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- PDB-7nq6: High resolution crystal structure of C-terminal domain (residues ... -

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Basic information

Entry
Database: PDB / ID: 7nq6
TitleHigh resolution crystal structure of C-terminal domain (residues 715-866) of Nucleoporin-98
ComponentsNuclear pore complex protein Nup96
KeywordsNUCLEAR PROTEIN / Nup98 / 1.5A resolution
Function / homology
Function and homology information


structural constituent of nuclear pore / mRNA transport / nuclear pore / protein transport / nuclear membrane
Similarity search - Function
Nuclear pore complex protein NUP98-NUP96 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like
Similarity search - Domain/homology
Nuclear pore complex protein Nup96
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTrakhanov, S. / Goerlich, D. / Huyton, T.
CitationJournal: To Be Published
Title: High resolution crystal structure of C-terminal domain (residues 715-866) of Nucleoporin-98
Authors: Trakhanov, S. / Huyton, T. / Goerlich, D.
History
DepositionMar 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
A: Nuclear pore complex protein Nup96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5698
Polymers17,2751
Non-polymers2947
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-49 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.070, 72.070, 91.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Nuclear pore complex protein Nup96 / Nuclear pore complex protein Nup98 / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin Nup96 / ...Nuclear pore complex protein Nup98 / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin Nup96 / Nucleoporin Nup98


Mass: 17275.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: nup98 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB Express / References: UniProt: F6ZMG3
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.45 Å3/Da / Density % sol: 66 % / Description: rods
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8% (v/w) PEG 6000, 8% (v/v) 2-methy-2,4-pentanediol, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2018 / Details: Dynamically bendable mirrow
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→44.6 Å / Num. obs: 39371 / % possible obs: 100 % / Redundancy: 90.2 % / Biso Wilson estimate: 20.85 Å2 / CC1/2: 1 / Rpim(I) all: 0.015 / Rrim(I) all: 0.148 / Net I/σ(I): 33.4
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 37.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2857 / CC1/2: 0.42 / Rpim(I) all: 1.1 / Rrim(I) all: 0.47 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E0Q

5e0q


Resolution: 1.5→44.56 Å / SU ML: 0.1976 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.694
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1919 1969 5 %
Rwork0.1712 37401 -
obs0.1722 39370 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.83 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 14 215 1444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841271
X-RAY DIFFRACTIONf_angle_d0.96221727
X-RAY DIFFRACTIONf_chiral_restr0.0604186
X-RAY DIFFRACTIONf_plane_restr0.007229
X-RAY DIFFRACTIONf_dihedral_angle_d5.25161064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.35951380.33162607X-RAY DIFFRACTION100
1.54-1.580.27121380.28152623X-RAY DIFFRACTION99.93
1.58-1.630.30071370.25252617X-RAY DIFFRACTION99.85
1.63-1.680.26351380.22922631X-RAY DIFFRACTION100
1.68-1.740.26911400.21472642X-RAY DIFFRACTION99.96
1.74-1.810.21031380.19582636X-RAY DIFFRACTION99.96
1.81-1.890.20781400.18762645X-RAY DIFFRACTION99.96
1.89-1.990.2121380.17212647X-RAY DIFFRACTION100
1.99-2.110.19611420.16652665X-RAY DIFFRACTION100
2.11-2.280.16221400.16122662X-RAY DIFFRACTION100
2.28-2.510.17581410.15152682X-RAY DIFFRACTION100
2.51-2.870.15651420.15112712X-RAY DIFFRACTION100
2.87-3.610.18991440.15692745X-RAY DIFFRACTION100
3.61-44.560.17751530.15882887X-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)
13.30773854224-3.88885690160.5224281149534.822482894430.356386205933.97405624064-0.09516420779510.421333265141-0.415662558014-0.2038599110290.1064703693460.5052139669430.621093272638-0.491322761519-0.09282745633990.374195126229-0.10869052732-0.02929728727970.249306539977-0.01810025259720.228896516976-10.893644623317.6256355066-12.0618823078
26.369018539985.45358460789-1.735644159238.56396188073-3.334896194816.81449189396-0.110649348325-0.106564678434-0.8513333406880.00462866540865-0.0790180916843-0.4267937103150.5744087340070.04102160119140.2057620263960.2912051004180.00741104106220.01906213363960.1791630955070.03034797782690.29969831461-4.8586230263713.9354901584-3.9856199541
33.083960836911.99819850737-1.383361411773.59211482514-1.67625885391.803657721340.0126699672644-0.14690937582-0.186923064776-0.100684938658-0.0267974070390.1337038077180.289219879552-0.1396270618510.06337317726630.205970321795-0.0591202905056-0.01207962676090.2006357416440.02032049878420.162289460695-10.390423277919.9724231313-2.42608063456
45.43371949844-0.4935181019723.927039878982.537363745220.4261708216733.101141645050.137165244901-0.1069991295570.06964713554750.01245042874410.004094211117040.35538992619-0.229630703457-0.658202490734-0.03022718859440.1642862144340.0305021211687-0.00659220819050.2619032280370.02008330100910.168059273539-12.326988217132.885243004-8.22571588221
53.147509243140.4915209529560.285752593831.154794099471.073712642281.006321919170.220588490169-0.4975394878660.3010684048160.259887351625-0.4982385324980.7329819810530.278337471779-1.18150115290.09656108974020.187945028275-0.08722558593830.02906110504560.575725199609-0.04258763601340.327444980997-18.812624275127.08067878791.1418230354
63.01882727182.43910939117-3.049526862982.6133335774-1.818454991263.65209527374-0.05557802749450.1716534337620.258572000605-0.1385109810970.06547544264450.0321792007275-0.2389037299370.17810964223-0.111758082960.226862051163-0.0838333022544-0.0386717929320.3492840403270.08259549636930.2404091462757.512156584740.3211224855-5.10369707874
76.65578437921-1.87957339255-4.649799737327.877096889143.439215906463.89839321963-0.293021065331-0.5235650178870.1606554056540.3248635566920.286618551192-0.4562752643560.004338789547121.00647032268-0.04129396574680.262633829582-0.114181103372-0.05059544980920.388459185630.03277111364350.24531895586413.286681381545.39899574134.2842125782
89.97391234524-3.47668202598-5.720435493594.273882157353.450909837484.122668916460.03356665879460.2183208988320.366908079041-0.0117078739036-0.00360283085054-0.0926721350906-0.5810329232230.0210639905329-0.06188814962950.207263293603-0.0114947585792-0.05448156764530.1901548112030.05870690370370.258052040575-0.61560810794944.79064068295.59093585963
97.390401156780.3691958975521.964320042272.996299763430.9387848331484.18549780171-0.05006889529180.1923085081230.2333652191730.0245872594173-0.09940475909290.107531478376-0.086935138056-0.1947365091550.1057893941850.152100647278-0.0243676129836-0.01686603516080.1731935499170.02489304712340.152802288772-2.0457195472135.47485394684.22109198757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 715 through 726 )
2X-RAY DIFFRACTION2chain 'A' and (resid 727 through 738 )
3X-RAY DIFFRACTION3chain 'A' and (resid 739 through 781 )
4X-RAY DIFFRACTION4chain 'A' and (resid 782 through 793 )
5X-RAY DIFFRACTION5chain 'A' and (resid 794 through 804 )
6X-RAY DIFFRACTION6chain 'A' and (resid 805 through 825 )
7X-RAY DIFFRACTION7chain 'A' and (resid 826 through 833 )
8X-RAY DIFFRACTION8chain 'A' and (resid 834 through 844 )
9X-RAY DIFFRACTION9chain 'A' and (resid 845 through 866 )

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