PDB-5c2u: Ferredoxin-like domain of nucleoporin Nup54 bound to a nanobody

ID or keywords:

Entry

Database: PDB / ID: 5c2u

Title

Ferredoxin-like domain of nucleoporin Nup54 bound to a nanobody

Components

Nanobody
Nup54

Keywords

TRANSPORT PROTEIN / Nucleoporin Nup54 / Nup54 alpha-beta domain / Ferredoxin-like fold

Function / homology

Function and homology information

protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / NLS-bearing protein import into nucleus / structural constituent of nuclear pore
Similarity search - Function

Biological species

Camelus dromedarius (Arabian camel)

Xenopus laevis (African clawed frog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Chug, H. / Trakhanov, S. / Hulsmann, B.B. / Pleiner, T. / Gorlich, D.

Citation

Journal: Science / Year: 2015
Title: Crystal structure of the metazoan Nup62Nup58Nup54 nucleoporin complex.
Authors: Chug, H. / Trakhanov, S. / Hulsmann, B.B. / Pleiner, T. / Gorlich, D.

History

Deposition	Jun 16, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 26, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 2, 2015	Group: Database references
Revision 1.2	Oct 14, 2015	Group: Database references
Revision 1.3	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
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5c2u.cif.gz	156.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5c2u.ent.gz	125.5 KB	Display	PDB format
PDBx/mmJSON format	5c2u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5c2u_validation.pdf.gz	427 KB	Display	wwPDB validaton report
Full document	5c2u_full_validation.pdf.gz	428 KB	Display
Data in XML	5c2u_validation.xml.gz	12.7 KB	Display
Data in CIF	5c2u_validation.cif.gz	18.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c2/5c2u ftp://data.pdbj.org/pub/pdb/validation_reports/c2/5c2u	HTTPS FTP

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Related structure data

Related structure data	5c3lC 4klmS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4drh-1 3g8x-d 3g8u-d 3573 2jjt-2 4n4h-d 3wof-10 3g6q-d 1za0-d 3rtl-6 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 (5) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

B: Nanobody

A: Nup54

30 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)	90.860, 90.860, 57.600
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	B-286- HOH
2	1	B-288- HOH

#1: Antibody	Nanobody Mass: 14341.810 Da / Num. of mol.: 1 / Fragment: Nanobody Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Gene: Immunoglobulin G / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Variant (production host): NEB SHuffle
#2: Protein	Nup54 Mass: 15671.594 Da / Num. of mol.: 1 Fragment: Nup54 ferredoxin-like domain, UNP residues 212-349 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Variant (production host): NEB Express / References: UniProt: K9ZTJ6
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: PEG 6000, Sodium acetate trihydrate

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2014 / Details: dynamically bendable mirror

Radiation

Monochromator: Double crystal fixed-exit monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.55→46.5 Å / Num. obs: 40071 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.9 % / B_iso Wilson estimate: 24.56 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.065 / R_rim(I) all: 0.067 / Χ²: 0.914 / Net I/σ(I): 22.9 / Num. measured all: 672687

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	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
1.55-1.59		15.9	0.434	2.212	1.7	26843	3240	3103	2.352	99.8
1.54-1.58			0.648	1.665	1.52	32823	3130	3107	1.75	99.3
1.58-1.63			0.805	1.299	2.25	42281	3080	3080	1.349	100
1.63-1.68			0.874	1.11	3.01	49328	2975	2975	1.145	100
1.68-1.73			0.912	0.883	3.93	47710	2886	2886	0.912	100
1.73-1.79			0.956	0.628	5.56	45778	2826	2826	0.649	100
1.79-1.86			0.973	0.435	7.75	41680	2700	2700	0.45	100
1.86-1.94			0.989	0.297	11.68	43896	2579	2578	0.306	100
1.94-2.02			0.995	0.201	16.18	42755	2509	2509	0.207	100
2.02-2.12			0.997	0.144	21.22	40219	2405	2405	0.148	100
2.12-2.24			0.998	0.11	25.24	36037	2270	2270	0.114	100
2.24-2.37			0.999	0.091	30.63	36809	2138	2138	0.094	100
2.37-2.54			0.999	0.073	36.28	35444	2066	2066	0.075	100
2.54-2.74			0.999	0.058	43.06	31443	1887	1887	0.06	100
2.74-3			0.999	0.046	50.64	28163	1760	1760	0.048	100
3-3.35			0.999	0.042	59.53	27232	1601	1601	0.043	100
3.35-3.87			0.999	0.04	64.36	22755	1404	1404	0.041	100
3.87-4.74			0.999	0.041	64.2	18660	1209	1209	0.042	100
4.74-6.71			0.999	0.043	63.42	15110	955	955	0.045	100
	6.71		0.999	0.043	61.12	7721	549	548	0.045	99.8

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
PHASER		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4klm

4klm

Resolution: 1.55→29.741 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2049	2002	5 %	Random selection
R_work	0.1764	38058	-	-
obs	0.1779	40060	99.97 %	-

Solvent computation

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

Displacement parameters

B_iso max: 93.37 Å² / B_iso mean: 39.5108 Å² / B_iso min: 16.89 Å²

Refinement step

Cycle: final / Resolution: 1.55→29.741 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1868	0	0	198	2066
B_iso mean	-	-	-	44.89	-
Num. residues	-	-	-	-	240

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1942
X-RAY DIFFRACTION	f_angle_d	1.051	2637
X-RAY DIFFRACTION	f_chiral_restr	0.043	287
X-RAY DIFFRACTION	f_plane_restr	0.005	347
X-RAY DIFFRACTION	f_dihedral_angle_d	14.477	714

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.55-1.5888	0.3104	140	0.3101	2662	2802
1.5888-1.6317	0.289	142	0.2727	2698	2840
1.6317-1.6797	0.3118	142	0.2614	2699	2841
1.6797-1.734	0.2943	141	0.246	2685	2826
1.734-1.7959	0.2649	142	0.2265	2696	2838
1.7959-1.8678	0.2381	142	0.212	2683	2825
1.8678-1.9528	0.2152	143	0.1908	2717	2860
1.9528-2.0557	0.1993	142	0.1841	2708	2850
2.0557-2.1845	0.2028	143	0.1815	2706	2849
2.1845-2.3531	0.2156	142	0.1791	2706	2848
2.3531-2.5898	0.2005	144	0.1791	2727	2871
2.5898-2.9642	0.218	144	0.1717	2744	2888
2.9642-3.7335	0.2172	145	0.1648	2763	2908
3.7335-29.7464	0.1607	150	0.1516	2864	3014

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	1.1541	0.3185	-0.6697	8.7159	-2.7593	1.6704	0.2474	-0.1343	0.0381	0.4385	-0.459	-0.6903	-0.1495	0.2498	0.1804	0.2537	0.0212	0.0044	0.238	0.0478	0.1825	18.5932	40.2341	17.8831
2	4.2672	-1.3176	-2.1921	6.8565	1.2518	8.1577	-0.0213	0.1208	0.3376	-0.7691	-0.108	-0.339	0.3042	0.5471	0.0534	0.3072	0.1369	0.09	0.2476	0.0553	0.2038	15.6344	45.4367	9.3551
3	6.777	1.6051	0.2434	3.581	2.4152	8.3342	0.1937	-0.444	0.431	-0.0875	-0.1166	0.5448	-0.9899	-0.4537	-0.0574	0.3879	0.0851	0.0589	0.2003	0.0185	0.2315	9.9683	43.0353	16.3334
4	6.0386	-0.9535	-0.364	2.9019	-2.6449	0.6337	0.2565	0.0932	0.0095	-0.3539	-0.2234	0.5073	-0.2872	-0.0082	0.0119	0.3045	0.0448	0.0315	0.2079	0.0383	0.1543	12.4251	36.0891	15.458
5	0.5635	-0.5513	-0.1306	3.7169	-0.9026	2.0415	0.1876	0.1085	0.1877	-0.3546	-0.3912	-0.7799	-0.1138	0.1689	0.2479	0.2389	0.0797	0.0511	0.2221	0.0699	0.3004	20.6259	45.5568	10.3475
6	9.673	4.448	5.247	8.077	2.2226	8.4798	0.0846	0.0803	-0.4056	0.103	-0.0608	-0.4648	0.381	0.3295	-0.1284	0.2577	0.1358	0.0508	0.2207	0.0031	0.2546	21.2268	60.5768	-2.3921
7	3.1018	-0.7527	-0.5165	2.5592	2.069	7.2014	-0.0775	0.3512	-0.3542	-0.8403	0.1859	0.0793	0.3979	-0.0055	0.0471	0.3228	-0.0088	0.0286	0.2293	0.0127	0.1852	17.0727	64.8145	-12.6891
8	2.5335	1.272	0.8986	7.7568	1.2354	2.398	-0.0189	0.1747	-0.4124	0.0022	0.1616	-0.5152	0.3723	0.195	-0.1626	0.2166	0.0584	0.0274	0.2175	0.0075	0.177	20.775	64.0756	-7.0115
9	5.9248	3.0808	1.2675	7.7129	2.3678	4.8257	-0.2179	-0.0661	0.3881	-0.0605	0.1462	-0.6002	-0.3365	0.4432	-0.0363	0.2222	0.0472	-0.0217	0.2917	0.0129	0.2545	25.6172	72.3479	-2.8424
10	7.6394	3.026	-4.2821	6.6955	-2.8477	7.0545	-0.0277	-0.7182	-0.1031	0.9654	0.0281	-0.113	0.0304	0.5288	0.0658	0.3531	0.1161	-0.0215	0.2313	0.0176	0.2191	20.4595	69.719	4.3019
11	3.0193	1.0755	-2.32	4.3592	4.3608	8.5663	-0.2372	0.0196	0.2032	-0.0308	0.1672	1.0587	-0.176	-0.2873	-0.0482	0.2823	0.0821	0.0766	0.1778	0.0788	0.4508	8.0957	65.1515	-1.0298
12	1.1912	1.1865	0.7466	1.3989	-1.8168	4.3683	0.1232	-0.3108	0.1548	0.5963	-0.1572	-0.0366	-0.6979	0.0433	-0.0121	0.5786	0.0723	0.0013	0.287	0.0097	0.422	19.0067	61.9305	13.7795

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 35 )	B
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 36 through 57 )	B
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 58 through 72 )	B
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 73 through 87 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 88 through 124 )	B
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 214 through 226 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 227 through 244 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 245 through 265 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 266 through 280 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 281 through 295 )	A
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 296 through 305 )	A
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 306 through 329 )	A

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