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- PDB-5yca: Crystal structure of inner membrane protein Bqt4 in complex with LEM2 -

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Basic information

Entry
Database: PDB / ID: 5yca
TitleCrystal structure of inner membrane protein Bqt4 in complex with LEM2
Components
  • Lap-Emerin-Man domain protein 2
  • Ubiquitin-like protein SMT3,Bouquet formation protein 4
KeywordsMEMBRANE PROTEIN / Chromosome organization / Membrane organization / Bouquet formation / Lap-Emerin-Man domain protein
Function / homology
Function and homology information


heterochromatin-nuclear membrane anchor activity / centromere-nuclear envelope anchor activity / subnuclear spatial organization of silent mating-type cassette heterochromatin / mitotic nuclear bridge midzone membrane domain / Sealing of the nuclear envelope (NE) by ESCRT-III / centromere clustering at the mitotic interphase nuclear envelope / meiotic telomere tethering at nuclear periphery / telomere-nuclear envelope anchor activity / nuclear membrane complex Bqt3-Bqt4 / CENP-A containing chromatin ...heterochromatin-nuclear membrane anchor activity / centromere-nuclear envelope anchor activity / subnuclear spatial organization of silent mating-type cassette heterochromatin / mitotic nuclear bridge midzone membrane domain / Sealing of the nuclear envelope (NE) by ESCRT-III / centromere clustering at the mitotic interphase nuclear envelope / meiotic telomere tethering at nuclear periphery / telomere-nuclear envelope anchor activity / nuclear membrane complex Bqt3-Bqt4 / CENP-A containing chromatin / pericentric heterochromatin organization / attachment of telomeric heterochromatin to nuclear envelope / protein localization to heterochromatin / mitotic telomere tethering at nuclear periphery / chromosome, centromeric core domain / nuclear membrane organization / meiotic attachment of telomere to nuclear envelope / nuclear inner membrane organization / chromosome, subtelomeric region / meiotic telomere clustering / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic spindle pole body / SUMO is proteolytically processed / SUMOylation of transcription factors / heterochromatin organization / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / centromeric DNA binding / rDNA heterochromatin / Transcriptional and post-translational regulation of MITF-M expression and activity / mitotic nuclear membrane reassembly / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / nuclear inner membrane / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / pericentric heterochromatin / telomere organization / telomere maintenance / nuclear periphery / condensed nuclear chromosome / meiotic cell cycle / protein tag activity / nuclear envelope / double-stranded DNA binding / nuclear membrane / cell division / chromatin binding / DNA binding / identical protein binding / nucleus / membrane / cytoplasm
Similarity search - Function
Bouquet formation protein 4 / Heh2/Src1-like / Transcription regulator HTH, APSES-type DNA-binding domain / KilA, N-terminal/APSES-type HTH, DNA-binding / HeH/LEM domain / HTH APSES-type DNA-binding domain superfamily / HeH/LEM domain / APSES-type HTH DNA-binding domain profile. / KilA-N / Man1/Src1, C-terminal ...Bouquet formation protein 4 / Heh2/Src1-like / Transcription regulator HTH, APSES-type DNA-binding domain / KilA, N-terminal/APSES-type HTH, DNA-binding / HeH/LEM domain / HTH APSES-type DNA-binding domain superfamily / HeH/LEM domain / APSES-type HTH DNA-binding domain profile. / KilA-N / Man1/Src1, C-terminal / MAN1, winged-helix domain / Man1-Src1p-C-terminal domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Bouquet formation protein 4 / Lap-Emerin-Man domain protein 2 / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Schizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsChen, Y. / Hu, C.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural insights into chromosome attachment to the nuclear envelope by an inner nuclear membrane protein Bqt4 in fission yeast.
Authors: Hu, C. / Inoue, H. / Sun, W. / Takeshita, Y. / Huang, Y. / Xu, Y. / Kanoh, J. / Chen, Y.
History
DepositionSep 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 22, 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

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Assembly

Deposited unit
A: Ubiquitin-like protein SMT3,Bouquet formation protein 4
C: Lap-Emerin-Man domain protein 2


Theoretical massNumber of molelcules
Total (without water)25,9432
Polymers25,9432
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The elution volume indicates that Bqt4-Lem2 complex is a monomer in Gel-filtration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-7 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.868, 53.128, 109.566
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-like protein SMT3,Bouquet formation protein 4


Mass: 23570.859 Da / Num. of mol.: 1 / Mutation: Q61E
Source method: isolated from a genetically manipulated source
Details: SUMO (residue 20 to 92) tagged Bqt4 (residue 8 to 140)
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: ATCC 204508 / S288c, 972 / ATCC 24843 / Gene: SMT3, YDR510W, D9719.15, bqt4, SPBC19C7.10 / Plasmid: pET28b-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12306, UniProt: O60158
#2: Protein/peptide Lap-Emerin-Man domain protein 2 / LEM domain protein 2


Mass: 2372.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Bqt4 binding motif of LEM2 protein
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: lem2, heh1, SPAC18G6.10 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q10109
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.51 Å3/Da / Density % sol: 50.96 % / Description: beautiful diamond
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1600 mM Sodium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.57→27.392 Å / Num. obs: 36534 / % possible obs: 99.9 % / Redundancy: 3 % / Biso Wilson estimate: 17.71 Å2 / Net I/σ(I): 3.7
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.264 / CC1/2: 0.978 / Rpim(I) all: 0.079 / Rrim(I) all: 0.276 / Χ2: 0.712 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.22data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YBX, 5YC2

5ybx

5yc2


Resolution: 1.57→27.392 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.69
RfactorNum. reflection% reflection
Rfree0.2136 1825 5 %
Rwork0.1894 --
obs0.1906 36534 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.96 Å2 / Biso mean: 23.33 Å2 / Biso min: 10.14 Å2
Refinement stepCycle: final / Resolution: 1.57→27.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 0 294 2068
Biso mean---31.38 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061823
X-RAY DIFFRACTIONf_angle_d1.1672470
X-RAY DIFFRACTIONf_chiral_restr0.046270
X-RAY DIFFRACTIONf_plane_restr0.006329
X-RAY DIFFRACTIONf_dihedral_angle_d13.4707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.57-1.61210.22571340.1856259699
1.6121-1.65950.23461430.18562620100
1.6595-1.71310.2281460.18562632100
1.7131-1.77430.21051390.18562640100
1.7743-1.84530.23681270.18562644100
1.8453-1.92930.20321220.18562661100
1.9293-2.03090.19851320.18562659100
2.0309-2.15810.20151510.18562636100
2.1581-2.32470.24771360.18562685100
2.3247-2.55850.23661440.20442687100
2.5585-2.92830.24251440.20442690100
2.9283-3.6880.18561500.18492725100
3.688-100.20441570.1732283499

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