PDB-4j77: Crystal structure of beta'-COP/hWbp1 complex

ID or keywords:

Entry

Database: PDB / ID: 4j77

Title

Crystal structure of beta'-COP/hWbp1 complex

Components

Coatomer subunit beta'
Wbp1

Keywords

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

Function / homology

Function and homology information

COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding / intracellular protein transport ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.756 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 12, 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	4j77.cif.gz	260.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4j77.ent.gz	212.8 KB	Display	PDB format
PDBx/mmJSON format	4j77.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4j77_validation.pdf.gz	445.3 KB	Display	wwPDB validaton report
Full document	4j77_full_validation.pdf.gz	448.4 KB	Display
Data in XML	4j77_validation.xml.gz	29 KB	Display
Data in CIF	4j77_validation.cif.gz	44.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j7/4j77 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/4j77	HTTPS FTP

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Related structure data

Related structure data	4j73C 4j78C 4j79C 4j81C 4j82C 4j84C 4j86C 4j87C 4j8bC 4j8gC C: citing same article (ref.)
Similar structure data	4j86-1 4j73-d 4j82-2 4j79-d 4j81-1 4j86-2 4j82-1 4j78-d 4j84-2 4j84-1 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

C: Wbp1

A: Coatomer subunit beta'

B: Coatomer subunit beta'

D: Wbp1

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

1

C: Wbp1

A: Coatomer subunit beta'

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

2

B: Coatomer subunit beta'

D: Wbp1

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

Unit cell

Length a, b, c (Å)	75.681, 50.935, 82.421
Angle α, β, γ (deg.)	90.00, 90.24, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein/peptide	Wbp1 / dolichyl-diphosphooligosaccharide--protein glycosyltransferase Mass: 678.732 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: 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
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.27 Å³/Da / Density % sol: 45.84 %

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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: 1.756→75.68 Å / Num. obs: 60204 / % possible obs: 97.8 % / Observed criterion σ(I): 8.4

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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: 1.756→36.129 Å / SU ML: 0.19 / σ(F): 1.33 / Phase error: 34.79 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2451	1632	3.34 %	RANDOM
R_work	0.2018	-	-	-
obs	0.2032	60204	95.58 %	-
all	-	61347	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.756→36.129 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4888	0	0	599	5487

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	5022
X-RAY DIFFRACTION	f_angle_d	1.557	6840
X-RAY DIFFRACTION	f_dihedral_angle_d	13.349	1784
X-RAY DIFFRACTION	f_chiral_restr	0.119	755
X-RAY DIFFRACTION	f_plane_restr	0.008	865

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 (%)
1.756-1.7998	0.3622	127	0.2549	3933	X-RAY DIFFRACTION	92
1.7998-1.8485	0.2835	144	0.2382	4138	X-RAY DIFFRACTION	96
1.8485-1.9029	0.2611	147	0.2197	4197	X-RAY DIFFRACTION	97
1.9029-1.9643	0.253	152	0.2127	4169	X-RAY DIFFRACTION	97
1.9643-2.0345	0.2855	129	0.2146	4174	X-RAY DIFFRACTION	96
2.0345-2.116	0.2328	164	0.2084	4192	X-RAY DIFFRACTION	96
2.116-2.2122	0.2437	150	0.198	4148	X-RAY DIFFRACTION	96
2.2122-2.3289	0.2274	134	0.2037	4163	X-RAY DIFFRACTION	96
2.3289-2.4747	0.2645	137	0.1988	4143	X-RAY DIFFRACTION	95
2.4747-2.6658	0.2489	148	0.2046	4153	X-RAY DIFFRACTION	95
2.6658-2.9339	0.2468	152	0.2033	4146	X-RAY DIFFRACTION	95
2.9339-3.3582	0.2668	146	0.1928	4187	X-RAY DIFFRACTION	96
3.3582-4.2299	0.1909	148	0.1798	4238	X-RAY DIFFRACTION	96
4.2299-36.1364	0.2444	134	0.1994	4211	X-RAY DIFFRACTION	94

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	1.2481	-0.4632	0.2896	3.4891	-0.682	1.7337	0.0792	0.1999	-0.1351	-0.1754	0.0022	-0.1074	0.2099	0.1007	-0.0307	0.4218	-0.0189	0.0845	0.9529	-0.2928	0.4919	-46.3938	-15.6979	-43.7426
2	1.5314	0.0028	0.2282	1.6625	-0.0202	0.9756	-0.0117	0.3334	0.1013	0.3573	0.0821	-0.1329	-0.0718	-0.0034	-0.0809	0.3312	0.0486	-0.0455	0.318	0.0095	0.2845	-47.5516	-5.2225	-20.6569
3	1.9596	0.0793	-0.4212	1.5945	-0.0151	1.8196	0.0521	0.6133	-0.4144	0.0554	0.087	0.0034	0.1271	0.0205	-0.1955	0.2696	0.0358	-0.0308	0.3737	-0.0849	0.2807	-51.6793	-19.6198	-24.6122
4	1.0387	0.2083	0.5348	1.1173	-0.2031	0.7745	0.083	0.4397	-0.4216	0.0829	0.1812	-0.0227	0.1536	-0.0131	-0.2132	0.2721	0.0378	-0.0131	0.4493	-0.1029	0.3248	-59.4138	-23.0379	-28.0215
5	0.3983	0.2871	-0.3485	0.6764	-0.1865	0.7095	0.0183	0.9295	-0.1127	-0.0116	0.2557	0.0794	-0.003	0.0478	-0.0587	0.2698	0.0416	-0.0297	0.8267	-0.1268	0.3496	-64.4544	-14.3476	-37.0861
6	0.7924	0.0419	0.2076	0.6419	0.0235	0.0566	-0.0068	0.4232	0.0721	-0.1608	0.0315	0.3432	-0.113	-0.0246	0.0031	0.2201	-0.0897	-0.1882	1.1381	-0.2574	0.343	-68.3578	-16.1577	-42.6314
7	1.3332	-0.3396	-0.1884	1.0523	0.2416	1.2061	0.0204	0.5716	0.2232	-0.1658	0.0506	0.0859	-0.195	0.2282	-0.1137	0.3332	0.0679	-0.0411	0.8494	0.0886	0.3514	-63.889	-4.3061	-39.2402
8	0.2765	-0.0978	-0.2328	1.1851	0.3774	0.6585	-0.0483	0.6709	0.1363	-0.2605	-0.2227	0.2815	0.0381	-0.0377	-0.137	0.3336	0.046	-0.0362	1.0065	0.3335	0.3465	-61.4528	0.0279	-40.1315
9	0.1825	-0.1428	0.056	0.3527	0.0138	0.2148	-0.052	0.3533	0.044	-0.1939	-0.0592	0.1132	-0.1866	-0.1288	0.0086	0.3727	0.1193	-0.0889	1.0187	0.6761	0.5231	-55.2613	7.6667	-37.0304
10	1.1156	0.1778	-0.0984	1.4588	0.202	1.67	-0.1002	0.4629	0.4359	0.1944	0.1139	-0.0965	-0.0812	0.128	-0.0256	0.3172	0.0264	-0.0122	0.5945	0.1342	0.2957	-50.1275	-2.163	-29.6469
11	2.6597	-1.5129	-0.7349	2.3755	1.1427	1.6933	-0.0856	0.3348	0.3073	0.1443	0.0489	-0.0565	-0.2844	0.0321	0.0376	0.3489	0.0349	-0.0205	0.3381	0.0835	0.3203	-50.1436	1.0786	-24.6655
12	1.3379	0.4925	0.1153	1.1913	-0.0736	0.3194	0.0241	0.3756	0.2592	-0.3919	-0.0191	0.1844	-0.2162	-0.001	0.0675	0.3081	0.0377	-0.0013	0.3043	0.0183	0.2519	-27.7969	-4.9941	-20.5128
13	1.2631	-0.1443	-0.1564	0.7799	0.1285	1.0774	0.161	0.4252	-0.4221	-0.1908	-0.107	0.0553	-0.0225	0.026	-0.1015	0.2522	0.0505	-0.0114	0.2962	-0.0952	0.2926	-23.573	-19.574	-16.6419
14	1.2386	-0.1798	0.2669	0.9799	0.134	0.9246	0.1236	0.4428	-0.4337	-0.2098	-0.0355	-0.0822	0.1876	0.0182	-0.1061	0.2452	0.0117	0.0195	0.2666	-0.0999	0.3308	-16.1113	-23.0254	-13.1872
15	1.4685	-0.0733	-0.3518	0.9347	0.0251	1.0657	0.0126	0.0232	-0.112	0.0509	-0.0175	-0.1537	0.0073	0.1063	-0.0272	0.1925	-0.0011	-0.0081	0.1887	-0.0182	0.2213	-11.0446	-14.34	-4.1186
16	1.4208	0.1696	0.6166	1.522	-0.2542	0.7584	0.0597	-0.1388	-0.1098	0.1076	-0.0724	-0.2937	-0.0255	0.053	0.0769	0.2119	-0.009	-0.0029	0.203	-0.0015	0.2466	-7.1493	-16.1568	1.4324
17	1.4	0.3832	-0.0363	1.2271	-0.1838	1.2376	0.0129	0.0193	0.1042	0.0529	-0.0286	-0.1483	-0.1606	-0.0223	0.0498	0.1965	0.0034	0.0282	0.171	-0.003	0.2096	-11.6262	-4.3232	-1.9684
18	1.807	0.3154	0.1182	0.9707	0.1629	1.0731	-0.015	-0.2522	0.0362	0.146	-0.0313	-0.0599	-0.1155	-0.0696	0.0398	0.2529	-0.0066	0.0026	0.1973	-0.0071	0.2015	-13.9796	-1.127	1.8793
19	1.3486	-0.2667	0.4427	1.5312	0.3372	0.7565	-0.0528	0.0307	0.427	-0.0994	-0.0058	-0.3285	-0.2781	0.051	0.0375	0.2369	0.005	0.0279	0.1571	0.0204	0.2821	-17.4568	5.075	-6.2915
20	0.8769	-1.0693	0.0016	1.6039	0.5026	1.1154	-0.0629	0.1233	0.2916	-0.0417	0.0874	0.0902	-0.1016	-0.1841	0.0251	0.2107	0.0359	0.0121	0.2055	-0.025	0.342	-27.5782	2.377	-7.5255
21	2.5765	0.1536	-0.0773	1.5602	0.3534	1.1039	-0.0704	0.304	0.3449	-0.3056	-0.041	0.0888	-0.2502	0.1302	0.0583	0.2748	0.0055	-0.0199	0.2695	0.0453	0.2972	-23.725	0.6264	-17.5328
22	1.9914	1.5012	-2.5124	1.1318	-1.8876	3.2875	0.0708	0.1503	-0.0918	-0.0256	-0.0808	-0.3185	0.054	0.2496	-0.0055	0.2957	-0.0079	0.0656	0.3986	0.021	0.242	-29.6115	-16.1655	3.0607

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 1 through 5 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 2 through 52 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 53 through 83 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 84 through 137 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 138 through 160 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 161 through 180 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 181 through 199 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 200 through 247 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 248 through 267 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 268 through 282 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 283 through 301 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1 through 52 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 53 through 83 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 84 through 137 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 138 through 160 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 161 through 180 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 181 through 199 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 200 through 235 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 236 through 261 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 262 through 278 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 279 through 301 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 0 through 5 )

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