PDB-5e0q: Crystal structure of the Nup98 C-terminal domain bound to nanobod...

ID or keywords:

Entry

Database: PDB / ID: 5e0q

Title

Crystal structure of the Nup98 C-terminal domain bound to nanobody TP377

Components

Anti-Nup98 Nanobody TP377
Nuclear pore complex protein Nup98-Nup96

Keywords

TRANSPORT PROTEIN / nuclear pore complex / nuclear transport / autoproteolytic domain / antibody

Function / homology

Function and homology information

Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Regulation of Glucokinase by Glucokinase Regulatory Protein / Separation of Sister Chromatids / Resolution of Sister Chromatid Cohesion / SUMOylation of DNA damage response and repair proteins / Nuclear Pore Complex (NPC) Disassembly / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins ...
Similarity search - Function

Biological species

Vicugna pacos (alpaca)

Xenopus tropicalis (tropical clawed frog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Pleiner, T. / Trakhanov, S. / Goerlich, D.

Funding support

Germany, 1items

Citation

Journal: Elife / Year: 2015
Title: Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation.
Authors: Pleiner, T. / Bates, M. / Trakhanov, S. / Lee, C.T. / Schliep, J.E. / Chug, H. / Bohning, M. / Stark, H. / Urlaub, H. / Gorlich, D.

History

Deposition	Sep 29, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 27, 2016	Group: Database references
Revision 1.2	Jan 10, 2024	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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PDBx/mmCIF format	5e0q.cif.gz	174.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5e0q_validation.pdf.gz	428.4 KB	Display	wwPDB validaton report
Full document	5e0q_full_validation.pdf.gz	429.1 KB	Display
Data in XML	5e0q_validation.xml.gz	13.2 KB	Display
Data in CIF	5e0q_validation.cif.gz	18.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e0/5e0q ftp://data.pdbj.org/pub/pdb/validation_reports/e0/5e0q	HTTPS FTP

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Related structure data

Related structure data	4krnS S: Starting model for refinement
Similar structure data	3m05-2 3l9j-d 6s9o-1 5cfa-2 5mfd-5 4mbo-d 3lra-d 2r5o-d 5z8x-2 4nv6-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
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (10) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Anti-Nup98 Nanobody TP377

B: Nuclear pore complex protein Nup98-Nup96

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	66.590, 66.590, 87.900
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

#1: Antibody	Anti-Nup98 Nanobody TP377 Mass: 13853.317 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR
#2: Protein	Nuclear pore complex protein Nup98-Nup96 Mass: 17316.389 Da / Num. of mol.: 1 / Mutation: C821S Source method: isolated from a genetically manipulated source Details: C-terminal domain, residues 715-866 Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog) Gene: nup98 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: J7I6Y1
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.15 Å³/Da / Density % sol: 60.96 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 45 % (w/v) Pentaerythritol propoxylate (17/8 PO/OH), 100 mM Tris

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 0.9787 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 25, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.9787 Å / Relative weight: 1

Reflection

Resolution: 1.9→47.01 Å / Num. obs: 30053 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 13.9 % / B_iso Wilson estimate: 27.44 Å² / R_merge F obs: 1 / R_merge(I) obs: 0.128 / R_rim(I) all: 0.13 / Χ²: 0.906 / Net I/σ(I): 27.72 / Num. measured all: 823111

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.9-1.95		0.773	1.633	2.59	59892	2206	2177	1.663	98.7
1.95-2		0.877	1.284	3.37	60443	2203	2180	1.307	99
2-2.06		0.927	0.976	4.5	56023	2078	2061	0.994	99.2
2.06-2.12		0.935	0.807	5.38	53380	2065	2048	0.823	99.2
2.12-2.19		0.957	0.617	6.69	49516	1983	1963	0.63	99
2.19-2.27		0.972	0.56	8.14	52328	1891	1878	0.57	99.3
2.27-2.36		0.981	0.464	9.59	53079	1877	1870	0.472	99.6
2.36-2.45		0.986	0.39	11.41	50885	1809	1795	0.397	99.2
2.45-2.56		0.99	0.323	13.27	48041	1722	1717	0.329	99.7
2.56-2.69		0.994	0.238	17.76	44020	1627	1621	0.242	99.6
2.69-2.83		0.996	0.185	21.59	39989	1560	1556	0.189	99.7
2.83-3		0.998	0.142	29.6	41869	1469	1466	0.145	99.8
3-3.21		0.999	0.1	41.29	40245	1401	1398	0.102	99.8
3.21-3.47		0.999	0.068	59.57	36739	1301	1301	0.07	100
3.47-3.8		1	0.053	74.51	32626	1191	1190	0.054	99.9
3.8-4.25		1	0.044	80.91	27245	1083	1083	0.045	100
4.25-4.91		1	0.035	102.82	27265	949	948	0.036	99.9
4.91-6.01		1	0.039	97.09	22987	807	807	0.039	100
6.01-8.5		1	0.036	95.32	16450	644	644	0.037	100
	8.5	1	0.021	158.69	10089	352	350	0.022	99.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4KRN

4krn

Resolution: 1.9→47 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1956	1503	5 %
R_work	0.1674	-	-
obs	0.1689	30054	99.46 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2176	0	0	145	2321

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2220
X-RAY DIFFRACTION	f_angle_d	1.068	3004
X-RAY DIFFRACTION	f_dihedral_angle_d	11.624	1331
X-RAY DIFFRACTION	f_chiral_restr	0.064	323
X-RAY DIFFRACTION	f_plane_restr	0.007	396

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-1.9613	0.2562	135	0.2364	2570	X-RAY DIFFRACTION	99
1.9613-2.0314	0.2401	134	0.2018	2547	X-RAY DIFFRACTION	99
2.0314-2.1128	0.2659	136	0.2011	2589	X-RAY DIFFRACTION	99
2.1128-2.2089	0.2299	136	0.1899	2567	X-RAY DIFFRACTION	99
2.2089-2.3254	0.228	136	0.1797	2593	X-RAY DIFFRACTION	99
2.3254-2.4711	0.2178	136	0.1768	2593	X-RAY DIFFRACTION	99
2.4711-2.6619	0.2198	138	0.1745	2612	X-RAY DIFFRACTION	100
2.6619-2.9297	0.2265	136	0.1872	2592	X-RAY DIFFRACTION	100
2.9297-3.3535	0.206	138	0.1757	2607	X-RAY DIFFRACTION	100
3.3535-4.2247	0.1681	138	0.15	2622	X-RAY DIFFRACTION	100
4.2247-47.1007	0.1495	140	0.1378	2659	X-RAY DIFFRACTION	100

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	3.7327	2.8561	-2.6093	5.4192	-3.2508	4.9543	0.3087	-0.4233	0.0997	0.5641	-0.6432	-0.2795	-0.3101	0.6738	0.2565	0.3627	-0.0436	0.0049	0.2891	0.0319	0.3209	12.1557	39.1714	33.019
2	5.158	-0.1181	0.6591	4.7711	-0.2135	6.5913	0.0452	0.6157	0.7964	-0.3255	-0.3201	0.4311	-0.5551	0.3457	0.2616	0.2998	-0.0081	-0.0223	0.2139	0.0697	0.344	4.2777	40.503	24.6512
3	3.2916	2.7338	-2.314	9.6642	-5.3541	3.3264	0.0723	0.3697	-0.0255	-1.1789	0.0764	0.1336	0.3251	-0.2156	0.0371	0.4526	0.0133	0.0219	0.2215	-0.0028	0.2762	7.025	29.087	25.7928
4	4.6421	1.8656	-2.2087	7.8428	-3.9391	4.2868	0.1381	-0.0925	-0.1184	-0.2391	-0.5838	-0.3258	0.0772	0.5492	0.4283	0.2848	0.0262	0.0149	0.2398	0.0472	0.3102	13.3767	36.5106	27.811
5	9.2495	0.654	-1.707	5.9741	-6.8591	7.9715	0.1651	0.1666	0.7284	0.4839	0.4095	0.8891	-0.3919	-0.6329	-0.6329	0.3298	0.0366	0.1004	0.2037	0.035	0.5494	-4.8951	36.0733	33.5377
6	4.3645	4.6384	-5.0359	6.4248	-5.8062	7.6747	0.4628	-0.1459	0.6367	0.415	-0.208	0.6812	-0.6666	0.319	-0.2071	0.3994	0.0273	0.0891	0.2184	0.0094	0.4701	7.8426	43.9327	29.1244
7	4.1406	1.6209	-0.9908	3.6288	4.1019	6.9597	0.1781	0.2294	0.6262	-0.3621	-0.0206	0.5066	-0.6186	-0.2884	-0.0681	0.2058	0.088	0.0061	0.2278	0.0311	0.2632	-7.9544	21.638	34.2378
8	3.6197	-2.931	0.0685	7.7034	2.3008	5.6803	0.3463	0.0542	0.5774	0.2206	0.037	0.5927	-0.5352	-0.5427	-0.2548	0.2601	0.0389	0.1413	0.2392	0.0163	0.4279	-13.0327	20.0996	41.1085
9	2.0689	-0.3439	-0.2983	4.6041	0.1065	0.942	0.3036	-0.2097	0.6163	0.4138	-0.0562	0.4681	-0.5883	-0.0509	-0.1909	0.4917	0.0033	0.1874	0.2731	-0.0706	0.3794	-7.8307	25.1255	45.9463
10	2.5699	-0.2322	-2.5501	6.141	0.3178	2.8695	0.2347	-0.1658	0.2903	0.5192	-0.1209	0.1657	-0.2761	0.1998	-0.0581	0.2377	-0.0211	0.0079	0.1929	-0.0287	0.1678	-4.2651	17.3215	44.4239
11	2.7478	2.4464	-0.6918	5.6015	-1.6626	4.0036	0.1896	-0.154	-0.0273	0.1479	-0.2886	-0.3558	-0.3594	0.3451	0.0563	0.1881	0.0001	0.0086	0.2087	0.002	0.1897	3.7933	13.8003	41.6488
12	7.0605	-3.8666	-3.9152	4.1875	4.7498	5.4469	-0.1966	0.1598	-0.547	-0.5655	-0.0482	0.3248	0.6717	0.1548	0.0361	0.4339	-0.026	0.0475	0.2554	-0.0437	0.2332	-3.6821	-10.08	37.6461
13	5.8664	-0.9459	1.5504	8.8046	5.5279	4.3151	0.1722	-0.2544	-0.4565	0.2259	-0.3846	-0.039	0.6088	-0.8662	0.1639	0.4767	-0.0686	0.0063	0.2973	0.0139	0.3131	-5.2888	-14.2929	42.7649
14	8.756	6.1194	5.0029	8.0529	4.0889	2.9576	0.2628	0.6257	-0.6487	-0.018	-0.104	-0.5894	0.3467	0.6733	-0.1343	0.2968	0.0632	0.006	0.3247	0.0165	0.301	4.8256	-5.6465	49.2945
15	0.9219	1.4187	-0.6915	6.7759	-2.316	4.5407	0.0498	-0.1323	-0.095	0.0346	-0.2285	-0.3712	-0.133	0.4499	0.1106	0.1557	-0.0254	0.0106	0.2387	0.0004	0.1604	-0.43	2.1467	49.3463

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 41 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 42 through 54 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 55 through 69 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 70 through 101 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 102 through 111 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 112 through 128 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 715 through 726 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 727 through 738 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 739 through 755 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 756 through 773 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 774 through 809 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 810 through 819 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 820 through 833 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 834 through 844 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 845 through 866 )

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