176-2.19216.85651.25188.1577-0.02130.12080.3376-0.7691-0.108-0.3390.30420.54710.05340.30720.13690.090.24760.05530.203815.634445.43679.3551
36.7771.60510.24343.5812.41528.33420.1937-0.4440.431-0.0875-0.11660.5448-0.9899-0.4537-0.05740.38790.08510.05890.20030.01850.23159.968343.035316.3334
46.0386-0.9535-0.3642.9019-2.64490.63370.25650.09320.0095-0.3539-0.22340.5073-0.2872-0.00820.01190.30450.04480.03150.20790.03830.154312.425136.089115.458
50.5635-0.5513-0.13063.7169-0.90262.04150.18760.10850.1877-0.3546-0.3912-0.7799-0.11380.16890.24790.23890.07970.05110.22210.06990.300420.625945.556810.3475
69.6734.4485.2478.0772.22268.47980.08460.0803-0.40560.103-0.0608-0.46480.3810.3295-0.12840.25770.13580.05080.22070.00310.254621.226860.5768-2.3921
73.1018-0.7527-0.51652.55922.0697.2014-0.07750.3512-0.3542-0.84030.18590.07930.3979-0.00550.04710.3228-0.00880.02860.22930.01270.185217.072764.8145-12.6891
82.53351.2720.89867.75681.23542.398-0.01890.1747-0.41240.00220.1616-0.51520.37230.195-0.16260.21660.05840.02740.21750.00750.17720.77564.0756-7.0115
95.92483.08081.26757.71292.36784.8257-0.2179-0.06610.3881-0.06050.1462-0.6002-0.33650.4432-0.03630.22220.0472-0.02170.29170.01290.254525.617272.3479-2.8424
107.63943.026-4.28216.6955-2.84777.0545-0.0277-0.7182-0.10310.96540.0281-0.1130.03040.52880.06580.35310.1161-0.02150.23130.01760.219120.459569.7194.3019
113.01931.0755-2.324.35924.36088.5663-0.23720.01960.2032-0.03080.16721.0587-0.176-0.2873-0.04820.28230.08210.07660.17780.07880.45088.095765.1515-1.0298
121.19121.18650.74661.3989-1.81684.36830.1232-0.31080.15480.5963-0.1572-0.0366-0.69790.0433-0.01210.57860.07230.00130.2870.00970.42219.006761.930513.7795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 35 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 36 through 57 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 58 through 72 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 73 through 87 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 88 through 124 )B0
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 226 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 227 through 244 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 245 through 265 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 266 through 280 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 281 through 295 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 296 through 305 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 306 through 329 )A0

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