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

ID or keywords:

Entry

Database: PDB / ID: 6a6w

Title

Crystal structure of fission yeast inner membrane protein Bqt4 in complex with Sad1

Components

Bouquet formation protein 4
Spindle pole body-associated protein sad1

Keywords

MEMBRANE PROTEIN / Chromosome organization / Inner nuclear membrane protein / Bouquet formation / Spindle pole boday

Function / homology

Function and homology information

old mitotic spindle pole body / spindle pole body-nuclear membrane anchor activity / mitotic spindle pole body insertion into the nuclear envelope / 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 ...
Similarity search - Function

Biological species

Schizosaccharomyces pombe (fission yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.601 Å

Authors

Chen, Y. / Hu, C.

Citation

Journal: 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

Deposition	Jun 29, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 5, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jul 10, 2019	Group: 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 1.3	Nov 22, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Full document	6a6w_full_validation.pdf.gz	433.2 KB	Display
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Related structure data

Related structure data	5yc2C 5ycaC 5ybxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ibj-d 6ibh-2 4c6s-d 5dnp-1 4z9a-d 7bf6-3 3n8i-d 6dzh-2 1dkd-4 7lg7-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Bouquet formation protein 4

B: Spindle pole body-associated protein sad1

17.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

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 number	182
Space group name H-M	P6₃22

Components on special symmetry positions

ID	Model	Components
1	1	A-208- HOH

#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 Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 6.42 Å³/Da / Density % sol: 80.84 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4M Sodium malonate, pH7.0

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Data collection

Diffraction

Mean temperature: 100 K / Ambient temp details: liquid nitrogen

Diffraction source

Source:

SYNCHROTRON / Site: NFPSS

/ Beamline: BL19U1 / Wavelength: 0.97775 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97775 Å / Relative weight: 1

Reflection

Resolution: 2.6→50 Å / Num. obs: 14717 / % possible obs: 100 % / Redundancy: 12.5 % / R_merge(I) obs: 0.115 / R_pim(I) all: 0.033 / R_rim(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 (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.6-2.64	12.8	0.712	721	0.893	0.207	0.742	0.534	100
2.64-2.69	12.6	0.64	714	0.896	0.188	0.668	0.656	100
2.69-2.74	12.1	0.611	722	0.91	0.182	0.639	0.546	100
2.74-2.8	12	0.487	724	0.934	0.147	0.51	0.617	100
2.8-2.86	12.4	0.395	717	0.961	0.116	0.412	0.648	100
2.86-2.93	13.4	0.32	714	0.978	0.09	0.333	0.702	100
2.93-3	13.4	0.277	712	0.983	0.077	0.288	0.853	100
3-3.08	13.3	0.245	727	0.986	0.068	0.254	0.847	100
3.08-3.17	13.2	0.225	724	0.985	0.064	0.234	0.986	100
3.17-3.28	13.1	0.193	725	0.984	0.055	0.201	1.305	100
3.28-3.39	13	0.167	727	0.988	0.049	0.174	1.46	100
3.39-3.53	12.3	0.159	730	0.988	0.047	0.166	1.839	100
3.53-3.69	11.6	0.128	726	0.991	0.039	0.134	2.106	100
3.69-3.88	12.8	0.12	731	0.995	0.035	0.125	2.276	100
3.88-4.13	13.2	0.103	737	0.996	0.029	0.107	2.474	99.9
4.13-4.45	12.8	0.098	748	0.997	0.028	0.102	2.695	100
4.45-4.89	12.6	0.091	741	0.997	0.026	0.094	2.488	100
4.89-5.6	11.3	0.082	759	0.997	0.025	0.086	2.059	100
5.6-7.05	12.6	0.075	773	0.998	0.021	0.078	1.647	99.9
7.05-50	10.3	0.054	845	0.999	0.017	0.057	1.437	99.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing
PDB_EXTRACT	3.24	data extraction

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.21	773	5.28 %
R_work	0.1822	13866	-
obs	0.1837	14639	99.4 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 147.43 Å² / B_iso mean: 66.396 Å² / B_iso min: 34.53 Å²

Refinement step

Cycle: final / Resolution: 2.601→43.846 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1195	0	0	15	1210
B_iso mean	-	-	-	65.88	-
Num. residues	-	-	-	-	152

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	1223
X-RAY DIFFRACTION	f_angle_d	0.795	1659
X-RAY DIFFRACTION	f_chiral_restr	0.049	183
X-RAY DIFFRACTION	f_plane_restr	0.009	219
X-RAY DIFFRACTION	f_dihedral_angle_d	15.703	764

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.6006-2.7635	0.3001	106	0.2569	2274	2380	99
2.7635-2.9768	0.2973	125	0.2438	2276	2401	100
2.9768-3.2763	0.2825	133	0.2249	2270	2403	100
3.2763-3.7502	0.2328	126	0.1856	2300	2426	100
3.7502-4.724	0.1761	129	0.1413	2336	2465	100
4.724-43.852	0.175	154	0.1747	2410	2564	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.5812	-0.8008	-0.9801	4.3859	4.6693	5.4418	0.2896	-0.1299	-0.3402	0.9223	0.0945	-0.8381	1.5468	-0.3353	-0.2116	1.1228	-0.0264	0.0605	0.6175	0.0476	0.548	-73.8925	7.8301	-0.7551
2	4.7631	-3.9018	3.6569	7.6846	-2.2913	5.6111	-0.0669	-0.21	-0.7395	0.116	0.2896	1.2765	0.599	-0.8664	-0.3656	0.5466	-0.0688	0.0189	0.5057	0.1183	0.5582	-78.8074	23.2193	-4.9297
3	2.0293	-0.8349	-1.4782	2.0023	0.575	1.3185	-1.0699	-0.0375	0.9162	0.4284	0.8827	-0.7672	-0.5395	0.2887	-0.1197	0.5054	0.0284	-0.0494	0.3717	0.0744	0.4696	-71.3592	31.9234	-10.3469
4	6.0468	-4.8134	-1.5621	3.9687	0.8361	2.6977	-0.304	0.5126	-0.1309	0.1498	0.5004	-1.1219	0.1752	0.8057	-0.3112	0.4746	-0.0219	0.0134	0.6679	-0.0825	0.7192	-51.9342	24.9173	-13.9974
5	8.7318	0.3565	-1.3749	5.2502	2.0311	7.2689	0.0515	-0.5084	-0.3543	0.7134	-0.1857	0.2391	0.0607	-0.5079	0.1258	0.6663	-0.0034	0.0069	0.3893	0.0244	0.4326	-63.2397	23.9123	-5.0576
6	2.7241	1.4422	0.0576	5.3897	-4.0659	4.4576	-0.1437	-0.229	-0.315	-0.0619	0.3155	-0.0203	0.1575	0.0276	-0.1763	0.5998	0.0068	-0.011	0.3988	0.0279	0.427	-65.6963	9.6623	-6.1297
7	6.3904	-1.4907	-0.6299	5.4288	1.6967	2.7305	-0.1655	0.1703	-0.1348	-0.1358	0.2481	0.2248	0.3716	-0.0808	-0.0064	0.64	-0.0685	-0.0196	0.3816	0.082	0.3621	-67.2346	16.6134	-13.4961
8	8.0402	1.8829	-3.9954	5.1133	0.2494	2.3723	0.4137	-1.3177	0.7966	2.0844	0.0897	-0.3156	-1.7582	0.4635	-0.7602	0.833	-0.1333	0.0155	0.7836	-0.1042	0.8589	-56.0248	32.8912	-2.7622
9	2.0467	-2.4334	-2.3358	3.4316	2.3082	3.0844	0.0096	-1.3773	-0.7377	1.2735	0.1339	-1.54	0.3493	0.2782	-0.2649	0.7476	0.0341	-0.223	0.7242	-0.0098	0.7244	-53.0011	21.0535	-4.7835

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 15 )	A	6 - 15
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 25 )	A	16 - 25
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 26 through 32 )	A	26 - 32
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 33 through 41 )	A	33 - 41
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 42 through 65 )	A	42 - 65
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 66 through 99 )	A	66 - 99
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 100 through 140 )	A	100 - 140
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 85 through 89 )	B	85 - 89
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 90 through 101 )	B	90 - 101

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