PDB-3pja: Crystal structure of human C3PO complex

ID or keywords:

Entry

Database: PDB / ID: 3pja

Title

Crystal structure of human C3PO complex

Components

Translin-associated protein X
Translin

Keywords

HYDROLASE / 7 alpha helical bundle /

Ribonuclease

Function / homology

Function and homology information

A2A adenosine receptor binding /

endoribonuclease complex / Small interfering RNA (siRNA) biogenesis / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / RNA endonuclease activity / male germ cell nucleus /

single-stranded DNA binding /

spermatogenesis /

endonuclease activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Huang, N. / Zhang, H.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structure of C3PO and mechanism of human RISC activation.
Authors: Ye, X. / Huang, N. / Liu, Y. / Paroo, Z. / Huerta, C. / Li, P. / Chen, S. / Liu, Q. / Zhang, H.

History

Deposition	Nov 9, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 11, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3pja.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb3pja.ent.gz	883.6 KB	Display	PDB format
PDBx/mmJSON format	3pja.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pj/3pja ftp://data.pdbj.org/pub/pdb/validation_reports/pj/3pja	HTTPS FTP

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Related structure data

Related structure data	3qb5C C: citing same article (ref.)
Similar structure data	3qb5-1 1j1j-5 1key-1 2irp-3 4dg7-d 4wyv-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#98 - Feb 2008 Small Interfering RNA similarity (1)

Deposited unit

A: Translin

B: Translin

C: Translin

D: Translin

E: Translin

F: Translin

G: Translin

H: Translin

I: Translin

J: Translin-associated protein X

K: Translin-associated protein X

L: Translin-associated protein X

335 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Translin

B: Translin

C: Translin

D: Translin

E: Translin

F: Translin

K: Translin-associated protein X

L: Translin-associated protein X

defined by author
224 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Translin

H: Translin

I: Translin

J: Translin-associated protein X

G: Translin

H: Translin

I: Translin

J: Translin-associated protein X

defined by author
224 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	171.250, 95.830, 232.885
Angle α, β, γ (deg.)	90.00, 104.58, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
1	2
2	2
3	2
1	3
2	3
3	3
1	4
2	4
3	4

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain A and (resseq 7:43 or resseq 57:59 or resseq...
2	1	1	chain D and (resseq 7:43 or resseq 57:59 or resseq...
3	1	1	chain G and (resseq 7:43 or resseq 57:59 or resseq...
1	1	2	chain B and (resseq 4:19 or resseq 21:34 or resseq...
2	1	2	chain E and (resseq 4:19 or resseq 21:34 or resseq...
3	1	2	chain H and (resseq 4:19 or resseq 21:34 or resseq...
1	1	3	chain C and (resseq 4:6 or resseq 12:21 or resseq...
2	1	3	chain F and (resseq 4:6 or resseq 12:21 or resseq...
3	1	3	chain I and (resseq 4:6 or resseq 12:21 or resseq...
1	1	4	chain J and (resseq 35:39 or resseq 41:42 or resseq...
2	1	4	chain K and (resseq 35:39 or resseq 41:42 or resseq...
3	1	4	chain L and (resseq 35:39 or resseq 41:42 or resseq...

NCS ensembles :

ID
1
2
3
4

#1: Protein	Translin / Mass: 26219.967 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Translin, TSN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15631
#2: Protein	Translin-associated protein X Mass: 33159.484 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Translin associated factor X, TRAX, TSNAX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99598
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.76 Å³/Da / Density % sol: 55.38 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 12% PEG 3350, 75mM potassium citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 9, 2010
Radiation	Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 3→30 Å / Num. obs: 73372 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / R_merge(I) obs: 0.093 / Net I/σ(I): 14.96
Reflection shell	Resolution: 3→3.11 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.683 / Mean I/σ(I) obs: 1.9 / Num. unique all: 7235 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_555)	refinement
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→29.916 Å / SU ML: 0.44 / σ(F): 1.33 / Phase error: 27.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2535	3676	5.03 %
R_work	0.2059	-	-
obs	0.2083	73084	99.7 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 37.536 Å² / k_sol: 0.31 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.8136 Å²	0 Å²	-1.1435 Å²
2-	-	1.6853 Å²	0 Å²
3-	-	-	-0.8718 Å²

Refinement step

Cycle: LAST / Resolution: 3→29.916 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21056	0	0	177	21233

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	22975
X-RAY DIFFRACTION	f_angle_d	0.823	28898
X-RAY DIFFRACTION	f_dihedral_angle_d	13.938	8026
X-RAY DIFFRACTION	f_chiral_restr	0.054	3309
X-RAY DIFFRACTION	f_plane_restr	0.003	3672

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1443	X-RAY DIFFRACTION	POSITIONAL
1	2	D	1443	X-RAY DIFFRACTION	POSITIONAL	0.039
1	3	G	1443	X-RAY DIFFRACTION	POSITIONAL	0.022
2	1	B	1406	X-RAY DIFFRACTION	POSITIONAL
2	2	E	1406	X-RAY DIFFRACTION	POSITIONAL	0.024
2	3	H	1406	X-RAY DIFFRACTION	POSITIONAL	0.019
3	1	C	1355	X-RAY DIFFRACTION	POSITIONAL
3	2	F	1355	X-RAY DIFFRACTION	POSITIONAL	0.027
3	3	I	1355	X-RAY DIFFRACTION	POSITIONAL	0.021
4	1	J	1344	X-RAY DIFFRACTION	POSITIONAL
4	2	K	1344	X-RAY DIFFRACTION	POSITIONAL	0.04
4	3	L	1344	X-RAY DIFFRACTION	POSITIONAL	0.054

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 (%)
3-3.0394	0.3519	138	0.2995	2591	X-RAY DIFFRACTION	99
3.0394-3.081	0.3703	143	0.3004	2669	X-RAY DIFFRACTION	100
3.081-3.125	0.3372	128	0.3	2648	X-RAY DIFFRACTION	100
3.125-3.1716	0.333	138	0.2929	2707	X-RAY DIFFRACTION	100
3.1716-3.2211	0.3509	122	0.2841	2623	X-RAY DIFFRACTION	100
3.2211-3.2739	0.3805	137	0.2922	2718	X-RAY DIFFRACTION	100
3.2739-3.3302	0.3661	140	0.2796	2611	X-RAY DIFFRACTION	100
3.3302-3.3907	0.3459	123	0.27	2728	X-RAY DIFFRACTION	100
3.3907-3.4558	0.3367	146	0.2512	2615	X-RAY DIFFRACTION	100
3.4558-3.5263	0.2829	153	0.2343	2664	X-RAY DIFFRACTION	100
3.5263-3.6028	0.302	138	0.2214	2641	X-RAY DIFFRACTION	100
3.6028-3.6865	0.2683	150	0.2078	2674	X-RAY DIFFRACTION	100
3.6865-3.7785	0.2685	145	0.2045	2679	X-RAY DIFFRACTION	100
3.7785-3.8804	0.2513	135	0.1978	2665	X-RAY DIFFRACTION	100
3.8804-3.9944	0.2568	147	0.1831	2674	X-RAY DIFFRACTION	100
3.9944-4.123	0.2189	153	0.1712	2629	X-RAY DIFFRACTION	100
4.123-4.27	0.2186	138	0.1623	2699	X-RAY DIFFRACTION	99
4.27-4.4404	0.19	137	0.1538	2635	X-RAY DIFFRACTION	100
4.4404-4.6418	0.2384	163	0.1592	2666	X-RAY DIFFRACTION	100
4.6418-4.8855	0.2233	149	0.1582	2668	X-RAY DIFFRACTION	100
4.8855-5.1901	0.1771	148	0.1565	2675	X-RAY DIFFRACTION	100
5.1901-5.5885	0.267	133	0.1844	2686	X-RAY DIFFRACTION	100
5.5885-6.1464	0.2985	136	0.2236	2714	X-RAY DIFFRACTION	100
6.1464-7.0258	0.2459	147	0.2052	2701	X-RAY DIFFRACTION	100
7.0258-8.814	0.1772	145	0.1539	2710	X-RAY DIFFRACTION	100
8.814-29.9174	0.1705	144	0.1772	2718	X-RAY DIFFRACTION	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	0.606	0.1136	-0.1066	0.164	0.4451	0.9751	-0.0502	0.0725	-0.1748	0.0368	0.0181	-0.1114	-0.156	0.054	0	0.3243	0.0515	-0.0477	0.1256	-0.032	0.3991	19.2761	4.7336	38.55
2	0.6729	-0.6793	-0.0817	1.2383	0.2001	0.8857	0.0038	-0.1855	-0.0637	-0.0787	0.0598	0.0058	-0.0386	-0.0377	-0	0.2918	0.0728	0.0282	0.2681	-0.0205	0.2495	21.7671	-18.7853	63.7
3	0.3183	-0.0988	-0.125	0.4967	0.2716	0.4715	-0.0919	-0.1511	0.0358	-0.1356	0.0789	0.1547	-0.1259	-0.1537	0.0159	0.1582	0.0828	-0.0505	0.1254	-0.0297	0.1654	-12.2441	-6.0685	31.1265
4	0.5118	-0.1473	-0.3641	0.5339	0.1767	0.5451	0.0801	0.0768	0.0126	-0.0341	-0.0356	0.0688	-0.0511	0.0819	-0	0.2508	0.1314	-0.0521	0.2846	-0.0707	0.409	43.7878	-35.8009	37.5184
5	0.3524	-0.7476	-0.1347	1.1736	0.377	0.4773	0.0177	0.0976	0.0588	-0.1396	0.0553	-0.0249	-0.1288	0.2964	-0	0.3621	0.0055	-0.0381	0.3145	-0.0697	0.4049	27.4379	-20.0309	11.4366
6	1.1246	-0.6542	0.1559	0.4855	-0.3732	0.4025	-0.0429	-0.1474	-0.1782	0.0796	0.1565	-0.0451	0.0692	-0.0649	0	0.4388	0.0846	-0.1517	0.1358	-0.0035	0.3163	18.647	-58.8037	39.4639
7	0.5978	-0.6035	-0.3357	0.2254	-0.198	0.8877	0.1213	-0.0806	0.0337	0.0701	0.026	0.0365	-0.2884	0.3865	0	0.4046	-0.2121	0.1263	0.5879	-0.1168	0.4123	-5.8208	14.771	113.5256
8	0.8679	0.0902	-0.6195	-0.0789	-0.1675	1.712	0.2427	0.0628	0.1085	-0.0439	0.0009	0.0086	-0.2073	-0.1589	-0	0.3199	0.0906	0.0914	0.4282	0.0016	0.3037	-25.9587	6.7958	86.5657
9	1.1227	0.5112	0.0338	0.0712	-0.2784	0.5919	0.0731	-0.5062	-0.1705	0.0388	-0.1848	0.018	0.2452	0.3547	-0	0.306	0.1921	0.0635	0.8424	0.0918	0.312	0.9688	-18.2397	118.5464
10	1.586	0.2176	-0.9729	0.045	0.0746	1.479	-0.1455	0.4472	-0.4384	-0.053	-0.0949	0.0562	0.422	-0.2726	0.0001	0.393	0.0367	0.1535	0.3938	-0.096	0.3936	-21.7731	-25.2283	95.1322
11	0.3665	-0.0763	0.2048	1.3086	1.2965	1.2388	-0.0933	-0.2972	-0.0038	0.2607	0.189	0.021	0.2423	-0.0316	0	0.3821	0.0535	0.0526	0.3807	0.0435	0.2745	-7.3101	-32.0199	52.5067
12	0.576	-0.0694	-0.3788	0.1817	0.3799	1.2325	0.0078	-0.0644	0.0173	-0.0385	0.151	-0.0646	0.1223	-0.0212	-0	0.2296	-0.009	-0.0621	0.1451	0.0116	0.2537	1.1908	-40.6188	17.0694
13	-0.1146	0.076	-0.0619	0.0957	0.0974	0.378	0.0534	-0.0176	0.0094	-0.0301	0.0087	-0.0201	-0.007	-0.108	0.0005	0.0984	0.0636	-0.0486	0.1564	0.0199	0.1145	4.5983	-22.6441	45.5637

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H
9	X-RAY DIFFRACTION	9	chain I
10	X-RAY DIFFRACTION	10	chain J
11	X-RAY DIFFRACTION	11	chain K
12	X-RAY DIFFRACTION	12	chain L
13	X-RAY DIFFRACTION	13	chain M

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