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- PDB-6x05: Nup133 (aa55-481) from S. cerevisiae bound by VHH-SAN4 -

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Basic information

Entry
Database: PDB / ID: 6x05
TitleNup133 (aa55-481) from S. cerevisiae bound by VHH-SAN4
Components
  • Nucleoporin NUP133
  • VHH-SAN4
KeywordsSTRUCTURAL PROTEIN / Nucleoporin / Nanobody
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / nuclear pore localization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / tRNA export from nucleus / SUMOylation of SUMOylation proteins ...mRNA export from nucleus in response to heat stress / nuclear pore localization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / tRNA export from nucleus / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / nuclear pore / subtelomeric heterochromatin formation / protein import into nucleus / nuclear envelope / double-strand break repair / cellular response to heat / nuclear membrane / chromosome, telomeric region / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Nuclear pore complex protein Nup133-like / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNordeen, S.A. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM077537 United States
CitationJournal: Nat Commun / Year: 2020
Title: Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif.
Authors: Nordeen, S.A. / Turman, D.L. / Schwartz, T.U.
History
DepositionMay 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_mon_prot_cis / struct_sheet_range
Item: _entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id ..._entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_close_contact.label_alt_id_1 / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 18, 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
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: Nucleoporin NUP133
K: VHH-SAN4


Theoretical massNumber of molelcules
Total (without water)62,0002
Polymers62,0002
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.381, 154.693, 41.423
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Nucleoporin NUP133 / Nuclear pore protein NUP133


Mass: 48493.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NUP133, RAT3, YKR082W, YKR402 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR / References: UniProt: P36161
#2: Antibody VHH-SAN4


Mass: 13505.921 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 24% PEG 3,350, 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→59.57 Å / Num. obs: 39093 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 32.43 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.052 / Net I/σ(I): 19.3
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.48 / Num. unique obs: 3828 / CC1/2: 0.51 / Rpim(I) all: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q9T

4q9t


Resolution: 2.1→59.57 Å / SU ML: 0.2187 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1084
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2188 1843 5.12 %
Rwork0.1742 34124 -
obs0.1765 35967 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→59.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 0 235 4147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824002
X-RAY DIFFRACTIONf_angle_d1.04785421
X-RAY DIFFRACTIONf_chiral_restr0.0595614
X-RAY DIFFRACTIONf_plane_restr0.0061688
X-RAY DIFFRACTIONf_dihedral_angle_d12.7118538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.28391390.24542574X-RAY DIFFRACTION99.82
2.16-2.220.29011400.22662586X-RAY DIFFRACTION99.89
2.22-2.290.25031390.20592591X-RAY DIFFRACTION99.89
2.29-2.370.27161390.20532559X-RAY DIFFRACTION99.89
2.37-2.470.23641400.19752606X-RAY DIFFRACTION100
2.47-2.580.26491420.192621X-RAY DIFFRACTION100
2.58-2.720.24491380.1892560X-RAY DIFFRACTION99.93
2.72-2.890.2441400.18842601X-RAY DIFFRACTION99.78
2.89-3.110.24431430.19412637X-RAY DIFFRACTION99.93
3.11-3.420.20531420.16352631X-RAY DIFFRACTION100
3.42-3.920.22171430.15232646X-RAY DIFFRACTION99.86
3.92-4.940.14411440.13162682X-RAY DIFFRACTION100
4.94-59.570.21731540.17882830X-RAY DIFFRACTION99.53
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)
14.72113900068-4.63530594813-2.318812529178.358231163242.557812572751.740708727290.2436699025590.07020027114220.725046362404-0.2868195904340.076324604323-0.297359443582-0.3161134026450.0213613521442-0.3378009407410.2677772159640.04467285179950.01255418039750.2870433617890.05696260771850.309630716289-5.2705343943.18211066787.54823542761
27.738160981622.295912470277.159793557561.110724127442.783649155278.19858393228-0.4963718511850.4714268922750.685531536087-0.1071186388170.0181917802790.0866075228689-0.3947140888890.5860242432750.470403804830.3718613184070.1037132817880.01866690615270.3252408459890.06250897446810.476882186652-22.568956932247.92893883419.63885573384
31.74869355032-1.663522138780.6821146313935.89144648992-1.024483369370.493651340624-0.150995886466-0.1316529384870.3131952659120.1679212275940.133356848730.151916314321-0.276356395022-0.2834462621960.005709159694210.3082650217540.1041690625170.04263730139810.3784968246510.01608393274150.303634074443-23.218603268237.916727824221.022960209
41.31662316607-0.174768786921-0.3976379457691.78525374631-1.665609096192.40081230994-0.07189602289660.0745854094718-0.0103074823886-0.05625186549870.07448183663810.06209077607690.0409454946378-0.142222409102-0.0002092573582150.2066153581830.02042141028860.0009963498377260.160238081247-0.02310764125970.15343362376-4.7547118547523.085968361917.6002102756
53.84661960704-1.107499011691.043187175696.9623836801-2.804154964272.926479798380.0105759336190.0789524527891-0.100841293993-0.4841062217280.3110395890070.6662083473090.275399197933-0.577446008969-0.3121311917180.227406244237-0.0292903738850.002631612219940.2924097605680.04798680524850.280508892689-17.9579233816-8.8536966902436.8567419971
68.54689995002-2.27504773776-1.971919094656.209937538073.007069085866.983788711880.356920275524-0.2628595252160.5921160747340.316063774711-0.1177139825540.149913728929-1.31540736274-0.0809467468376-0.2696717560540.3990272673230.06562908028650.010638568880.2128273299320.004479108912220.281014124744-12.200860426-2.1153635511341.2683485769
75.51274386301-1.641167252980.157356932815.26157041191-1.025228582067.55385887865-0.0991298826423-0.03068879769560.121958338370.01240702517240.158720897285-0.0839950133992-0.04880777010070.149348410707-0.04467799073440.1669323913690.00883942914786-0.004750652586970.1309900022450.02168537620620.175657863386-11.2098795787-10.230049732541.3860196596
82.74221086812-0.8119499991481.004473063668.27861780142-7.283092791447.86483426274-0.065035190481-0.1581541661990.03951652184910.2270518502130.3679524076860.639517448819-0.171120350423-0.340322446196-0.2891257602380.2007498879210.04916894796020.055598987710.2239914206970.002893791662230.241508573064-20.35962977160.20555395461637.6112671617
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 59 through 123 )AA59 - 1232 - 60
22chain 'A' and (resid 124 through 175 )AA124 - 17561 - 105
33chain 'A' and (resid 176 through 318 )AA176 - 318106 - 234
44chain 'A' and (resid 319 through 481 )AA319 - 481235 - 381
55chain 'K' and (resid 3 through 40 )KB3 - 401 - 38
66chain 'K' and (resid 41 through 60 )KB41 - 6039 - 58
77chain 'K' and (resid 61 through 98 )KB61 - 9859 - 96
88chain 'K' and (resid 99 through 122 )KB99 - 12297 - 120

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