PDB-4cyj: Chaetomium thermophilum Pan2:Pan3 complex

ID or keywords:

Entry

Database: PDB / ID: 4cyj

Title

Chaetomium thermophilum Pan2:Pan3 complex

Components

PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN
PAN2

Keywords

TRANSFERASE /

DEADENYLATION

Function / homology

Function and homology information

PAN complex /

poly(A)-specific ribonuclease /

poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening /

mRNA processing /

nucleic acid binding /

protein kinase activity /

RNA binding /

ATP binding /

metal ion binding
Similarity search - Function

Biological species

CHAETOMIUM THERMOPHILUM (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.59 Å

Authors

Wolf, J. / Valkov, E. / Allen, M.D. / Meineke, B. / Gordiyenko, Y. / McLaughlin, S.H. / Olsen, T.M. / Robinson, C.V. / Bycroft, M. / Stewart, M. / Passmore, L.A.

Citation

Journal: Embo J. / Year: 2014
Title: Structural Basis for Pan3 Binding to Pan2 and its Function in Mrna Recruitment and Deadenylation
Authors: Wolf, J. / Valkov, E. / Allen, M.D. / Meineke, B. / Gordiyenko, Y. / Mclaughlin, S.H. / Olsen, T.M. / Robinson, C.V. / Bycroft, M. / Stewart, M. / Passmore, L.A.

History

Deposition	Apr 11, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 11, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 25, 2014	Group: Atomic model / Database references / Other
Revision 1.2	Jul 30, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4cyj.cif.gz	1015.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4cyj.ent.gz	890.6 KB	Display	PDB format
PDBx/mmJSON format	4cyj.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/cy/4cyj ftp://data.pdbj.org/pub/pdb/validation_reports/cy/4cyj	HTTPS FTP

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Related structure data

Related structure data	4cyiC 4cykC C: citing same article (ref.)
Similar structure data	4cyi-4 4c5m-d 5yew-1 4c5k-d 4c5l-d 4bwk-d 4ldv-1 4c5n-d 4cyi-3 2rbe-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	#86 - Feb 2007 Exosomes similarity (1) #245 - May 2020 Spliceosomes similarity (2)

Deposited unit

A: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN

B: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN

C: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN

D: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN

E: PAN2

F: PAN2

hetero molecules

229 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN

B: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN

E: PAN2

hetero molecules

defined by author&software
114 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN

D: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN

F: PAN2

hetero molecules

defined by author&software
114 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	89.094, 145.359, 101.811
Angle α, β, γ (deg.)	90.00, 94.86, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN / PAN3 Mass: 50047.871 Da / Num. of mol.: 4 / Fragment: PKC, RESIDUES 203-640 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Description: SEE PUBLICATION FOR FULL DETAILS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S0Y3*PLUS
#2: Protein	PAN2 Mass: 13099.340 Da / Num. of mol.: 2 / Fragment: RESIDUES 343-458 Source method: isolated from a genetically manipulated source Details: SEE PUBLICATION FOR DETAILS / Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Description: SEE PUBLICATION FOR DETAILS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0SAK8
#3: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.9 Å³/Da / Density % sol: 57.64 % / Description: NONE
Crystal grow	Details: SEE PUBLICATION FOR DETAILS

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763
Detector	Type: DECTRIS PIXEL / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.59→100 Å / Num. obs: 80131 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / B_iso Wilson estimate: 55 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 12
Reflection shell	Resolution: 2.59→2.68 Å / R_merge(I) obs: 0.66 / Mean I/σ(I) obs: 1.77 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.59→47.89 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 23.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2206	4021	5 %
R_work	0.183	-	-
obs	0.1849	80120	99.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.59→47.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14004	0	128	150	14282

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	14443
X-RAY DIFFRACTION	f_angle_d	1.146	19571
X-RAY DIFFRACTION	f_dihedral_angle_d	15.36	5359
X-RAY DIFFRACTION	f_chiral_restr	0.069	2178
X-RAY DIFFRACTION	f_plane_restr	0.005	2484

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 (%)
2.59-2.6205	0.3862	144	0.3183	2639	X-RAY DIFFRACTION	100
2.6205-2.6524	0.3519	129	0.2895	2586	X-RAY DIFFRACTION	100
2.6524-2.686	0.339	150	0.2578	2634	X-RAY DIFFRACTION	99
2.686-2.7214	0.2659	131	0.2441	2588	X-RAY DIFFRACTION	100
2.7214-2.7586	0.279	147	0.2341	2617	X-RAY DIFFRACTION	100
2.7586-2.798	0.2889	157	0.225	2584	X-RAY DIFFRACTION	100
2.798-2.8398	0.3028	135	0.2271	2591	X-RAY DIFFRACTION	100
2.8398-2.8842	0.2216	114	0.2231	2670	X-RAY DIFFRACTION	100
2.8842-2.9314	0.2684	127	0.2311	2618	X-RAY DIFFRACTION	100
2.9314-2.982	0.2742	136	0.2158	2632	X-RAY DIFFRACTION	100
2.982-3.0362	0.2493	135	0.2116	2587	X-RAY DIFFRACTION	100
3.0362-3.0946	0.221	125	0.2008	2677	X-RAY DIFFRACTION	100
3.0946-3.1577	0.227	131	0.1931	2614	X-RAY DIFFRACTION	100
3.1577-3.2264	0.2275	138	0.1865	2610	X-RAY DIFFRACTION	100
3.2264-3.3014	0.2504	130	0.1956	2658	X-RAY DIFFRACTION	100
3.3014-3.384	0.2676	134	0.197	2594	X-RAY DIFFRACTION	100
3.384-3.4754	0.2136	149	0.1861	2610	X-RAY DIFFRACTION	100
3.4754-3.5777	0.238	154	0.1926	2596	X-RAY DIFFRACTION	100
3.5777-3.6931	0.2109	128	0.177	2635	X-RAY DIFFRACTION	100
3.6931-3.825	0.2142	132	0.1671	2643	X-RAY DIFFRACTION	100
3.825-3.9781	0.1869	147	0.168	2609	X-RAY DIFFRACTION	100
3.9781-4.1591	0.1985	151	0.1603	2618	X-RAY DIFFRACTION	100
4.1591-4.3782	0.1901	146	0.1554	2612	X-RAY DIFFRACTION	100
4.3782-4.6523	0.1966	150	0.1546	2627	X-RAY DIFFRACTION	100
4.6523-5.0112	0.1727	147	0.1494	2631	X-RAY DIFFRACTION	100
5.0112-5.5148	0.2432	133	0.1674	2633	X-RAY DIFFRACTION	100
5.5148-6.3113	0.2309	143	0.1964	2666	X-RAY DIFFRACTION	100
6.3113-7.9456	0.2075	140	0.1917	2632	X-RAY DIFFRACTION	100
7.9456-47.8985	0.1816	138	0.1572	2688	X-RAY DIFFRACTION	99

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	3.2717	0.0423	-0.3134	1.5954	0.3664	1.6388	-0.2032	0.1506	-0.2443	0.0192	0.0814	-0.0508	0.1311	-0.2186	0.0843	0.3198	-0.0305	0.0085	0.371	-0.0173	0.3081	-29.3113	17.291	125.7159
2	1.8487	-0.1053	0.03	1.2779	0.1739	1.0253	-0.1017	-0.3554	-0.058	0.1724	0.1494	0.0113	0.0524	-0.0598	-0.0282	0.286	0.0282	-0.0122	0.4012	0.004	0.333	-21.8512	27.6094	139.2677
3	1.8731	0.1848	-0.3555	0.8196	0.401	0.9927	-0.1488	0.4705	-0.5933	-0.7612	-0.0169	-0.381	0.4575	0.1146	0.1373	0.8773	-0.0735	0.3273	0.652	-0.2606	0.9056	1.0337	0.7197	95.1496
4	3.4026	1.2896	0.1755	1.3289	0.5598	0.8884	-0.3134	0.6122	-0.0033	-0.1448	0.1812	0.0497	-0.0315	0.0539	0.099	0.4968	-0.081	0.014	0.5511	-0.0258	0.3928	-0.688	23.5016	108.2886
5	2.7172	-0.1527	-0.0635	0.8897	0.1452	1.6265	-0.0896	0.1503	0.2806	-0.1076	0.0183	-0.0525	-0.0323	0.1357	0.0854	0.2711	-0.0429	-0.0495	0.3219	0.0022	0.2991	11.9221	36.7145	125.7489
6	1.6608	0.3606	-0.1628	1.3678	0.5504	1.1618	-0.1875	0.1868	-0.1304	-0.1258	0.022	0.0435	0.1023	-0.0882	0.1238	0.2801	-0.0196	0.0338	0.3182	0.0058	0.3064	-7.9391	22.4287	118.2833
7	0.9062	0.381	-0.4357	1.5501	-0.8377	2.2784	0.0667	0.0047	0.0902	0.1046	-0.1088	-0.1254	-0.0867	0.2642	0.0312	0.2695	-0.0174	-0.038	0.3813	-0.0165	0.3332	35.5346	25.2762	156.0978
8	1.0062	-0.1305	-0.1755	1.4403	-0.5647	1.7444	-0.1273	0.0464	-0.1866	-0.1744	-0.1154	-0.3455	0.3175	0.4549	0.1594	0.3332	0.0418	0.0552	0.3806	0.0154	0.4071	40.6421	5.9665	152.4105
9	1.1017	-0.1128	-0.615	1.1004	-0.0931	2.105	0.1952	-0.1657	0.2313	0.1593	-0.1009	0.029	-0.6304	0.062	-0.0666	0.6576	-0.0657	0.0453	0.4892	-0.0815	0.3736	16.0096	33.6429	195.2132
10	1.1895	-0.1221	-0.7851	3.7099	-0.4658	1.2752	-0.1692	-0.0858	-0.3388	0.4352	0.142	0.6275	0.1734	0.0197	0.0557	0.4865	0.0143	0.0322	0.4737	-0.0377	0.4952	14.6985	1.3072	184.0063
11	1.0564	0.2704	-0.6376	2.1107	0.2842	2.585	-0.1727	-0.2944	-0.2041	0.279	0.1574	0.0815	0.1453	0.0016	-0.0159	0.4024	0.0836	0.0481	0.2723	0.0852	0.4051	20.1862	-10.6704	175.5507
12	0.6031	0.5069	-0.1397	1.8228	0.4224	1.7806	0.0264	-0.1243	-0.0206	-0.0953	0.0666	-0.0728	-0.2044	0.1593	-0.0689	0.2583	0.0338	-0.0164	0.324	0.0173	0.3023	23.7005	12.7757	172.5696
13	1.4244	0.0338	0.333	1.2563	-0.1337	0.8416	0.0709	0.3905	-0.1087	-0.3312	-0.2666	0.3104	0.1222	0.0586	0.1217	0.6532	-0.1869	0.0134	1.1184	-0.2109	0.5214	-16.1655	13.8355	98.9815
14	0.949	0.7129	-0.0362	0.6701	0.152	0.3669	-0.0288	0.143	-0.1758	-0.0515	-0.0614	0.2016	0.6397	-0.3205	-0.0031	1.1632	-0.4002	-0.0645	1.0069	-0.3584	1.4536	-33.3727	-10.4327	106.0979
15	1.3179	0.6319	0.2499	3.5019	-1.171	0.5254	0.2393	0.1962	-0.1817	-0.1051	0.0923	0.7026	0.5266	-0.2774	-0.1605	0.9793	-0.3562	-0.0622	1.0949	-0.4039	1.0515	-29.7167	-6.2105	94.9591
16	4.3419	0.1607	-5.2395	0.0055	-0.1842	6.3241	-0.0335	0.1004	-0.1366	0.0276	-0.0521	-0.0595	0.2643	0.075	0.0916	1.3833	-0.175	-0.0036	1.1921	-0.1561	0.9521	-31.023	6.3358	99.5894
17	0.6552	0.2737	-0.2712	1.0314	-0.6114	2.0312	0.1525	0.0656	0.1668	0.0666	0.1141	0.062	-0.4264	-0.0544	-0.1957	0.6584	0.0789	0.0344	0.4992	-0.0707	0.5893	15.1814	34.704	174.4822
18	6.5803	4.4034	-0.4404	9.3865	-4.62	2.9289	0.2337	0.1493	0.218	-0.3845	0.2471	0.015	-0.3517	0.0702	-0.0914	1.6743	-0.1568	0.1008	0.6	0.1378	1.074	32.8665	55.1589	166.4201
19	1.667	-0.2231	-0.0218	2.0319	-0.3784	1.4021	0.0033	-0.0904	0.1926	-0.472	0.0768	0.0208	-0.5721	0.1064	0.0339	1.3493	-0.2496	0.082	0.6879	-0.1319	1.0177	35.1435	56.3742	176.4245
20	0.7015	-0.0233	-0.5082	1.5906	1.5617	2.7249	0.4544	0.5376	-0.1217	-0.2532	0.4012	0.2125	-0.0744	0.1171	-0.1725	1.3971	0.1781	0.1228	0.5829	-0.023	0.8667	20.7912	48.2946	169.9635

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 207:344)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 345:527)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 528:630)
4	X-RAY DIFFRACTION	4	(CHAIN B AND RESID 207:249)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 250:394)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 395:631)
7	X-RAY DIFFRACTION	7	(CHAIN C AND RESID 210:344)
8	X-RAY DIFFRACTION	8	(CHAIN C AND RESID 345:520)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 521:632)
10	X-RAY DIFFRACTION	10	(CHAIN D AND RESID 207:297)
11	X-RAY DIFFRACTION	11	(CHAIN D AND RESID 298:390)
12	X-RAY DIFFRACTION	12	(CHAIN D AND RESID 391:631)
13	X-RAY DIFFRACTION	13	(CHAIN E AND RESID 355:372)
14	X-RAY DIFFRACTION	14	(CHAIN E AND RESID 373:390)
15	X-RAY DIFFRACTION	15	(CHAIN E AND RESID 391:402)
16	X-RAY DIFFRACTION	16	(CHAIN E AND RESID 403:406)
17	X-RAY DIFFRACTION	17	(CHAIN F AND RESID 354:373)
18	X-RAY DIFFRACTION	18	(CHAIN F AND RESID 374:379)
19	X-RAY DIFFRACTION	19	(CHAIN F AND RESID 380:398)
20	X-RAY DIFFRACTION	20	(CHAIN F AND RESID 399:408)

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