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- PDB-4i79: Crystal structure of human NUP43 -

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Basic information

Entry
Database: PDB / ID: 4i79
TitleCrystal structure of human NUP43
Components
  • Nucleoporin Nup43
  • floating chain, unknown sequence
KeywordsCELL CYCLE / Structural Genomics Consortium / SGC / WD40 repeat
Function / homology
Function and homology information


nuclear pore outer ring / Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript ...nuclear pore outer ring / Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / HCMV Late Events / chromosome segregation / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / kinetochore / HCMV Early Events / Separation of Sister Chromatids / protein transport / nuclear envelope / snRNP Assembly / nuclear speck / cell division / SARS-CoV-2 activates/modulates innate and adaptive immune responses / nucleoplasm / cytosol
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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. ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsXu, C. / Tempel, W. / Li, Z. / He, H. / Wernimont, A.K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Febs Lett. / Year: 2015
Title: Crystal structure of human nuclear pore complex component NUP43.
Authors: Xu, C. / Li, Z. / He, H. / Seitova, A. / Wernimont, A. / Li, Y. / Loppnau, P. / Min, J.
History
DepositionNov 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Other
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Dec 30, 2015Group: Database references
Revision 1.4May 10, 2017Group: Other / Structure summary
Revision 1.5Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin Nup43
B: Nucleoporin Nup43
C: floating chain, unknown sequence


Theoretical massNumber of molelcules
Total (without water)89,24235
Polymers89,2423
Non-polymers032
Water5,008278
1
A: Nucleoporin Nup43


Theoretical massNumber of molelcules
Total (without water)44,22914
Polymers44,2291
Non-polymers013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoporin Nup43


Theoretical massNumber of molelcules
Total (without water)44,22920
Polymers44,2291
Non-polymers019
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: floating chain, unknown sequence


  • defined by software
  • 784 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)7841
Polymers7841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.736, 161.964, 58.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsbiological unit has not been determined.

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Components

#1: Protein Nucleoporin Nup43 / Nup107-160 subcomplex subunit Nup43 / p42


Mass: 44228.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP43 / Plasmid: pFBOH-LIC / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NFH3
#2: Protein/peptide floating chain, unknown sequence


Mass: 783.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFBOH-LIC / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 32 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG-3350, 0.1 M ammonium sulfate, 0.1 M sodium Hepes, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→80.982 Å / Num. all: 77846 / Num. obs: 77846 / % possible obs: 100 % / Redundancy: 7.4 % / Rsym value: 0.078 / Net I/σ(I): 15.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.847.40.940.883285112240.94100
1.84-1.967.40.5311.478984106160.531100
1.96-2.097.50.2992.674622100130.299100
2.09-2.267.40.2083.76932993370.208100
2.26-2.477.50.1445.36425186080.144100
2.47-2.777.40.0957.95835678490.095100
2.77-3.27.40.0611.95105369280.06100
3.2-3.917.20.03915.44267959150.039100
3.91-5.537.10.03215.93317946510.032100
5.53-47.216.70.03312.51820427050.03399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3cfs, 4aow, 2xzm.

3cfs

4aow

2xzm
PDB Unreleased entry


Resolution: 1.75→45 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1992 / WRfactor Rwork: 0.1694 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8631 / SU B: 4.722 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1022 / SU Rfree: 0.1011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: COMMENT BY AUTHOR: AMBIGUOUS ELECTRON DENSITY AROUND RESIDUES 329 THROUGH 331 OF CHAINS A AND B.
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 2490 3.2 %thin shells (sftools)
Rwork0.1811 ---
obs0.1821 77783 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.15 Å2 / Biso mean: 29.118 Å2 / Biso min: 13.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å2-0 Å20 Å2
2---1.65 Å2-0 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4911 0 32 278 5221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195303
X-RAY DIFFRACTIONr_bond_other_d0.0030.024810
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9217316
X-RAY DIFFRACTIONr_angle_other_deg0.79311073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2625705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47124.351239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36215802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5871524
X-RAY DIFFRACTIONr_chiral_restr0.0950.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021273
X-RAY DIFFRACTIONr_mcbond_it1.5421.4972656
X-RAY DIFFRACTIONr_mcbond_other1.5421.4962655
X-RAY DIFFRACTIONr_mcangle_it2.4682.2313325
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 295 -
Rwork0.269 5361 -
all-5656 -
obs--99.98 %
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)
10.7620.04930.32393.761-0.42240.9047-0.00660.0430.0063-0.06380.02240.0324-0.02080.0008-0.01580.03020.0042-0.00220.0865-0.00180.049519.0376-23.7957-16.613
20.99690.401-0.46183.10340.35781.2953-0.03460.0585-0.0422-0.07120.0336-0.0060.0777-0.01770.0010.01460.0078-0.01260.0617-0.00090.031820.412412.131312.685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 380
2X-RAY DIFFRACTION1A401 - 413
3X-RAY DIFFRACTION1A501 - 630
4X-RAY DIFFRACTION2B4 - 380
5X-RAY DIFFRACTION2B401 - 428
6X-RAY DIFFRACTION2B501 - 648

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