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- PDB-5yc2: Crystal structure of inner membrane protein Bqt4 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5yc2
TitleCrystal structure of inner membrane protein Bqt4 in complex with telomeric protein Rap1
Components
  • DNA-binding protein rap1
  • Ubiquitin-like protein SMT3,Bouquet formation protein 4
KeywordsMEMBRANE PROTEIN / Choromosome organization / Teleomere bouquet / Nuclear envelope / Spore formation
Function / homology
Function and homology information


meiotic telomere tethering at nuclear periphery / telomere-nuclear envelope anchor activity / nuclear membrane complex Bqt3-Bqt4 / meiotic attachment of telomeric heterochromatin to spindle pole body / meiotic spindle pole body / nucleus leading edge / mitotic telomere tethering at nuclear periphery / meiotic attachment of telomere to nuclear envelope / chromosome, telomeric repeat region / protection from non-homologous end joining at telomere ...meiotic telomere tethering at nuclear periphery / telomere-nuclear envelope anchor activity / nuclear membrane complex Bqt3-Bqt4 / meiotic attachment of telomeric heterochromatin to spindle pole body / meiotic spindle pole body / nucleus leading edge / mitotic telomere tethering at nuclear periphery / meiotic attachment of telomere to nuclear envelope / chromosome, telomeric repeat region / protection from non-homologous end joining at telomere / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / meiotic telomere clustering / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / telomere maintenance via telomere lengthening / shelterin complex / SUMOylation of DNA replication proteins / septin ring / SUMOylation of SUMOylation proteins / nuclear telomere cap complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / telomere capping / SUMOylation of chromatin organization proteins / nuclear inner membrane / telomeric DNA binding / ubiquitin-like protein ligase binding / protein sumoylation / telomere organization / telomere maintenance / condensed nuclear chromosome / PML body / protein tag activity / nuclear envelope / cell division / regulation of DNA-templated transcription / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Bouquet formation protein 4 / S. pombe DNA-binding protein Rap1, C-terminal / Transcription regulator HTH, APSES-type DNA-binding domain / KilA, N-terminal/APSES-type HTH, DNA-binding / HTH APSES-type DNA-binding domain superfamily / APSES-type HTH DNA-binding domain profile. / KilA-N / Rap1, DNA-binding domain / Rap1, DNA-binding / TE2IP/Rap1 ...Bouquet formation protein 4 / S. pombe DNA-binding protein Rap1, C-terminal / Transcription regulator HTH, APSES-type DNA-binding domain / KilA, N-terminal/APSES-type HTH, DNA-binding / HTH APSES-type DNA-binding domain superfamily / APSES-type HTH DNA-binding domain profile. / KilA-N / Rap1, DNA-binding domain / Rap1, DNA-binding / TE2IP/Rap1 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / BRCT domain profile. / BRCT domain / Homeobox-like domain superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Bouquet formation protein 4 / Ubiquitin-like protein SMT3 / DNA-binding protein rap1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Schizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 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 6, 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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like protein SMT3,Bouquet formation protein 4
B: DNA-binding protein rap1
C: Ubiquitin-like protein SMT3,Bouquet formation protein 4
D: DNA-binding protein rap1


Theoretical massNumber of molelcules
Total (without water)51,1484
Polymers51,1484
Non-polymers00
Water59433
1
A: Ubiquitin-like protein SMT3,Bouquet formation protein 4
B: DNA-binding protein rap1


Theoretical massNumber of molelcules
Total (without water)25,5742
Polymers25,5742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-7 kcal/mol
Surface area11700 Å2
MethodPISA
2
C: Ubiquitin-like protein SMT3,Bouquet formation protein 4
D: DNA-binding protein rap1


Theoretical massNumber of molelcules
Total (without water)25,5742
Polymers25,5742
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-7 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.154, 51.293, 79.669
Angle α, β, γ (deg.)94.920, 100.560, 105.000
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 23570.859 Da / Num. of mol.: 2 / 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12306, UniProt: O60158
#2: Protein/peptide DNA-binding protein rap1


Mass: 2003.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Bqt4 binding motif of telomeric protein Rap1
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: rap1, SPBC1778.02 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96TL7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.5 Å3/Da / Density % sol: 50.71 % / Description: Snowflake
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethyleneglycol 4000.
Temp details: crystal culture in cold room

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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: Dec 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.7→39.056 Å / Num. obs: 12761 / % possible obs: 98 % / Redundancy: 1 % / Biso Wilson estimate: 46.84 Å2 / Net I/σ(I): 1.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.428 / CC1/2: 0.894 / Rpim(I) all: 0.216 / Rrim(I) all: 0.391 / Χ2: 0.501 / % possible all: 94.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YBX

5ybx


Resolution: 2.704→39.056 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 28.09
RfactorNum. reflection% reflection
Rfree0.2493 626 4.91 %
Rwork0.2022 --
obs0.2044 12761 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.01 Å2 / Biso mean: 53.5988 Å2 / Biso min: 26.7 Å2
Refinement stepCycle: final / Resolution: 2.704→39.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 0 33 3410
Biso mean---43.45 -
Num. residues----431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023448
X-RAY DIFFRACTIONf_angle_d0.4814665
X-RAY DIFFRACTIONf_chiral_restr0.043517
X-RAY DIFFRACTIONf_plane_restr0.004615
X-RAY DIFFRACTIONf_dihedral_angle_d11.7942156
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.704-2.9760.32411560.2759296896
2.976-3.40640.26071630.234304598
3.4064-4.29090.2491490.1836307398
4.2909-100.21941580.182304998
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)
16.3323-0.85912.94776.79342.25244.69170.3872-0.68190.23641.0369-0.13670.2328-0.2053-0.4555-0.19520.5979-0.15210.0660.5006-0.05930.427934.788643.995693.4983
24.82871.18470.07132.13712.42088.0290.1759-0.2413-0.33790.4499-0.55960.4720.1024-1.14390.31920.46320.0141-0.0580.5168-0.09470.471227.269940.606786.9811
31.57981.13042.09640.93681.43346.13350.22720.0288-0.09460.36590.0093-0.17090.4848-0.1606-0.24930.38460.0391-0.00370.32290.01360.438825.904633.578372.235
42.82222.39761.50635.48950.46555.67750.390.11750.4643-0.00450.43090.6009-0.0024-0.4353-0.75470.2790.00490.03260.42350.05580.45518.986237.073856.85
54.14771.006-1.90562.50870.29744.94060.0601-0.1791-0.0420.05390.3057-0.4126-0.2120.1627-0.37950.2208-0.02330.03150.3474-0.04830.365124.504842.641365.046
62.1313.1329-2.00327.7956-4.46872.6304-0.02630.9845-0.0875-0.17660.36090.78970.0465-0.8388-0.21360.5069-0.03780.02950.60530.06020.558410.30638.59753.6082
73.11131.2611-2.12694.36571.09648.970.34110.1633-0.21640.6556-0.1728-0.67360.4844-0.0558-0.22330.5642-0.084-0.09630.34910.06250.437118.165145.1612129.3321
88.44651.2166-0.62795.06850.11195.23460.67450.0227-0.5660.8538-0.003-1.47150.68250.502-0.35470.5795-0.0085-0.18770.3527-0.07080.760524.494154.5202132.5875
90.186-0.36190.86230.5803-1.75335.7139-0.1650.02490.0780.36970.1167-0.1236-0.7898-0.38850.11450.7258-0.0652-0.02250.4079-0.16030.533316.495860.789117.1384
103.7179-0.12671.12154.2337-0.60775.2036-0.1049-0.25480.20430.21470.04540.1065-0.20310.05490.05720.3768-0.06240.0290.3521-0.01560.30913.550959.2044100.6755
118.0146-3.2473-0.48282.0324-1.92978.3027-0.2110.7564-0.02250.7617-0.14570.227-0.02570.75490.26730.4674-0.05080.03610.4951-0.03180.567319.526866.721490.0454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 44 )A11 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 64 )A45 - 64
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 114 )A65 - 114
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 145 )A115 - 145
5X-RAY DIFFRACTION5chain 'A' and (resid 146 through 212 )A146 - 212
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 17 )B4 - 17
7X-RAY DIFFRACTION7chain 'C' and (resid 13 through 54 )C13 - 54
8X-RAY DIFFRACTION8chain 'C' and (resid 55 through 74 )C55 - 74
9X-RAY DIFFRACTION9chain 'C' and (resid 75 through 98 )C75 - 98
10X-RAY DIFFRACTION10chain 'C' and (resid 99 through 212 )C99 - 212
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 17 )D3 - 17

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