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- PDB-3i4r: Nup107(aa658-925)/Nup133(aa517-1156) complex, H.sapiens -

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Basic information

Entry
Database: PDB / ID: 3i4r
TitleNup107(aa658-925)/Nup133(aa517-1156) complex, H.sapiens
Components
  • Nuclear pore complex protein Nup107Nuclear pore
  • Nuclear pore complex protein Nup133
KeywordsPROTEIN TRANSPORT / STRUCTURAL PROTEIN / Kinetochore / mRNA transport / Nuclear pore complex / Nucleus / Phosphoprotein / Translocation / Transport / Polymorphism
Function / homology
Function and homology information


nephron development / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / somite development / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / paraxial mesoderm development / Transport of Ribonucleoproteins into the Host Nucleus ...nephron development / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / somite development / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / paraxial mesoderm development / 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 / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / 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 / neural tube development / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / female gonad development / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / neurogenesis / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / kinetochore / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / nuclear membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / membrane / cytosol
Similarity search - Function
Delta-Endotoxin; domain 1 - #50 / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Delta-Endotoxin; domain 1 / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear pore complex protein Nup107 / Nuclear pore complex protein Nup133
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53 Å
AuthorsWhittle, J.R.R. / Schwartz, T.U.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Architectural nucleoporins Nup157/170 and Nup133 are structurally related and descend from a second ancestral element.
Authors: Whittle, J.R. / Schwartz, T.U.
History
DepositionJul 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Nuclear pore complex protein Nup107
B: Nuclear pore complex protein Nup133


Theoretical massNumber of molelcules
Total (without water)106,0872
Polymers106,0872
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-15 kcal/mol
Surface area45000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.554, 133.047, 176.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear pore complex protein Nup107 / Nuclear pore / Nucleoporin Nup107 / 107 kDa nucleoporin


Mass: 32049.789 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FRAGMENT (UNP residues 658-925)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP107 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P57740
#2: Protein Nuclear pore complex protein Nup133 / / Nucleoporin Nup133 / 133 kDa nucleoporin


Mass: 74036.891 Da / Num. of mol.: 1 / Fragment: HELICAL DOMAIN (UNP residues 517-1156)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP133 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q8WUM0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 6.39 Å3/Da / Density % sol: 80.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.8 M sodium/potassium phosphate, 15 % glycerol, 2% PEG 3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. all: 29866 / Num. obs: 29866 / % possible obs: 85.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 115.2 Å2 / Rsym value: 0.157 / Net I/σ(I): 11.6
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 0.59 / % possible all: 40

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX1.4_4refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.53→37.63 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: -0 / σ(F): 1.34 / Phase error: 46.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.37 2336 9.96 %
Rwork0.315 21110 -
obs0.32 23446 68.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 136.409 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso max: 496.94 Å2 / Biso mean: 174.62 Å2 / Biso min: 42.69 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.53→37.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5161 0 0 0 5161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045540
X-RAY DIFFRACTIONf_angle_d0.8357435
X-RAY DIFFRACTIONf_dihedral_angle_d14.7531964
X-RAY DIFFRACTIONf_chiral_restr0.058880
X-RAY DIFFRACTIONf_plane_restr0.003937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5302-3.60220.4648150.448480X-RAY DIFFRACTION5
3.6022-3.68040.5481210.4163153X-RAY DIFFRACTION9
3.6804-3.7660.4203270.3889271X-RAY DIFFRACTION15
3.766-3.86010.5195420.4242389X-RAY DIFFRACTION22
3.8601-3.96430.3946550.4068540X-RAY DIFFRACTION30
3.9643-4.08080.4412680.3683785X-RAY DIFFRACTION43
4.0808-4.21240.34131170.35751074X-RAY DIFFRACTION60
4.2124-4.36270.4122040.35831523X-RAY DIFFRACTION87
4.3627-4.53710.37212000.32891732X-RAY DIFFRACTION97
4.5371-4.74320.36211890.32151751X-RAY DIFFRACTION98
4.7432-4.99280.36622030.31981767X-RAY DIFFRACTION99
4.9928-5.30480.40712000.3211804X-RAY DIFFRACTION100
5.3048-5.71310.42471900.34161806X-RAY DIFFRACTION100
5.7131-6.28560.44921800.34671840X-RAY DIFFRACTION100
6.2856-7.18960.39082180.33391801X-RAY DIFFRACTION100
7.1896-9.03740.322120.26111843X-RAY DIFFRACTION100
9.0374-37.63250.31871950.2831951X-RAY DIFFRACTION99
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)
11.68480.5059-2.12421.7132-0.27032.9384-0.33340.60520.1897-0.7356-0.09860.78640.3137-1.4378-1.42841.05890.7803-0.94651.1431-0.74570.6292-29.1259-17.183-22.0447
21.5255-1.67860.1173.87762.53473.4862-0.6603-0.8365-0.87461.86391.56780.91281.6774-0.24440.01630.4349-0.06750.26311.08650.10040.6613-39.512717.5915-9.0792
32.8852-0.89071.47920.4214-0.3662.34860.56090.6999-0.15010.5131-0.3711-0.4939-0.0927-0.3014-0.12460.65520.0131-0.10720.52380.09950.7234-18.2921.1521-5.2115
42.38180.59973.37261.63642.26835.35710.22650.4788-0.14240.21560.0768-0.1960.25260.60670.00130.55680.0193-0.05470.37370.18560.575-7.295666.14330.6403
51.87842.3205-0.15724.18190.76852.6986-0.5794-0.0895-0.68-0.04891.0856-1.20870.44250.3780.00120.55190.2031-0.0160.4544-0.01240.519-5.170814.82885.8031
62.31871.75970.84242.693-1.32132.85250.7292-0.00430.5649-0.5296-0.21150.89530.8493-0.4407-0.11150.1830.5791-0.5295-0.39470.62390.0611-11.6051-17.408125.2259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 667:746)A667 - 746
2X-RAY DIFFRACTION2(chain A and resid 747:803)A747 - 803
3X-RAY DIFFRACTION3(chain A and resid 804:924)A804 - 924
4X-RAY DIFFRACTION4(chain B and resid 518:871)B518 - 871
5X-RAY DIFFRACTION5(chain B and resid 872:1008)B872 - 1008
6X-RAY DIFFRACTION6(chain B and resid 1009:1156)B1009 - 1156

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