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- PDB-6a6w: Crystal structure of fission yeast inner membrane protein Bqt4 in... -

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Basic information

Entry
Database: PDB / ID: 6a6w
TitleCrystal structure of fission yeast inner membrane protein Bqt4 in complex with Sad1
Components
  • Bouquet formation protein 4
  • Spindle pole body-associated protein sad1
KeywordsMEMBRANE PROTEIN / Chromosome organization / Inner nuclear membrane protein / Bouquet formation / Spindle pole boday
Function / homology
Function and homology information


old mitotic spindle pole body / new mitotic spindle pole body / spindle pole body-nuclear membrane anchor activity / mitotic spindle pole body localization / Sad1-Kms1 LINC complex / inner plaque of mitotic spindle pole body / centromere clustering at the mitotic interphase nuclear envelope / meiotic telomere tethering at nuclear periphery / telomere-nuclear envelope anchor activity / nuclear membrane complex Bqt3-Bqt4 ...old mitotic spindle pole body / new mitotic spindle pole body / spindle pole body-nuclear membrane anchor activity / mitotic spindle pole body localization / Sad1-Kms1 LINC complex / inner plaque of mitotic spindle pole body / centromere clustering at the mitotic interphase nuclear envelope / 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 / mitotic telomere tethering at nuclear periphery / meiotic attachment of telomere to nuclear envelope / meiotic nuclear membrane microtubule tethering complex / mitotic spindle pole body / meiotic telomere clustering / nuclear envelope organization / interphase microtubule organizing center / nuclear inner membrane / protein-membrane adaptor activity / telomere organization / telomere maintenance / nuclear envelope / site of double-strand break / microtubule / cell division / DNA binding / nucleus / cytoplasm
Similarity search - Function
Bouquet formation protein 4 / 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 / SUN domain profile. / SUN domain / Sad1 / UNC-like C-terminal / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Bouquet formation protein 4 / Spindle pole body-associated protein sad1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.601 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
DepositionJun 29, 2018Deposition 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: Bouquet formation protein 4
B: Spindle pole body-associated protein sad1


Theoretical massNumber of molelcules
Total (without water)17,6872
Polymers17,6872
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-6 kcal/mol
Surface area8210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.951, 133.951, 87.394
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-208-

HOH

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Components

#1: Protein Bouquet formation protein 4


Mass: 15799.956 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Bqt4 (residue 2 to 140)
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: bqt4, SPBC19C7.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60158
#2: Protein/peptide Spindle pole body-associated protein sad1


Mass: 1886.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sad1 residues 88 to 101 with three extra residues (GPL) from N-terminal tag
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: sad1, SPBC12D12.01, SPBC16H5.01c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q09825
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 6.42 Å3/Da / Density % sol: 80.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4M Sodium malonate, pH7.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14717 / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.033 / Rrim(I) all: 0.12 / Χ2: 1.412 / Net I/σ(I): 6.2 / Num. measured all: 184255
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6412.80.7127210.8930.2070.7420.534100
2.64-2.6912.60.647140.8960.1880.6680.656100
2.69-2.7412.10.6117220.910.1820.6390.546100
2.74-2.8120.4877240.9340.1470.510.617100
2.8-2.8612.40.3957170.9610.1160.4120.648100
2.86-2.9313.40.327140.9780.090.3330.702100
2.93-313.40.2777120.9830.0770.2880.853100
3-3.0813.30.2457270.9860.0680.2540.847100
3.08-3.1713.20.2257240.9850.0640.2340.986100
3.17-3.2813.10.1937250.9840.0550.2011.305100
3.28-3.39130.1677270.9880.0490.1741.46100
3.39-3.5312.30.1597300.9880.0470.1661.839100
3.53-3.6911.60.1287260.9910.0390.1342.106100
3.69-3.8812.80.127310.9950.0350.1252.276100
3.88-4.1313.20.1037370.9960.0290.1072.47499.9
4.13-4.4512.80.0987480.9970.0280.1022.695100
4.45-4.8912.60.0917410.9970.0260.0942.488100
4.89-5.611.30.0827590.9970.0250.0862.059100
5.6-7.0512.60.0757730.9980.0210.0781.64799.9
7.05-5010.30.0548450.9990.0170.0571.43799.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YBX

5ybx


Resolution: 2.601→43.846 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 773 5.28 %
Rwork0.1822 13866 -
obs0.1837 14639 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.43 Å2 / Biso mean: 66.396 Å2 / Biso min: 34.53 Å2
Refinement stepCycle: final / Resolution: 2.601→43.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 0 15 1210
Biso mean---65.88 -
Num. residues----152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051223
X-RAY DIFFRACTIONf_angle_d0.7951659
X-RAY DIFFRACTIONf_chiral_restr0.049183
X-RAY DIFFRACTIONf_plane_restr0.009219
X-RAY DIFFRACTIONf_dihedral_angle_d15.703764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6006-2.76350.30011060.25692274238099
2.7635-2.97680.29731250.243822762401100
2.9768-3.27630.28251330.224922702403100
3.2763-3.75020.23281260.185623002426100
3.7502-4.7240.17611290.141323362465100
4.724-43.8520.1751540.17472410256498
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)
10.5812-0.8008-0.98014.38594.66935.44180.2896-0.1299-0.34020.92230.0945-0.83811.5468-0.3353-0.21161.1228-0.02640.06050.61750.04760.548-73.89257.8301-0.7551
24.7631-3.90183.65697.6846-2.29135.6111-0.0669-0.21-0.73950.1160.28961.27650.599-0.8664-0.36560.5466-0.06880.01890.50570.11830.5582-78.807423.2193-4.9297
32.0293-0.8349-1.47822.00230.5751.3185-1.0699-0.03750.91620.42840.8827-0.7672-0.53950.2887-0.11970.50540.0284-0.04940.37170.07440.4696-71.359231.9234-10.3469
46.0468-4.8134-1.56213.96870.83612.6977-0.3040.5126-0.13090.14980.5004-1.12190.17520.8057-0.31120.4746-0.02190.01340.6679-0.08250.7192-51.934224.9173-13.9974
58.73180.3565-1.37495.25022.03117.26890.0515-0.5084-0.35430.7134-0.18570.23910.0607-0.50790.12580.6663-0.00340.00690.38930.02440.4326-63.239723.9123-5.0576
62.72411.44220.05765.3897-4.06594.4576-0.1437-0.229-0.315-0.06190.3155-0.02030.15750.0276-0.17630.59980.0068-0.0110.39880.02790.427-65.69639.6623-6.1297
76.3904-1.4907-0.62995.42881.69672.7305-0.16550.1703-0.1348-0.13580.24810.22480.3716-0.0808-0.00640.64-0.0685-0.01960.38160.0820.3621-67.234616.6134-13.4961
88.04021.8829-3.99545.11330.24942.37230.4137-1.31770.79662.08440.0897-0.3156-1.75820.4635-0.76020.833-0.13330.01550.7836-0.10420.8589-56.024832.8912-2.7622
92.0467-2.4334-2.33583.43162.30823.08440.0096-1.3773-0.73771.27350.1339-1.540.34930.2782-0.26490.74760.0341-0.2230.7242-0.00980.7244-53.001121.0535-4.7835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 15 )A6 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 25 )A16 - 25
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 32 )A26 - 32
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 41 )A33 - 41
5X-RAY DIFFRACTION5chain 'A' and (resid 42 through 65 )A42 - 65
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 99 )A66 - 99
7X-RAY DIFFRACTION7chain 'A' and (resid 100 through 140 )A100 - 140
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 89 )B85 - 89
9X-RAY DIFFRACTION9chain 'B' and (resid 90 through 101 )B90 - 101

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