PDB-3lkx: Human nac dimerization domain

ID or keywords:

Entry

Database: PDB / ID: 3lkx

Title

Human nac dimerization domain

Components

Nascent polypeptide-associated complex subunit alpha
Transcription factor BTF3

Keywords

CHAPERONE / beta-barrel

Function / homology

Function and homology information

negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / regulation of skeletal muscle fiber development / negative regulation of striated muscle cell apoptotic process / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of skeletal muscle tissue growth / cardiac ventricle development / skeletal muscle tissue regeneration / heart trabecula morphogenesis / protein targeting to membrane ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Liu, Y. / Hu, Y. / Li, X. / Niu, L. / Teng, M.

Citation

Journal: Biochemistry / Year: 2010
Title: The crystal structure of the human nascent polypeptide-associated complex domain reveals a nucleic acid-binding region on the NACA subunit
Authors: Liu, Y. / Hu, Y. / Li, X. / Niu, L. / Teng, M.

History

Deposition	Jan 28, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 23, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Feb 12, 2014	Group: Database references
Revision 1.3	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.4	Nov 1, 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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3lkx.cif.gz	37.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3lkx.ent.gz	26.8 KB	Display	PDB format
PDBx/mmJSON format	3lkx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3lkx_validation.pdf.gz	433.7 KB	Display	wwPDB validaton report
Full document	3lkx_full_validation.pdf.gz	435.2 KB	Display
Data in XML	3lkx_validation.xml.gz	6.9 KB	Display
Data in CIF	3lkx_validation.cif.gz	8.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lk/3lkx ftp://data.pdbj.org/pub/pdb/validation_reports/lk/3lkx	HTTPS FTP

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Related structure data

Related structure data	1tr8S S: Starting model for refinement
Similar structure data	6gba-d 4kuk-d 2p6v-d 1sj6-d 2qgo-d 5w88-d 4hp9-d 1nnx-d 6y7q-d 4x6s-1 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	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Transcription factor BTF3

B: Nascent polypeptide-associated complex subunit alpha

13.1 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)	59.755, 59.755, 176.823
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

#1: Protein	Transcription factor BTF3 / RNA polymerase B transcription factor 3 Mass: 7089.922 Da / Num. of mol.: 1 / Fragment: UNP residues 97-162 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NACA / Production host: Escherichia coli (E. coli) / References: UniProt: P20290
#2: Protein	Nascent polypeptide-associated complex subunit alpha / NAC-alpha / Alpha-NAC Mass: 6047.907 Da / Num. of mol.: 1 / Fragment: UNP residues 84-136 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BTF3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13765
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.47 Å³/Da / Density % sol: 64.54 % / Mosaicity: 0.754 °
Crystal grow	Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 6000, Sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site: BSRF

/ Beamline: 3W1A / Wavelength: 1 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 16, 2009

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.5→50 Å / Num. obs: 7011 / % possible obs: 98.8 % / Redundancy: 17.1 % / R_merge(I) obs: 0.067 / Χ²: 0.591 / Net I/σ(I): 9.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.5-2.54	5.3	0.443	280	0.266	1	86.4
2.54-2.59	7.9	0.429	336	0.287	1	93.6
2.59-2.64	9.3	0.378	313	0.291	1	96.9
2.64-2.69	11.7	0.402	344	0.305	1	100
2.69-2.75	13.9	0.312	337	0.291	1	99.4
2.75-2.82	16.2	0.239	340	0.323	1	100
2.82-2.89	18.1	0.233	351	0.329	1	100
2.89-2.96	19.5	0.22	345	0.355	1	100
2.96-3.05	19.7	0.171	339	0.365	1	100
3.05-3.15	20.8	0.144	349	0.366	1	100
3.15-3.26	20.4	0.113	338	0.405	1	100
3.26-3.39	20.6	0.092	351	0.483	1	100
3.39-3.55	20.5	0.077	355	0.595	1	100
3.55-3.73	20	0.065	363	0.644	1	100
3.73-3.97	20.5	0.063	352	0.665	1	100
3.97-4.27	19.7	0.051	359	0.955	1	100
4.27-4.7	19.7	0.045	359	1.023	1	99.7
4.7-5.38	19.5	0.045	374	0.939	1	100
5.38-6.78	18.8	0.048	384	0.952	1	100
6.78-50	16	0.041	442	0.965	1	98.9

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
MAR345dtb		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TR8

1tr8

Resolution: 2.5→19.56 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.928 / WR_factor R_free: 0.232 / WR_factor R_work: 0.2 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.814 / SU B: 16.066 / SU ML: 0.172 / SU R Cruickshank DPI: 0.336 / SU R_free: 0.251 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.315 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.253	529	7.6 %	RANDOM
R_work	0.215	-	-	-
obs	0.218	6936	98.48 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 68.14 Å² / B_iso mean: 26.468 Å² / B_iso min: 15.75 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.66 Å²	0.83 Å²	0 Å²
2-	-	1.66 Å²	0 Å²
3-	-	-	-2.49 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→19.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	884	0	0	19	903

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	894
X-RAY DIFFRACTION	r_angle_refined_deg	1.374	1.949	1215
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.117	5	116
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.071	25.946	37
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.047	15	145
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	27.623	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	152
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	658
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	314
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	580
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.139	0.2	39
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.222	0.2	36
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.183	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	0.46	1.5	598
X-RAY DIFFRACTION	r_mcangle_it	0.831	2	949
X-RAY DIFFRACTION	r_scbond_it	0.96	3	318
X-RAY DIFFRACTION	r_scangle_it	1.442	4.5	266

LS refinement shell

Resolution: 2.501→2.566 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.471	29	-
R_work	0.415	403	-
all	-	432	-
obs	-	-	88.52 %

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	7.9502	10.296	3.5708	23.156	-5.7116	14.7934	-0.1355	-1.1203	1.7579	0.0267	-0.1589	2.3831	0.384	-1.0124	0.2944	0.2048	-0.0225	0.0557	0.2315	-0.0863	0.2947	16.3617	-13.4205	9.8835
2	5.242	-0.2272	-0.75	3.039	-1.811	5.94	-0.2224	0.82	0.2042	0.4714	0.2002	0.031	-0.0007	0.664	0.0221	0.0458	0.0234	-0.0066	0.299	0.0238	0.1109	25.3558	-19.5478	-1.1035
3	6.8804	-4.7014	-4.9002	4.8048	1.4023	5.868	-0.2033	1.1482	0.1578	-1.3565	0.1876	0.0148	0.2207	0.3193	0.0157	0.1557	0.002	0.0306	0.4105	-0.0077	0.1886	26.0921	-23.6609	-8.3801
4	18.6783	-7.1926	-14.9242	10.2495	3.8624	12.3995	0.5013	-0.231	0.4136	-0.2496	-0.5524	-0.834	-1.6465	0.2512	0.0511	0.1614	0.0005	-0.0609	0.31	0.0409	0.2156	20.3862	-12.5695	0.4327
5	11.9386	19.1615	-12.4121	36.0607	-10.6856	28.9793	0.1103	-0.5204	-0.1171	4.2309	1.3347	2.9968	-1.3559	0.5722	-1.445	0.4369	-0.0343	0.0351	0.4694	0.0641	0.5045	12.75	-22.6069	10.4484
6	10.5865	10.0424	-7.1608	43.5049	-45.1961	48.2478	0.296	-1.3165	0.5484	0.3927	-0.4563	0.7492	-0.3222	-0.4949	0.1603	0.145	0.0229	0.0838	0.125	-0.0831	0.1396	14.2123	-19.4163	3.4273
7	33.6207	-25.3004	-9.6206	19.7471	11.767	31.7046	-0.1577	3.0069	2.6854	-0.1483	-0.3279	-1.6366	-1.9538	-0.2314	0.4856	0.2612	-0.0684	0.0506	0.3387	0.2026	0.2878	22.9138	-14.7477	-8.6434
8	4.1495	-0.9426	7.5015	2.5464	7.3896	49.0164	0.0771	1.1126	1.3393	-1.1449	-0.1629	-0.3403	-0.5287	0.6237	0.0858	0.0921	0.0298	0.082	0.417	0.0778	0.1826	33.4394	-20.1029	-9.1656
9	14.6413	0.5256	-7.7624	0.0375	-0.3207	4.2102	-0.3865	-0.1833	0.0114	0.1026	-0.1388	-0.8205	-0.3681	0.1343	0.5253	0.0177	-0.015	0.0198	0.25	0.0066	0.2125	35.8259	-20.8634	0.0651
10	10.9707	6.0098	1.611	3.382	-1.3348	54.9808	0.4544	1.2775	-2.1307	-1.4158	-1.7606	-1.4777	1.8767	0.4596	1.3062	0.173	0.2086	0.0305	0.3561	-0.1277	0.6489	33.4454	-30.901	-1.5053
11	17.5919	6.0256	-5.7428	7.8471	7.7807	18.3046	-0.9196	0.0671	0.0412	0.2237	0.4164	0.802	-0.2909	0.0403	0.5032	0.1262	-0.0526	0.0009	0.2307	-0.0223	0.113	9.9775	-26.288	-8.1028
12	12.3588	1.5413	1.4477	7.1583	3.3777	1.6369	-0.4435	0.1762	-0.4618	-0.4263	0.2785	-0.0958	0.3336	0.5686	0.165	0.0749	0.0292	0.0515	0.1998	-0.0071	0.1721	24.1422	-27.0986	-0.8287
13	1.8597	-0.4463	5.3924	2.2227	-2.3269	16.1406	0.2354	0.4721	0.6738	0.4526	-0.1354	0.0631	-0.5848	0.3366	-0.1	0.1822	-0.0164	0.0076	0.2015	-0.016	0.2994	27.4739	-14.8448	8.6888
14	13.4426	0.6227	6.2929	0.6608	-1.2229	6.5747	0.2961	0.032	-0.3952	-0.0049	-0.1734	-0.0798	-0.1479	-0.1896	-0.1227	0.1347	-0.0169	0.0848	0.1946	-0.0019	0.1547	24.8173	-22.0987	8.4215
15	28.7915	4.3164	3.346	3.2507	4.5784	6.7724	0.2521	-0.5563	-1.483	0.2925	0.1578	-0.132	0.8156	-0.7741	-0.4099	0.1276	-0.0753	0.006	0.2894	-0.0359	0.2292	16.7515	-29.2398	-0.4033
16	2.3249	-0.2996	2.6076	0.0386	-0.3361	2.9246	-0.3061	-0.5441	1.5401	-1.6386	-0.7068	1.6811	-1.1325	0.6279	1.013	0.4206	-0.0035	-0.1203	0.6251	0.1179	0.5381	10.1767	-17.6227	-7.5396
17	4.9938	2.7541	-2.662	20.8462	-18.8046	19.3399	0.0273	0.1953	-0.0422	-0.2083	0.376	0.8776	0.1015	0.4402	-0.4033	0.0325	-0.0374	-0.0029	0.2664	-0.0853	0.2612	14.2764	-24.6124	0.9335
18	21.3843	4.1057	3.0724	4.9826	1.8656	8.7612	0.8639	-0.3235	-0.8288	-0.2349	-0.6091	-0.0881	0.6634	-0.3844	-0.2548	0.182	0.016	-0.0077	0.2455	0.0587	0.135	26.1596	-25.4378	11.6907
19	42.4019	-8.6758	4.0555	15.5066	1.6394	2.3594	-0.4483	-1.751	0.2234	1.3368	0.5944	-0.4737	0.0248	1.0611	-0.1461	0.1537	0.0425	0.0315	0.3888	-0.0089	0.1074	38.793	-22.2063	12.2763

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	25 - 31
2	X-RAY DIFFRACTION	2	A	32 - 38
3	X-RAY DIFFRACTION	3	A	39 - 45
4	X-RAY DIFFRACTION	4	A	46 - 51
5	X-RAY DIFFRACTION	5	A	52 - 58
6	X-RAY DIFFRACTION	6	A	59 - 63
7	X-RAY DIFFRACTION	7	A	64 - 69
8	X-RAY DIFFRACTION	8	A	70 - 74
9	X-RAY DIFFRACTION	9	A	75 - 81
10	X-RAY DIFFRACTION	10	A	82 - 88
11	X-RAY DIFFRACTION	11	B	24 - 30
12	X-RAY DIFFRACTION	12	B	31 - 36
13	X-RAY DIFFRACTION	13	B	37 - 42
14	X-RAY DIFFRACTION	14	B	43 - 47
15	X-RAY DIFFRACTION	15	B	48 - 53
16	X-RAY DIFFRACTION	16	B	54 - 60
17	X-RAY DIFFRACTION	17	B	61 - 65
18	X-RAY DIFFRACTION	18	B	66 - 71
19	X-RAY DIFFRACTION	19	B	72 - 77

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