PDB-3mzk: Sec13/Sec16 complex, S.cerevisiae

ID or keywords:

Entry

Database: PDB / ID: 3mzk

Title

Sec13/Sec16 complex, S.cerevisiae

Components

Protein transport protein SEC13
Protein transport protein SEC16

Keywords

PROTEIN TRANSPORT / alpha-helical-stack / beta-propeller

Function / homology

Function and homology information

Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein localization to endoplasmic reticulum exit site / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / COPII vesicle coat ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.69 Å

Authors

Whittle, J.R. / Schwartz, T.U.

Citation

Journal: J.Cell Biol. / Year: 2010
Title: Structure of the Sec13-Sec16 edge element, a template for assembly of the COPII vesicle coat.
Authors: Whittle, J.R. / Schwartz, T.U.

History

Deposition	May 12, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 18, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 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
Revision 1.3	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3mzk.cif.gz	551.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3mzk.ent.gz	454.5 KB	Display	PDB format
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Validation report

Summary document	3mzk_validation.pdf.gz	461.1 KB	Display	wwPDB validaton report
Full document	3mzk_full_validation.pdf.gz	498.1 KB	Display
Data in XML	3mzk_validation.xml.gz	49.9 KB	Display
Data in CIF	3mzk_validation.cif.gz	68.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mz/3mzk ftp://data.pdbj.org/pub/pdb/validation_reports/mz/3mzk	HTTPS FTP

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Related structure data

Related structure data	3mzlC C: citing same article (ref.)
Similar structure data	5hj5-d 4dve-4 3am1-1 5hr4-d 6fls-d 2wp6-d 2woi-d 2wp5-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 (3)

Deposited unit

A: Protein transport protein SEC13

B: Protein transport protein SEC16

C: Protein transport protein SEC16

D: Protein transport protein SEC13

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	56.734, 139.012, 205.424
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2
1	3
2	3
1	4
2	4
1	5
2	5
1	6
2	6

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain B and (resseq 1040:1090)
2	1	1	chain C and (resseq 1040:1090)
1	1	2	chain B and (resseq 1123:1183)
2	1	2	chain C and (resseq 1123:1183)
1	1	3	chain B and (resseq 1194:1242)
2	1	3	chain C and (resseq 1194:1242)
1	1	4	chain B and (resseq 1309:1323)
2	1	4	chain C and (resseq 1309:1323)
1	1	5	chain B and (resseq 1332:1367)
2	1	5	chain C and (resseq 1332:1367)
1	1	6	chain B and (resseq 1377:1390)
2	1	6	chain C and (resseq 1377:1390)

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Protein transport protein SEC13 Mass: 33082.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ANU3, L8167.4, SEC13, YLR208W / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q04491
#2: Protein	Protein transport protein SEC16 / COPII coat assembly protein SEC16 Mass: 49905.078 Da / Num. of mol.: 2 / Fragment: UNP residues 984-1420 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: LPF1W, SEC16, YPL085W / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P48415
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.44 Å³/Da / Density % sol: 49.6 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1mM bis-Tris propane, 0.2M NaBr, 12% polyethylene glycol 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
Detector	Type: ADSC QUANTUM 315 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2.65→30 Å / Num. obs: 45333 / % possible obs: 99.8 % / Redundancy: 3.7 % / R_merge(I) obs: 0.074 / Net I/σ(I): 20.7
Reflection shell	Resolution: 2.65→2.74 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.653 / Mean I/σ(I) obs: 1.9 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6.1_357)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD
Starting model: PARTIAL MODEL FROM SEMET CRYSTAL

Resolution: 2.69→30.713 Å / SU ML: 0.37 / σ(F): 0.1 / Phase error: 25.23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2434	2158	5.07 %
R_work	0.1979	-	-
obs	0.2002	42594	92.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 58.022 Å² / k_sol: 0.281 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.0657 Å²	0 Å²	-0 Å²
2-	-	20.512 Å²	0 Å²
3-	-	-	-15.4463 Å²

Refinement step

Cycle: LAST / Resolution: 2.69→30.713 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10487	0	0	175	10662

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	10747
X-RAY DIFFRACTION	f_angle_d	0.836	14669
X-RAY DIFFRACTION	f_dihedral_angle_d	13.165	3735
X-RAY DIFFRACTION	f_chiral_restr	0.054	1682
X-RAY DIFFRACTION	f_plane_restr	0.003	1847

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	B	367	X-RAY DIFFRACTION	POSITIONAL
1	2	C	367	X-RAY DIFFRACTION	POSITIONAL	0.016
2	1	B	474	X-RAY DIFFRACTION	POSITIONAL
2	2	C	474	X-RAY DIFFRACTION	POSITIONAL	0.016
3	1	B	371	X-RAY DIFFRACTION	POSITIONAL
3	2	C	371	X-RAY DIFFRACTION	POSITIONAL	0.017
4	1	B	139	X-RAY DIFFRACTION	POSITIONAL
4	2	C	139	X-RAY DIFFRACTION	POSITIONAL	0.015
5	1	B	279	X-RAY DIFFRACTION	POSITIONAL
5	2	C	279	X-RAY DIFFRACTION	POSITIONAL	0.014
6	1	B	109	X-RAY DIFFRACTION	POSITIONAL
6	2	C	109	X-RAY DIFFRACTION	POSITIONAL	0.015

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 (%)
2.6895-2.752	0.3232	99	0.2512	1692	X-RAY DIFFRACTION	60
2.752-2.8208	0.3464	117	0.2421	2390	X-RAY DIFFRACTION	82
2.8208-2.897	0.3158	122	0.2353	2474	X-RAY DIFFRACTION	86
2.897-2.9822	0.2951	152	0.2118	2529	X-RAY DIFFRACTION	89
2.9822-3.0784	0.2822	150	0.2101	2619	X-RAY DIFFRACTION	92
3.0784-3.1883	0.2752	132	0.208	2741	X-RAY DIFFRACTION	93
3.1883-3.3158	0.2427	162	0.1943	2747	X-RAY DIFFRACTION	96
3.3158-3.4665	0.2411	158	0.1851	2776	X-RAY DIFFRACTION	96
3.4665-3.649	0.2336	143	0.1866	2845	X-RAY DIFFRACTION	97
3.649-3.8772	0.2091	145	0.1848	2870	X-RAY DIFFRACTION	99
3.8772-4.1759	0.242	155	0.17	2861	X-RAY DIFFRACTION	98
4.1759-4.5949	0.1939	158	0.1636	2887	X-RAY DIFFRACTION	99
4.5949-5.2569	0.2124	156	0.1703	2926	X-RAY DIFFRACTION	99
5.2569-6.6122	0.2561	163	0.2127	2950	X-RAY DIFFRACTION	99
6.6122-30.7154	0.2297	146	0.2035	3129	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	3.2127	0.2618	-0.8351	0.7554	0.116	3.4203	0.0118	-0.0897	-0.1734	0.0361	0.1569	-0.0976	0.1642	0.3758	-0.1559	0.0344	0.0131	-0.0216	0.0431	0.0046	0.2229	32.1473	-36.5253	-94.1671
2	2.1816	-0.3013	-0.1239	1.9011	0.7816	3.5258	0.0113	-0.1972	-0.0249	-0.0187	-0.1557	0.107	0.1171	-0.5036	0.1112	0.0108	-0.01	-0.023	0.1099	-0.0489	0.2209	11.0158	-29.9466	-88.3274
3	0.9956	-0.4458	-0.171	2.3765	0.3317	3.2297	-0.0241	0.0029	0.4098	-0.0226	-0.0477	0.0111	-0.318	0.2011	0.0651	0.1443	-0.0872	0.0037	0.079	-0.2013	0.2441	24.8269	-16.6793	-78.2884
4	0.0617	-0.5102	-0.856	0.8956	1.6501	3.6124	-0.0991	-0.2396	0.2608	0.1452	0.4773	-0.2563	0.3572	0.9563	-0.3946	0.0537	-0.0177	-0.0601	0.5014	-0.2341	0.2519	31.6773	-15.378	-52.5116
5	1.6425	-1.4949	-2.1237	1.0608	1.7583	2.7958	-0.1414	0.392	0.3244	-0.3612	0.2352	0.1046	-0.4031	-0.3187	-0.0026	0.2538	0.1368	-0.0605	0.1533	-0.2569	0.1887	10.5675	3.4773	-37.0298
6	0.1247	0.497	0.196	2.2815	1.9244	2.6909	-0.1023	-0.3702	0.0502	0.1899	-0.0984	0.1851	0.3273	0.0931	0.166	0.3153	-0.004	0.0281	0.3054	-0.1201	0.2019	19.2921	-26.6814	-56.4053
7	0.1335	0.4077	0.0768	1.4967	1.1294	2.7785	-0.907	0.2346	0.697	2.1166	0.3347	-0.2064	0.6264	-0.792	0.5179	2.5841	0.7636	-0.432	2.0853	0.2568	1.0508	-36.8845	-8.7923	22.8965
8	0.2664	0.5459	-0.0611	0.9308	-1.0773	2.5818	0.0047	-0.0798	0.2812	0.0214	0.5893	0.6153	0.0433	-1.1407	-0.5517	0.491	0.0569	-0.105	0.9381	0.2629	0.8242	-25.2983	-0.0964	-12.897
9	2.2591	-0.9182	1.0469	1.584	0.1369	1.3367	0.008	-0.8491	0.0237	0.1237	0.7047	-0.2472	-0.035	0.0083	-0.4687	0.2932	-0.0031	0.0212	0.625	-0.1598	0.3545	17.1973	8.4379	-25.687
10	1.1469	0.3297	-0.0783	2.1519	-1.1816	1.0866	0.1642	-0.3235	-0.5082	-0.1319	0.1338	-0.2157	0.1298	0.2213	-0.2238	0.4074	0.1374	-0.1153	0.4856	-0.0266	0.5181	-3.3948	0.2971	-13.151
11	0.8433	0.3024	-1.0814	0.7564	0.8535	3.7623	-0.0007	0.3948	0.1082	0.4553	0.0783	0.0043	1.2731	-0.7815	-0.2109	0.9854	-0.0938	-0.1819	0.813	0.228	0.6665	-22.9249	-18.8327	-1.3014
12	0.6522	-0.9409	0.0466	2.071	0.3103	0.2533	-0.9398	-1.1111	-0.5918	1.8734	0.3982	0.3664	0.3902	-1.4075	0.5772	2.8465	0.4229	0.5084	2.2215	0.5537	0.8629	-35.5479	-23.7594	33.6665
13	2.1258	-0.1752	-1.1949	0.8734	0.9176	1.3999	-1.5556	-1.9712	-0.0985	1.3738	0.0366	-0.5759	0.3031	2.6126	1.3827	1.2645	0.7017	-0.938	1.5905	0.9687	-0.669	-15.3666	-26.3996	25.9748
14	1.3999	1.1089	0.1078	2.143	-1.5778	2.1935	-0.5887	0.3644	0.8312	2.6136	0.3026	-0.1591	-0.5095	0.294	0.3114	3.0555	-0.0421	-0.8359	1.0321	0.2581	1.0321	-20.5479	-7.8064	19.849

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:89)
2	X-RAY DIFFRACTION	2	(chain A and resid 90:200)
3	X-RAY DIFFRACTION	3	(chain A and resid 201:297)
4	X-RAY DIFFRACTION	4	(chain B and resid 990:1135)
5	X-RAY DIFFRACTION	5	(chain B and resid 1136:1252)
6	X-RAY DIFFRACTION	6	(chain B and resid 1253:1390)
7	X-RAY DIFFRACTION	7	(chain C and resid 990:1042)
8	X-RAY DIFFRACTION	8	(chain C and resid 1043:1115)
9	X-RAY DIFFRACTION	9	(chain C and resid 1116:1182)
10	X-RAY DIFFRACTION	10	(chain C and resid 1183:1271)
11	X-RAY DIFFRACTION	11	(chain C and resid 1272:1390)
12	X-RAY DIFFRACTION	12	(chain D and resid 1:118)
13	X-RAY DIFFRACTION	13	(chain D and resid 119:218)
14	X-RAY DIFFRACTION	14	(chain D and resid 219:297)

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