PDB-4j81: Crystal structure of beta'-COP/Insig-1 complex

ID or keywords:

Entry

Database: PDB / ID: 4j81

Title

Crystal structure of beta'-COP/Insig-1 complex

Components

Coatomer subunit beta'
Insulin-induced gene 1 protein

Keywords

PROTEIN TRANSPORT / Beta propeller domain / dilysine motif / COPI / ER retrieval

Function / homology

Function and homology information

negative regulation of protein exit from endoplasmic reticulum / negative regulation of cargo loading into COPII-coated vesicle / SREBP-SCAP complex retention in endoplasmic reticulum / SREBP-SCAP-Insig complex / cranial suture morphogenesis / negative regulation of steroid biosynthetic process / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / sterol biosynthetic process ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.745 Å

Authors

Ma, W. / Goldberg, J.

Citation

Journal: Embo J. / Year: 2013
Title: Rules for the recognition of dilysine retrieval motifs by coatomer.
Authors: Ma, W. / Goldberg, J.

History

Deposition	Feb 14, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	4j81.cif.gz	258.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4j81.ent.gz	212.4 KB	Display	PDB format
PDBx/mmJSON format	4j81.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4j81_validation.pdf.gz	435.3 KB	Display	wwPDB validaton report
Full document	4j81_full_validation.pdf.gz	436.9 KB	Display
Data in XML	4j81_validation.xml.gz	28.2 KB	Display
Data in CIF	4j81_validation.cif.gz	42.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j8/4j81 ftp://data.pdbj.org/pub/pdb/validation_reports/j8/4j81	HTTPS FTP

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Related structure data

Related structure data	4j73C 4j77C 4j78C 4j79C 4j82C 4j84C 4j86C 4j87C 4j8bC 4j8gC C: citing same article (ref.)
Similar structure data	4j77-1 4j78-d 4j79-d 4j73-d 4j84-2 4j84-1 4j86-1 4j82-1 4j77-2 4j82-2 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	#205 - Jan 2017 Nuclear Pore Complex similarity (1) #85 - Jan 2007 Importins similarity (1)

Deposited unit

A: Coatomer subunit beta'

B: Coatomer subunit beta'

C: Insulin-induced gene 1 protein

D: Insulin-induced gene 1 protein

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

1

A: Coatomer subunit beta'

D: Insulin-induced gene 1 protein

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

2

B: Coatomer subunit beta'

C: Insulin-induced gene 1 protein

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

Unit cell

Length a, b, c (Å)	48.661, 48.758, 75.208
Angle α, β, γ (deg.)	89.75, 89.63, 63.95
Int Tables number	1
Space group name H-M	P1

#1: Protein	Coatomer subunit beta' / Beta'-coat protein / Beta'-COP Mass: 34293.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41811
#2: Protein/peptide	Insulin-induced gene 1 protein / INSIG-1 Mass: 584.622 Da / Num. of mol.: 2 / Fragment: UNP residues 273-277 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15503
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.48 %

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E
Detector	Type: ADSC QUANTUM 315 / Detector: CCD
Radiation	Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 1.74→50 Å / Num. all: 60481 / Num. obs: 60453 / % possible obs: 95.9 % / Observed criterion σ(I): 3.4

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Processing

Software

Name	Version	Classification
ADSC		data collection
PHENIX	(phenix.refine: 1.7.3_928)	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.745→37.713 Å / SU ML: 0.17 / σ(F): 1.98 / Phase error: 18.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1983	1984	3.28 %	RANDOM
R_work	0.1584	-	-	-
obs	0.1597	60453	95.64 %	-
all	-	60481	-	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 45.207 Å² / k_sol: 0.372 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.6606 Å²	2.1321 Å²	5.0794 Å²
2-	-	-1.4218 Å²	3.34 Å²
3-	-	-	0.7612 Å²

Refinement step

Cycle: LAST / Resolution: 1.745→37.713 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4873	0	0	588	5461

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5013
X-RAY DIFFRACTION	f_angle_d	1.178	6843
X-RAY DIFFRACTION	f_dihedral_angle_d	12.477	1768
X-RAY DIFFRACTION	f_chiral_restr	0.092	756
X-RAY DIFFRACTION	f_plane_restr	0.006	870

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 (%)
1.745-1.7886	0.2412	132	0.2221	3987	X-RAY DIFFRACTION	90
1.7886-1.8369	0.24	122	0.1956	4173	X-RAY DIFFRACTION	96
1.8369-1.891	0.2241	147	0.1747	4197	X-RAY DIFFRACTION	96
1.891-1.952	0.1908	142	0.1595	4239	X-RAY DIFFRACTION	96
1.952-2.0218	0.2204	130	0.1486	4184	X-RAY DIFFRACTION	96
2.0218-2.1027	0.1674	168	0.1488	4184	X-RAY DIFFRACTION	97
2.1027-2.1984	0.2025	154	0.1484	4245	X-RAY DIFFRACTION	97
2.1984-2.3143	0.1787	124	0.1563	4276	X-RAY DIFFRACTION	97
2.3143-2.4593	0.2196	151	0.1536	4244	X-RAY DIFFRACTION	97
2.4593-2.6491	0.2261	119	0.16	4232	X-RAY DIFFRACTION	98
2.6491-2.9156	0.1896	160	0.1508	4270	X-RAY DIFFRACTION	98
2.9156-3.3373	0.1673	141	0.1502	4236	X-RAY DIFFRACTION	97
3.3373-4.2038	0.1857	167	0.1458	4040	X-RAY DIFFRACTION	93
4.2038-37.7215	0.2179	127	0.1725	3962	X-RAY DIFFRACTION	90

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	0.3568	0.2002	-0.0744	0.6444	0.0027	0.4719	-0.0335	-0.0602	-0.075	0.0478	0.1024	0.2594	-0.0644	0.0028	0.0503	0.0825	-0.0002	0.0005	0.0908	0.0221	0.1355	-119.9227	68.3294	122.1343
2	0.3029	-0.1427	-0.2905	0.1359	0.0102	0.2548	-0.0655	-0.1193	0.0123	0.025	-0.0091	0.1367	0.0587	0.0969	-0.0419	0.1038	-0.0077	-0.0077	0.1088	0.0036	0.1146	-109.4545	58.281	117.838
3	0.3884	-0.1101	-0.2083	0.5917	-0.3532	0.427	-0.0558	-0.0336	-0.0965	-0.1426	-0.0033	0.0138	0.1489	0.0802	-0.0256	0.1212	0.0022	-0.004	0.0959	-0.0081	0.0996	-104.3156	57.4535	110.2213
4	0.0224	-0.0946	0.0571	0.1411	0.0019	0.1014	0.0274	0.0705	0.0153	-0.1304	-0.0121	-0.1099	-0.0732	0.115	0.0001	0.1239	0.0027	-0.0001	0.1372	0.0097	0.1158	-100.694	69.3958	105.2432
5	0.1197	-0.0158	-0.1818	0.0846	-0.0499	0.0868	0.0589	0.0547	0.0074	-0.084	-0.0581	-0.1928	0.0289	0.1886	-0.0043	0.1314	0.0153	0.0329	0.1342	0.0054	0.1193	-95.7212	71.3736	101.2268
6	0.0087	-0.0678	0.0447	0.071	-0.0175	0.0656	0.0821	0.0158	0.2516	0.0199	-0.1555	0.0222	-0.0664	0.0959	0.0014	0.1117	-0.0212	-0.0171	0.1379	0.008	0.0992	-104.9033	79.1831	105.4328
7	0.1975	-0.3532	-0.0107	0.6448	-0.1038	0.1371	0.092	0.0372	0.0634	-0.0079	-0.0842	-0.0341	-0.0887	0.035	0.007	0.1105	-0.0161	-0.0044	0.106	0.0107	0.1145	-106.5214	83.4669	108.1759
8	0.1644	-0.0445	-0.0211	0.1568	0.0261	0.0626	0.0318	0.0377	0.1364	0.0848	-0.0128	0.0406	-0.3395	0.1025	0.0015	0.1879	0.0082	0.0064	0.0964	0.0096	0.1249	-113.1724	88.2153	114.8262
9	0.2782	-0.0443	-0.4034	0.9222	0.0359	0.6884	-0.0234	-0.0215	-0.0128	0.016	0.1415	0.243	-0.2526	-0.0854	0.1523	0.1375	0.0053	-0.0133	0.0871	0.0203	0.128	-117.9882	76.226	119.0324
10	0.4475	0.0111	0.0863	0.1884	0.0348	0.2973	0.0869	-0.0175	0.236	-0.1216	-0.0235	-0.2061	-0.036	-0.0896	0.0314	0.0984	0.0029	0.02	0.106	-0.0151	0.1634	-123.5113	69.3889	67.9998
11	0.0503	-0.1098	-0.0947	0.2601	-0.0359	0.1703	0.1021	0.0009	0.2406	-0.1819	-0.1105	-0.0935	-0.0119	-0.0185	0.0581	0.1365	0.0009	0.0362	0.0856	-0.0057	0.1825	-116.3201	66.0481	63.3519
12	0.0714	-0.1002	-0.0316	0.4228	-0.3403	0.3773	-0.0112	-0.0325	0.0906	-0.0926	-0.0359	-0.0879	0.1311	0.0509	-0.0269	0.0967	-0.0051	0.0006	0.1202	-0.0104	0.1211	-116.1268	54.2389	70.5625
13	0.6295	-0.127	-0.3572	0.696	-0.0125	0.4194	-0.093	-0.1649	-0.0761	-0.0449	0.0119	-0.1031	0.1432	0.1285	-0.0551	0.1007	0.0135	-0.0064	0.1154	0.0015	0.0955	-117.499	49.2256	77.7975
14	0.0727	-0.1606	0.0259	0.1469	-0.0529	0.0806	-0.0748	-0.0961	-0.0931	0.1382	0.0591	0.1215	0.0809	-0.0584	0.0005	0.1194	-0.0014	0.0024	0.1172	-0.0034	0.1045	-129.9721	51.1084	82.883
15	0.1192	0.0154	-0.1896	0.1457	-0.1308	0.1661	-0.0591	-0.016	-0.1403	0.1394	0.0548	0.1147	0.0639	-0.0054	-0.0037	0.131	0.0085	0.0188	0.108	0.023	0.127	-133.941	47.4789	86.89
16	0.0487	-0.0149	-0.1223	0.0328	0.016	0.1057	-0.0952	0.1037	0.0267	0.1064	0.0972	0.1514	0.0327	-0.0792	0.0167	0.1103	-0.006	-0.0084	0.1265	-0.018	0.0894	-136.9658	59.4117	82.9493
17	0.5097	-0.5117	-0.2591	0.5421	-0.1766	0.3857	-0.0222	0.0603	0.0032	0.1137	0.0426	0.1054	-0.0755	-0.0967	0.022	0.0984	-0.0142	0.0019	0.1285	-0.011	0.1146	-140.0366	62.5578	79.9928
18	0.2292	0.0419	-0.0052	0.187	-0.1802	0.2826	0.0773	0.075	0.1988	0.034	0.0183	0.1579	-0.1921	-0.3536	0.006	0.1483	0.0386	0.0179	0.1708	-0.0061	0.1388	-141.6389	70.9114	73.6987
19	0.6681	-0.5131	-0.2494	0.3822	-0.1138	0.5083	0.1222	-0.009	0.3232	-0.082	0.031	-0.0496	-0.1422	-0.1403	0.1124	0.1107	0.0175	0.0163	0.1029	-0.0339	0.1458	-128.5263	69.6109	69.163
20	0.0166	-0.0088	0.0067	0.0077	-0.004	0.0008	-0.0025	-0.0087	-0.0848	-0.1274	-0.2656	0.0904	-0.0718	-0.2159	0.0002	0.2273	-0.0173	-0.0131	0.1548	-0.0278	0.1443	-134.3111	49.0169	64.2347
21	-0.0033	0.0025	-0.0033	0.0061	0.0092	0.0008	-0.2876	-0.0732	0.0359	-0.0688	-0.1752	-0.083	-0.1457	0.0284	-0.0005	0.133	0.0152	-0.032	0.201	0.0202	0.1626	-96.7814	72.3341	123.8327

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:52)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 53:83)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 84:136)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 137:160)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 161:180)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 181:199)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 200:247)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 248:267)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 268:301)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 2:32)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 33:52)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 53:83)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 84:136)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 137:160)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 161:180)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 181:199)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 200:247)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 248:267)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 268:301)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 1:5)
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 1:5)

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