PDB-4b6h: Structure of hDcp1a in complex with proline rich sequence of PNRC2

ID or keywords:

Entry

Database: PDB / ID: 4b6h

Title

Structure of hDcp1a in complex with proline rich sequence of PNRC2

Components

MRNA-DECAPPING ENZYME 1A
PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2

Keywords

HYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX /

DECAPPING

Function / homology

Function and homology information

mRNA methylguanosine-cap decapping / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / protein localization to cytoplasmic stress granule / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.6 Å

Authors

Lai, T. / Song, H.

Citation

Journal: Structure / Year: 2012
Title: Structural Basis of the Pnrc2-Mediated Link between Mrna Surveillance and Decapping.
Authors: Lai, T. / Cho, H. / Liu, Z. / Bowler, M.W. / Piao, S. / Parker, R. / Kim, Y.K. / Song, H.

History

Deposition	Aug 13, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 6, 2013	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4b6h.cif.gz	124.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4b6h.ent.gz	103.2 KB	Display	PDB format
PDBx/mmJSON format	4b6h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b6/4b6h ftp://data.pdbj.org/pub/pdb/validation_reports/b6/4b6h	HTTPS FTP

-
Related structure data

Similar structure data	6mu0-d 5fie-d 1hhq-d 2vvw-3 5nvi-d 3mtk-1 4jgb-2 1pae-d 6y41-9 6xy6-4 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (2) #86 - Feb 2007 Exosomes similarity (2) #60 - Dec 2004 Ubiquitin similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: MRNA-DECAPPING ENZYME 1A

B: MRNA-DECAPPING ENZYME 1A

C: PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2

D: PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2

61.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: MRNA-DECAPPING ENZYME 1A

C: PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2

defined by author&software
30.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: MRNA-DECAPPING ENZYME 1A

D: PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2

defined by author&software
30.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.091, 97.639, 109.688
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A AND (RESSEQ 27:43 OR RESSEQ 48:75 OR RESSEQ 81:130 )
2	1	1	CHAIN B AND (RESSEQ 27:43 OR RESSEQ 48:75 OR RESSEQ 81:130 )
1	1	2	CHAIN C AND (RESSEQ 170:180 )
2	1	2	CHAIN D AND (RESSEQ 170:180 )

NCS ensembles :

ID
1
2

#1: Protein	MRNA-DECAPPING ENZYME 1A / HDCP1A / SMAD4-INTERACTING TRANSCRIPTIONAL CO-ACTIVATOR / TRANSCRIPTION FACTOR SMIF Mass: 15492.594 Da / Num. of mol.: 2 / Fragment: EVH1 DOMAIN, RESIDUES 1-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: Q9NPI6, Hydrolases
#2: Protein	PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2 / PNRC2 Mass: 15125.746 Da / Num. of mol.: 2 / Fragment: PROLINE RICH SEQUENCE, RESIDUES 1-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: Q9NPJ4
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.18 Å³/Da / Density % sol: 61.4 % / Description: NONE
Crystal grow	Details: 27% PEG3350, 0.15M AMMONIUM ACETATE, 0.1M BIS TRIS PH5.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9793
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.6→72 Å / Num. obs: 12614 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / R_merge(I) obs: 0.04 / Net I/σ(I): 19.1
Reflection shell	Resolution: 2.6→2.6 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.17 / Mean I/σ(I) obs: 4.9 / % possible all: 91

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.6.1_357)	refinement
MOSFLM		data reduction
SCALA		data scaling
SnB		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2.6→72.931 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 30.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2847	1262	10 %
R_work	0.2335	-	-
obs	0.2388	12614	97.58 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 80.522 Å² / k_sol: 0.369 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.3046 Å²	0 Å²	0 Å²
2-	-	-6.005 Å²	0 Å²
3-	-	-	4.7004 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→72.931 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2086	0	0	66	2152

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2137
X-RAY DIFFRACTION	f_angle_d	1.239	2902
X-RAY DIFFRACTION	f_dihedral_angle_d	17.725	771
X-RAY DIFFRACTION	f_chiral_restr	0.082	319
X-RAY DIFFRACTION	f_plane_restr	0.004	366

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	782	X-RAY DIFFRACTION	POSITIONAL
1	2	B	782	X-RAY DIFFRACTION	POSITIONAL	0.241
2	1	C	89	X-RAY DIFFRACTION	POSITIONAL
2	2	D	89	X-RAY DIFFRACTION	POSITIONAL	0.196

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 (%)
2.6001-2.7042	0.4158	141	0.3174	1267	X-RAY DIFFRACTION	100
2.7042-2.8272	0.354	142	0.2972	1275	X-RAY DIFFRACTION	99
2.8272-2.9763	0.3459	139	0.2869	1258	X-RAY DIFFRACTION	100
2.9763-3.1628	0.3364	141	0.2729	1275	X-RAY DIFFRACTION	100
3.1628-3.407	0.3169	140	0.2528	1255	X-RAY DIFFRACTION	99
3.407-3.7498	0.264	143	0.2302	1279	X-RAY DIFFRACTION	99
3.7498-4.2924	0.2742	140	0.1876	1264	X-RAY DIFFRACTION	98
4.2924-5.4077	0.1957	140	0.1705	1264	X-RAY DIFFRACTION	97
5.4077-72.9592	0.3018	136	0.2456	1215	X-RAY DIFFRACTION	88

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	1.8331	-0.2796	3.9697	2.9482	-0.5451	8.4976	-0.1856	0.2046	-1.0936	-0.7506	-0.3247	0.0442	-0.2097	-1.4543	0.7435	0.4396	0.0793	-0.0445	0.1384	-0.104	0.3876	-4.5729	-43.517	-0.7444
2	8.4808	-1.3124	-3.6641	0.4138	0.5213	1.7932	-0.0049	-0.2919	-2.1642	-0.0077	-0.4915	-0.0536	-0.2969	0.5242	0.3347	0.5104	-0.0628	-0.0362	0.3198	0.0717	0.591	-11.792	-44.6617	14.8732
3	2.863	-0.714	2.5189	3.8209	0.4834	3.6975	0.3341	-0.2444	0.9582	-0.3044	-0.3087	-1.0368	0.2461	-0.3593	-0.1182	0.2456	-0.0056	0.021	0.3484	-0.1956	0.5943	2.817	-25.6851	19.8896
4	3.399	0.4573	-1.3298	4.0965	-0.3591	7.6443	0.1052	-0.2897	0.0423	-0.0534	0.2717	0.1401	0.417	0.4243	-0.4175	0.2563	-0.0399	-0.0334	0.1742	0.0495	0.2409	-11.0937	-36.5628	15.663
5	4.4977	-1.1697	0.9542	2.7462	1.3076	1.4845	-0.2559	0.4781	-0.8661	1.4467	0.279	-0.3137	1.0955	-0.2445	0.0054	0.4804	0.0058	-0.0367	0.4666	-0.043	0.2868	-2.3556	-36.7856	19.2284
6	2.3347	-1.5426	1.2855	2.7841	-2.1077	1.9485	0.037	-0.7362	1.1589	-0.6575	-1.377	0.2714	-0.1173	0.1674	-0.6465	0.4441	-0.2292	0.1346	0.5069	-0.3964	-0.0032	-10.3542	-21.5088	19.1481
7	3.176	-0.9856	-0.0168	4.0419	2.0881	3.2579	0.6601	-0.7524	0.6525	0.408	0.5276	-0.9835	-0.784	0.4223	-0.9002	0.1891	-0.0914	0.0842	0.3301	-0.1086	0.3702	-3.3916	-24.4893	18.8981
8	7.016	-3.6768	-2.6762	4.5536	0.1938	2.8838	0.2236	0.6687	0.4593	-0.8712	-0.2854	-0.5975	-0.3179	-0.7086	-0.1049	0.2725	0.01	-0.0836	0.3646	-0.054	0.2239	-13.2603	-25.6884	11.0533
9	5.2427	-4.0798	0.5285	4.7907	-3.064	1.9913	0.3109	0.4406	1.1219	-0.7401	-0.6889	-1.2758	2.3816	-1.3799	0.5203	0.1557	-0.0242	0.204	0.5906	-0.1204	0.5959	-10.0155	-3.6494	25.5909
10	4.3727	0.2196	-4.1579	3.9767	-0.654	5.6488	0.5067	3.2345	-0.0132	-0.6046	-0.1657	-1.1031	0.368	0.418	-0.0855	0.6152	0.3574	-0.0608	0.7113	0.0155	0.6186	-29.1931	-6.97	15.0311
11	9.7894	-6.8401	0.3113	9.769	4.6183	6.8632	1.0606	0.9966	1.4577	-4.4992	-1.8829	0.6526	-1.6734	-0.5369	1.2829	1.0234	0.4202	-0.3605	0.9319	-0.1956	0.1175	-29.8843	-3.9446	12.7605
12	5.3854	-3.8971	-3.658	8.3027	6.4159	5.0639	0.5856	-0.2413	1.7442	-0.0834	1.3002	-2.7089	-0.1854	0.6553	-1.9384	0.4415	-0.1215	0.1284	0.5213	-0.2333	0.7972	-14.3517	-3.5946	28.9943
13	2.1016	0.2499	-0.8906	7.7556	1.3013	1.023	1.1195	0.2877	3.9286	-2.454	-0.7439	1.0326	0.8276	-0.4149	-0.4197	0.7375	-0.0126	0.2193	0.4612	0.191	1.4414	-18.6038	2.4761	16.0705
14	5.1882	2.3814	3.9402	6.3126	7.216	8.6444	1.2861	0.7356	-0.2069	1.3676	-0.4532	-1.0853	1.7885	-1.5465	0.7137	0.3562	0.1124	0.1416	0.4084	-0.1021	0.3883	-24.9094	-9.6431	27.1241
15	8.0618	0.6079	-1.9812	3.5572	0.8749	3.6004	-0.052	1.4602	1.2278	-0.1544	-0.6962	-0.3561	-0.5206	-1.2551	0.6722	0.5249	0.2994	-0.0136	0.8619	-0.0281	0.4572	-26.3347	-9.7116	20.0063
16	0.5126	1.5359	0.5377	3.8377	1.5115	0.5298	0.4257	0.2183	-0.3172	0.6539	-0.7185	-0.0242	0.4091	-0.1669	0.0185	0.5381	-0.0444	0.1433	0.5998	-0.1129	0.3184	-17.0855	-15.8407	24.379
17	5.6818	-0.2202	-1.9383	1.3063	1.8165	4.2018	0.699	-0.2745	2.3812	-0.5263	0.5591	-0.4213	0.0547	0.3144	-1.1695	0.361	-0.0002	0.0775	0.3788	-0.1116	0.7989	0.1781	-17.296	21.4707
18	6.3896	3.8512	4.6697	9.5799	8.3488	7.73	0.7629	-1.1785	-0.0715	1.7965	-2.0941	1.2788	2.8557	-1.484	0.0238	0.4234	0.1707	-0.038	0.5376	-0.1169	0.2377	-34.2789	-13.8288	18.8035

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 4:15)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 16:31)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 32:54)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 55:74)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 75:87)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 88:96)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 97:114)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 115:134)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 24:35)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 36:46)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 47:55)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 56:71)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 72:81)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 82:96)
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 97:115)
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 116:130)
17	X-RAY DIFFRACTION	17	(CHAIN C AND RESID 167:180)
18	X-RAY DIFFRACTION	18	(CHAIN D AND RESID 167:180)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi