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- PDB-5hay: Crystal structure of Chaetomium thermophilum Nup170 CTD Y905M L10... -

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Basic information

Entry
Database: PDB / ID: 5hay
TitleCrystal structure of Chaetomium thermophilum Nup170 CTD Y905M L1007M L1183M V1292M mutant
ComponentsNucleoporin NUP170
KeywordsTRANSPORT PROTEIN / Nucleocytoplasmic transport / Protein transport
Function / homology
Function and homology information


protein localization to nuclear inner membrane / nuclear pore inner ring / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / RNA export from nucleus / mRNA transport / protein import into nucleus / nuclear membrane
Similarity search - Function
Nucleoporin, helical domain, central subdomain / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup155-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Nucleoporin, helical domain, central subdomain / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup155-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsLin, D.H. / Fan, Y. / Hoelz, A.
Funding support United States, Germany, China, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM111461 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 T32 GM07616 United States
V Foundation for Cancer Research United States
Edward Mallinckrodt Jr. Foundation United States
Sidney Kimmel Foundation for Cancer Research United States
Heritage Medical Research Institute United States
German Research Foundation (DFG) Germany
Boehringer Ingelheim Fonds Germany
China Scholarship Council China
CitationJournal: Science / Year: 2016
Title: Architecture of the symmetric core of the nuclear pore.
Authors: Lin, D.H. / Stuwe, T. / Schilbach, S. / Rundlet, E.J. / Perriches, T. / Mobbs, G. / Fan, Y. / Thierbach, K. / Huber, F.M. / Collins, L.N. / Davenport, A.M. / Jeon, Y.E. / Hoelz, A.
History
DepositionDec 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2May 4, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
Revision 1.6Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoporin NUP170
B: Nucleoporin NUP170
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,3153
Polymers132,2922
Non-polymers231
Water86548
1
A: Nucleoporin NUP170
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1692
Polymers66,1461
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoporin NUP170


Theoretical massNumber of molelcules
Total (without water)66,1461
Polymers66,1461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.790, 101.700, 193.800
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 Nucleoporin NUP170 / Nuclear pore protein NUP170


Mass: 66145.867 Da / Num. of mol.: 2 / Mutation: Y905M, L1007M, L1183M, V1292M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: NUP170, CTHT_0036270 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S7B6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1 M MES (pH 6.3), 10 % PEG 20000, 10 % (v/v) ethylene glycol, 0.2 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 30966 / % possible obs: 98.2 % / Redundancy: 16.2 % / Net I/σ(I): 22.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 2.8→49.185 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 1544 5.01 %
Rwork0.2092 --
obs0.2113 30817 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→49.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8564 0 1 48 8613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038726
X-RAY DIFFRACTIONf_angle_d0.55511840
X-RAY DIFFRACTIONf_dihedral_angle_d12.0025296
X-RAY DIFFRACTIONf_chiral_restr0.0281338
X-RAY DIFFRACTIONf_plane_restr0.0031548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.89040.3761370.30772557X-RAY DIFFRACTION98
2.8904-2.99370.31461380.24222638X-RAY DIFFRACTION100
2.9937-3.11350.32961330.23712619X-RAY DIFFRACTION100
3.1135-3.25520.29491420.24442623X-RAY DIFFRACTION100
3.2552-3.42680.27821300.21952648X-RAY DIFFRACTION100
3.4268-3.64140.23421310.20832667X-RAY DIFFRACTION100
3.6414-3.92240.23861350.2112645X-RAY DIFFRACTION100
3.9224-4.3170.26191320.19132658X-RAY DIFFRACTION100
4.317-4.94110.21211450.17582683X-RAY DIFFRACTION100
4.9411-6.22330.26731530.22472717X-RAY DIFFRACTION100
6.2233-49.19270.21991680.19662818X-RAY DIFFRACTION100

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