PDB-6f9n: CRYSTAL STRUCTURE OF THE HUMAN CPSF160-WDR33 COMPLEX

ID or keywords:

Entry

Database: PDB / ID: 6f9n

Title

CRYSTAL STRUCTURE OF THE HUMAN CPSF160-WDR33 COMPLEX

Components

Cleavage and polyadenylation specificity factor subunit 1
pre-mRNA 3' end processing protein WDR33

Keywords

RNA BINDING PROTEIN / Polyadenylation / mRNA / beta propeller / cpsf / 3' end processing

Function / homology

Function and homology information

co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / collagen trimer / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / tRNA processing in the nucleus / DNA damage tolerance ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Clerici, M. / Jinek, M.

Funding support

Belgium, 1items

Citation

Journal: Elife / Year: 2017
Title: Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex.
Authors: Clerici, M. / Faini, M. / Aebersold, R. / Jinek, M.

History

Deposition	Dec 14, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 3, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 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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Download

PDBx/mmCIF format	6f9n.cif.gz	634.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6f9n.ent.gz	520.3 KB	Display	PDB format
PDBx/mmJSON format	6f9n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6f9n_validation.pdf.gz	441.4 KB	Display	wwPDB validaton report
Full document	6f9n_full_validation.pdf.gz	460.7 KB	Display
Data in XML	6f9n_validation.xml.gz	53.1 KB	Display
Data in CIF	6f9n_validation.cif.gz	71.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f9/6f9n ftp://data.pdbj.org/pub/pdb/validation_reports/f9/6f9n	HTTPS FTP

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Related structure data

Related structure data	3ei1S S: Starting model for refinement
Similar structure data	6bly-d 6bm0-d 7112 7113 2hpa-d 3dfh-d 4225 6b2e-d 4cff-1 6dnh-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 (2) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1)

Deposited unit

A: Cleavage and polyadenylation specificity factor subunit 1

B: pre-mRNA 3' end processing protein WDR33

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

1

Idetical with deposited unit
defined by author&software
Evidence: cross-linking, assay for oligomerization, pulldown, gel filtration

Unit cell

Length a, b, c (Å)	67.910, 77.400, 104.020
Angle α, β, γ (deg.)	87.56, 76.41, 67.00
Int Tables number	1
Space group name H-M	P1

#1: Protein	Cleavage and polyadenylation specificity factor subunit 1 / Cleavage and polyadenylation specificity factor 160 kDa subunit / CPSF 160 kDa subunit Mass: 161074.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF1, CPSF160 / Plasmid: pML-5B (addgene #30122) Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) References: UniProt: Q10570
#2: Protein	pre-mRNA 3' end processing protein WDR33 / WD repeat-containing protein 33 / WD repeat-containing protein WDC146 Mass: 43326.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR33, WDC146 Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) References: UniProt: Q9C0J8
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.39 Å³/Da / Density % sol: 48.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 11% w/v PEG3400 37.5 mM Ammonium Formate 112.5 mM Magnesium Formate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 5, 2016
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→47.312 Å / Num. obs: 65410 / % possible obs: 100 % / Redundancy: 7.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.09 / Net I/σ(I): 18.3
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.773 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6519 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3EI1

3ei1

Resolution: 2.5→47.312 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0.88 / Phase error: 32.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2627	6504	5 %
R_work	0.2275	-	-
obs	0.2292	65402	99.39 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→47.312 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12162	0	0	102	12264

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	12457
X-RAY DIFFRACTION	f_angle_d	0.555	16912
X-RAY DIFFRACTION	f_dihedral_angle_d	14.759	7404
X-RAY DIFFRACTION	f_chiral_restr	0.044	1898
X-RAY DIFFRACTION	f_plane_restr	0.004	2156

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 (%)
2.4999-2.5283	0.4664	244	0.4059	4039	X-RAY DIFFRACTION	99
2.5283-2.5581	0.3896	186	0.3704	4043	X-RAY DIFFRACTION	99
2.5581-2.5893	0.408	212	0.3524	4237	X-RAY DIFFRACTION	100
2.5893-2.6221	0.365	199	0.3432	4028	X-RAY DIFFRACTION	99
2.6221-2.6566	0.3833	210	0.3482	4106	X-RAY DIFFRACTION	99
2.6566-2.6929	0.3896	225	0.327	4242	X-RAY DIFFRACTION	99
2.6929-2.7314	0.3705	246	0.308	4005	X-RAY DIFFRACTION	99
2.7314-2.7722	0.4048	214	0.3164	4106	X-RAY DIFFRACTION	99
2.7722-2.8155	0.3613	227	0.3037	4166	X-RAY DIFFRACTION	99
2.8155-2.8616	0.3649	210	0.2961	4092	X-RAY DIFFRACTION	99
2.8616-2.911	0.3584	199	0.3121	4096	X-RAY DIFFRACTION	100
2.911-2.9639	0.3733	208	0.2988	4236	X-RAY DIFFRACTION	99
2.9639-3.0209	0.2961	240	0.2814	4016	X-RAY DIFFRACTION	99
3.0209-3.0826	0.3372	222	0.2659	4129	X-RAY DIFFRACTION	99
3.0826-3.1496	0.2916	207	0.2675	4098	X-RAY DIFFRACTION	100
3.1496-3.2228	0.3342	220	0.2691	4229	X-RAY DIFFRACTION	99
3.2228-3.3034	0.3139	214	0.2521	3996	X-RAY DIFFRACTION	99
3.3034-3.3927	0.2857	225	0.2449	4173	X-RAY DIFFRACTION	100
3.3927-3.4925	0.2821	225	0.2402	4142	X-RAY DIFFRACTION	100
3.4925-3.6052	0.2645	205	0.229	4094	X-RAY DIFFRACTION	100
3.6052-3.734	0.2728	218	0.2244	4132	X-RAY DIFFRACTION	100
3.734-3.8834	0.273	218	0.2257	4167	X-RAY DIFFRACTION	100
3.8834-4.0601	0.2427	220	0.1971	4131	X-RAY DIFFRACTION	99
4.0601-4.274	0.2004	212	0.1869	4121	X-RAY DIFFRACTION	99
4.274-4.5416	0.2126	216	0.1723	4157	X-RAY DIFFRACTION	99
4.5416-4.8919	0.1575	224	0.1593	4105	X-RAY DIFFRACTION	100
4.8919-5.3836	0.1935	209	0.1753	4058	X-RAY DIFFRACTION	99
5.3836-6.1611	0.1908	218	0.191	4138	X-RAY DIFFRACTION	99
6.1611-7.7568	0.2374	216	0.2021	4130	X-RAY DIFFRACTION	100
7.7568-47.3207	0.2117	215	0.181	4138	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	0.9889	-0.4251	-0.0682	1.3776	0.1665	1.2664	-0.027	0.2938	0.1553	0.0386	0.0596	-0.2218	-0.3144	0.7328	0.0434	0.379	-0.1672	-0.0285	0.803	0.0718	0.4129	8.2496	-30.0379	-9.4501
2	2.127	-0.0935	0.0277	1.8467	-0.2313	2.2107	0.0613	-0.2682	0.3905	0.3815	-0.0865	-0.176	-0.49	0.4306	-0.0028	0.5363	-0.1736	-0.0398	0.5336	-0.0671	0.4164	1.9369	-21.1641	12.6772
3	0.7867	0.1732	0.2309	0.9957	0.3484	3.93	-0.019	0.4283	0.0792	-0.4119	0.1169	0.0822	-0.4244	-0.2046	-0.1121	0.4506	-0.0427	-0.0773	0.818	0.1594	0.444	-11.4652	-28.6009	-38.2076
4	1.974	0.7108	0.1045	2.1347	-0.4401	2.2582	0.025	0.4064	0.2689	-0.2582	-0.1385	-0.2145	-0.5205	0.7414	0.131	0.5957	-0.2186	-0.0172	1.1171	0.1934	0.4861	11.3748	-24.253	-42.4652
5	1.0531	-0.0475	-0.2209	0.732	-0.5734	3.7901	0.0687	0.4095	-0.1188	-0.1981	0.0123	0.16	-0.3046	-0.1556	-0.0697	0.3856	-0.1208	-0.1267	0.7988	0.1161	0.4398	-13.1334	-35.6468	-29.7916
6	1.7917	0.0325	-0.0564	1.8877	2.102	3.667	-0.1109	-0.1556	0.1368	0.3319	-0.0289	0.4485	0.1437	-0.7629	0.0767	0.3473	0.0336	0.0404	0.7565	0.1362	0.5342	-30.0236	-38.236	4.8962
7	2.5989	-0.7306	1.0403	1.1971	-0.0791	2.0369	0.2103	-0.1774	-0.2134	0.0261	0.1292	0.6105	0.5503	-0.8405	-0.3423	0.4459	-0.2436	-0.0846	0.9532	0.2734	0.6722	-32.255	-54.8392	-2.5567
8	2.9814	0.6788	-1.1869	1.225	-0.834	3.2109	-0.0179	0.1546	-0.2762	-0.2293	0.0668	-0.0191	0.4696	0.1182	-0.0506	0.317	0.0148	-0.0863	0.4851	0.0122	0.3982	-1.7592	-56.1257	-11.2844
9	2.1322	1.1984	0.856	3.3347	0.3487	0.3574	0.2385	0.0177	-0.0995	0.422	-0.1326	0.3995	-0.0801	-0.0289	-0.1081	0.2812	0.0208	0.0291	0.4937	0.1168	0.3978	-16.3132	-39.8448	11.6568
10	2.7158	0.3086	0.313	5.3158	-0.7737	4.9531	0.0843	-0.1898	-0.2414	0.6086	0.0688	0.2266	0.4366	-0.2991	-0.1684	0.4028	-0.0472	-0.0898	0.682	0.1227	0.4163	-13.6051	-54.5842	25.4036
11	6.2998	-2.4222	-1.087	3.457	-0.0655	2.1275	0.4314	-0.3945	-0.7756	0.2923	0.0333	0.4263	0.6561	-0.5088	-0.4173	0.8044	-0.1956	-0.246	0.8079	0.2646	0.6403	-13.7815	-68.2873	25.9917
12	6.2823	1.0976	-0.0127	2.1468	-0.3558	2.5958	0.0945	0.0104	-0.9643	0.1201	-0.0403	-0.141	0.7726	0.0517	0.0014	0.8171	-0.0097	-0.2928	0.6508	0.1051	0.798	-0.3817	-76.2117	24.329
13	3.1157	-2.6544	-0.451	4.1466	0.3747	0.0634	0.3375	-0.4042	-0.3244	0.9816	-0.0233	-0.4867	0.3528	1.3354	-0.0855	0.7755	0.0343	-0.2826	0.8871	0.1306	0.6919	10.1465	-66.2452	29.3613
14	4.4968	-1.5511	1.3901	3.7334	0.5007	5.4315	-0.0146	-0.6171	-0.3145	0.844	0.123	-0.4579	0.1584	0.7021	-0.1657	0.6362	-0.0407	-0.2274	0.8604	0.1203	0.5687	10.6454	-56.6973	29.2798
15	6.1778	-0.216	1.3062	6.6489	-3.281	6.6121	0.1689	-0.1773	-0.1381	0.8891	0.1338	0.1076	0.3002	0.1755	-0.3292	0.524	-0.078	-0.0822	0.6418	0.1272	0.3124	-0.7923	-48.1167	28.4766
16	3.3379	-1.875	0.3672	7.0347	-4.0665	3.9051	0.0494	-0.7126	0.2148	1.2123	0.1867	0.1873	-0.8832	-0.0547	-0.1826	0.6876	-0.1792	-0.0658	0.8637	0.1048	0.417	-12.3398	-50.9861	31.063

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 129 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 130 through 380 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 381 through 652 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 653 through 895 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 896 through 1043 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1044 through 1109 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1110 through 1207 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 1208 through 1443 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 54 through 91 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 92 through 138 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 139 through 180 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 181 through 240 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 241 through 269 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 270 through 333 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 334 through 367 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 368 through 410 )

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