PDB-4j8g: Crystal structure of alpha-COP/E19 complex

ID or keywords:

Entry

Database: PDB / ID: 4j8g

Title

Crystal structure of alpha-COP/E19 complex

Components

coatomer subunit alpha
membrane glycoprotein E3 gp19K

Keywords

PROTEIN TRANSPORT / beta propeller domain / dilysine motif / ER retrieval / vesicle trafficking

Function / homology

Function and homology information

COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / cargo receptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity ...
Similarity search - Function

Biological species

Schizosaccharomyces pombe (fission yeast)
unidentified (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.895 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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PDBx/mmCIF format	4j8g.cif.gz	259.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4j8g.ent.gz	211.3 KB	Display	PDB format
PDBx/mmJSON format	4j8g.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4j8g_validation.pdf.gz	446.2 KB	Display	wwPDB validaton report
Full document	4j8g_full_validation.pdf.gz	449.5 KB	Display
Data in XML	4j8g_validation.xml.gz	27.8 KB	Display
Data in CIF	4j8g_validation.cif.gz	41.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j8/4j8g ftp://data.pdbj.org/pub/pdb/validation_reports/j8/4j8g	HTTPS FTP

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Related structure data

Related structure data	4j73C 4j77C 4j78C 4j79C 4j81C 4j82C 4j84C 4j86C 4j87C 4j8bC C: citing same article (ref.)
Similar structure data	2pse-d 2pgb-d 5gx5-d 4d8l-d 1h2j-d 1x2r-d 2ckr-1 4blv-2 3o0d-2 5d9b-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

Deposited unit

A: coatomer subunit alpha

B: coatomer subunit alpha

C: membrane glycoprotein E3 gp19K

D: membrane glycoprotein E3 gp19K

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

1

A: coatomer subunit alpha

C: membrane glycoprotein E3 gp19K

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

2

B: coatomer subunit alpha

D: membrane glycoprotein E3 gp19K

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

Unit cell

Length a, b, c (Å)	64.881, 62.629, 77.261
Angle α, β, γ (deg.)	90.00, 93.64, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	coatomer subunit alpha Mass: 37525.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q96WV5
#2: Protein/peptide	membrane glycoprotein E3 gp19K Mass: 1180.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.02 Å³/Da / Density % sol: 39.22 %

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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: 1.895→50 Å / Num. all: 73818 / Num. obs: 49039 / % possible obs: 99.8 % / Observed criterion σ(I): 2.4

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Processing

Software

Name	Version	Classification
ADSC		data collection
PHENIX	(phenix.refine: 1.8_1069)	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.895→48.104 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 21.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2094	2017	4.12 %	RANDOM
R_work	0.167	-	-	-
obs	0.1687	48995	99.38 %	-
all	-	54368	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.895→48.104 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4953	0	0	469	5422

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	5101
X-RAY DIFFRACTION	f_angle_d	1.475	6937
X-RAY DIFFRACTION	f_dihedral_angle_d	12.977	1767
X-RAY DIFFRACTION	f_chiral_restr	0.109	751
X-RAY DIFFRACTION	f_plane_restr	0.007	877

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 (%)
1.895-1.9424	0.3053	138	0.2513	3081	X-RAY DIFFRACTION	93
1.9424-1.9949	0.2589	144	0.2074	3363	X-RAY DIFFRACTION	100
1.9949-2.0536	0.2458	138	0.1935	3340	X-RAY DIFFRACTION	100
2.0536-2.1199	0.2289	152	0.1802	3376	X-RAY DIFFRACTION	100
2.1199-2.1956	0.2155	137	0.1768	3358	X-RAY DIFFRACTION	100
2.1956-2.2835	0.2929	143	0.213	3363	X-RAY DIFFRACTION	100
2.2835-2.3875	0.2471	149	0.1867	3355	X-RAY DIFFRACTION	100
2.3875-2.5133	0.2455	142	0.1919	3373	X-RAY DIFFRACTION	100
2.5133-2.6708	0.2648	141	0.1896	3370	X-RAY DIFFRACTION	100
2.6708-2.877	0.24	145	0.1821	3386	X-RAY DIFFRACTION	100
2.877-3.1664	0.2065	145	0.1652	3364	X-RAY DIFFRACTION	100
3.1664-3.6245	0.1868	144	0.1491	3416	X-RAY DIFFRACTION	100
3.6245-4.5659	0.1488	149	0.1294	3398	X-RAY DIFFRACTION	100
4.5659-48.1195	0.176	150	0.1474	3435	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	0.0188	-0.017	0.0206	0.0144	-0.0177	0.022	0.0154	0.0053	-0.071	-0.0551	-0.0939	-0.0235	0.0764	0.0627	-0.0001	0.1248	-0.0074	0.0086	0.138	0.0154	0.1279	-6.8532	5.6095	-22.3197
2	0.0247	0.0006	-0.0012	0.0155	-0.0094	0.0036	0.0046	-0.0121	-0.1091	-0.015	-0.0744	-0.0382	0.0452	0.0914	-0.001	0.1519	0.032	-0.0023	0.1102	0.0176	0.1423	-8.1572	-2.8471	-24.5236
3	0.0405	0.0237	0.0334	0.0691	-0.0598	0.1208	-0.0197	0.0725	-0.0123	-0.0622	-0.0077	0.0486	0.014	-0.161	-0.0765	0.0976	-0.0037	0.032	0.0051	0.0128	0.0855	-23.4558	7.4803	-33.2996
4	0.0069	-0.0014	0.0149	0.0069	0.0056	0.0343	-0.0712	0.0055	0.0187	-0.0082	-0.0268	0.0503	-0.0977	-0.0177	-0.0026	0.1377	0.016	0.0026	0.0923	0.0057	0.1747	-26.9793	22.1311	-36.6405
5	0.0092	0.0103	0.0121	0.0177	0.0105	0.0148	-0.033	0.0376	0.075	-0.0392	-0.0319	-0.0961	-0.1585	-0.01	-0	0.1893	-0.0014	-0.0085	0.099	0.0092	0.144	-18.4457	25.2647	-33.0715
6	0.1336	-0.0062	0.0867	0.0061	-0.0051	0.2151	-0.1153	0.0639	0.171	0.1742	-0.0747	-0.2235	-0.2519	0.0429	-0.0295	0.2408	-0.0351	-0.038	0.1052	0.0297	0.2231	-11.2923	26.8886	-28.8642
7	0.0746	-0.0486	0.0942	0.0449	-0.0722	0.1117	-0.0542	0.1134	0.0944	0.0433	-0.1206	-0.1424	-0.1575	0.1732	-0.0199	0.1439	-0.0305	-0.0189	0.1327	0.021	0.1801	-2.922	16.6608	-25.002
8	0.0271	-0.0023	-0.0004	0.0052	-0.0013	0.0095	-0.0079	0.0688	0.0204	-0.031	-0.0029	0.0497	-0.0191	-0.0541	-0	0.1216	-0.0012	0.0127	0.1334	0.0137	0.0988	-23.1597	20.424	-61.4018
9	0.0256	-0.014	0.0356	0.0407	-0.0273	0.0918	-0.0769	0.0913	0.1611	0.0417	0.1171	0.0582	-0.263	-0.0929	-0.0004	0.1357	-0.0076	-0.002	0.1297	0.0297	0.1083	-18.5911	29.0096	-63.8661
10	0.0471	-0.0547	-0.0123	0.1947	-0.0197	0.0199	-0.1792	0.3848	0.0899	-0.0946	0.1741	-0.049	-0.0324	0.0009	0.0058	0.1576	-0.0846	0.002	0.2508	0.0031	0.1545	-7.2673	29.498	-68.5547
11	0.0719	0.1078	0.0593	0.1459	0.0874	0.0474	-0.0389	0.282	-0.099	0.0059	0.2122	-0.2289	0.0472	0.175	0.1567	0.0494	-0.1714	-0.0979	0.3639	-0.2553	0.049	-0.8142	19.3196	-72.6883
12	0.0685	0.0084	0.008	0.1236	0.018	0.0321	-0.0097	0.1003	-0.0064	0.0391	0.0873	-0.1621	0.0512	-0.0078	0.0307	0.1337	-0.0184	0.0142	0.3381	-0.2133	0.209	1.0545	11.7752	-69.6541
13	0.1652	0.0261	-0.0733	0.2469	-0.2399	0.2674	-0.0486	0.2157	-0.2608	0.1299	0.2358	-0.0931	0.1479	0.1204	0.1833	0.1973	0.039	-0.0144	0.2165	-0.1609	0.2354	-10.7916	3.0988	-69.2086
14	0.0212	0.0187	0.0012	0.0188	0.0147	0.0279	-0.0335	0.173	-0.1361	0.0563	0.0445	0.0148	0.0713	-0.0617	-0	0.1629	-0.0268	0.0148	0.1811	-0.024	0.1925	-22.4847	5.6852	-68.8749
15	0.0041	-0.0024	-0.005	0.0098	0.0036	0.0047	-0.0552	0.0489	-0.0267	0.0646	-0.0092	-0.0405	0.0252	0.0198	-0.0001	0.1682	0.0084	0.0252	0.1715	0.004	0.1631	-22.7102	14.9005	-60.8572
16	0.001	0.0002	-0.0015	0.0006	-0.002	0.0048	0.0253	0.0085	-0.0169	-0.0713	0.0297	0.0016	0.0065	0.0071	0	0.2846	-0.1288	-0.0001	0.5267	-0.0007	0.2057	-17.1064	18.3206	-87.409
17	0.0069	-0.0098	0.0045	0.1265	-0.0306	0.0083	0.0089	0.0645	0.0125	-0.0421	-0.0259	-0.0461	0.0044	0.0145	-0.0007	0.1581	0.0483	0.0496	0.3827	0.1502	0.32	-7.1809	12.0629	-47.8244

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 30 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 31 through 50 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 51 through 156 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 157 through 202 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 203 through 225 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 226 through 275 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 276 through 327 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 30 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 31 through 72 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 73 through 114 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 115 through 165 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 166 through 225 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 226 through 275 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 276 through 306 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 307 through 327 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 0 through 10 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 10 )

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