PDB-4in3: Crystal Structure of the Chs5-Bch1 Exomer Cargo Adaptor Complex

ID or keywords:

Entry

Database: PDB / ID: 4in3

Title

Crystal Structure of the Chs5-Bch1 Exomer Cargo Adaptor Complex

Components

Chitin biosynthesis protein CHS5
Protein BCH1

Keywords

PROTEIN TRANSPORT / OB fold / TPR domain / Trans-Golgi Network / TGN

Function / homology

Function and homology information

: / exomer complex / : / conjugation with cellular fusion / cellular bud site selection / ascospore wall assembly / Golgi to plasma membrane transport / mating projection tip / trans-Golgi network / small GTPase binding ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.936 Å

Authors

Richardson, B.C. / Fromme, J.C.

Citation

Journal: Structure / Year: 2013
Title: The exomer cargo adaptor features a flexible hinge domain.
Authors: Richardson, B.C. / Fromme, J.C.

History

Deposition	Jan 3, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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	4in3.cif.gz	551.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4in3.ent.gz	459.5 KB	Display	PDB format
PDBx/mmJSON format	4in3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4in3_validation.pdf.gz	464.3 KB	Display	wwPDB validaton report
Full document	4in3_full_validation.pdf.gz	497.1 KB	Display
Data in XML	4in3_validation.xml.gz	49.5 KB	Display
Data in CIF	4in3_validation.cif.gz	66.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/in/4in3 ftp://data.pdbj.org/pub/pdb/validation_reports/in/4in3	HTTPS FTP

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Related structure data

Related structure data	4gns PDB Unreleased entryS S: Starting model for refinement
Similar structure data	3avw-d 3agp-d 3avt-d 6sda-1 3mmp-1 3avx-d 3agq-d 3avv-d 3vnv-d 3avu-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	#55 - Jul 2004 DNA Ligase similarity (5) #150 - Jun 2012 Sliding Clamps similarity (5)

Deposited unit

A: Chitin biosynthesis protein CHS5

B: Protein BCH1

C: Chitin biosynthesis protein CHS5

D: Protein BCH1

186 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)	141.391, 155.686, 99.054
Angle α, β, γ (deg.)	90.00, 95.34, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Chitin biosynthesis protein CHS5 / Protein CAL3 Mass: 9272.695 Da / Num. of mol.: 2 / Fragment: UNP residues 1-77 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CHS5, CAL3, YLR330W, L8543.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12114
#2: Protein	Protein BCH1 / BUD7 and CHS6 homolog 1 Mass: 83972.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: BCH1, YMR237W, YM9959.19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05029
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.91 Å³/Da / Density % sol: 57.74 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15% PEG8000, 19% glycerol, 0.1 M Tris, pH 8.0, 0.2 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CHESS

/ Beamline: A1 / Wavelength: 0.987 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 29, 2012

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.987 Å / Relative weight: 1

Reflection

Resolution: 2.9→50 Å / Num. all: 43750 / Num. obs: 43750 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / B_iso Wilson estimate: 70.41 Å² / R_sym value: 0.111 / Net I/σ(I): 8.59

Reflection shell

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
2.9-2.95	3	2.51	0.567	1	68.7
2.95-3				1	99.2
3-3.06				1	99.9
3.06-3.12				1	100
3.12-3.19				1	100
3.19-3.27				1	99.9
3.27-3.35				1	99.9
3.35-3.44				1	99.8
3.44-3.54				1	99.8
3.54-3.65				1	99.6
3.65-3.78				1	99.7
3.78-3.94				1	99.4
3.94-4.11				1	99.5
4.11-4.33				1	99.2
4.33-4.6				1	99
4.6-4.96				1	98.8
4.96-5.46				1	98.4
5.46-6.24				1	98
6.24-7.86				1	97.6
7.86-50				1	94.2

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	3.11 Å	49.31 Å
Translation	3.11 Å	49.31 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.3.0	phasing
RESOLVE		phasing
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GNS

4gns
PDB Unreleased entry

Resolution: 2.936→38.73 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 34.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2889	2305	5.28 %
R_work	0.2367	-	-
obs	0.2396	43672	95.86 %
all	-	43761	-

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 96.226 Å²

Refinement step

Cycle: LAST / Resolution: 2.936→38.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11069	0	0	18	11087

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	11268
X-RAY DIFFRACTION	f_angle_d	0.907	15251
X-RAY DIFFRACTION	f_dihedral_angle_d	16.947	4182
X-RAY DIFFRACTION	f_chiral_restr	0.063	1790
X-RAY DIFFRACTION	f_plane_restr	0.005	1916

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 (%)
2.936-2.9997	0.4256	78	0.3325	1387	X-RAY DIFFRACTION	51
2.9997-3.0694	0.3827	155	0.331	2608	X-RAY DIFFRACTION	99
3.0694-3.1461	0.4004	139	0.3244	2689	X-RAY DIFFRACTION	100
3.1461-3.2312	0.4076	151	0.307	2700	X-RAY DIFFRACTION	100
3.2312-3.3262	0.3428	157	0.2913	2662	X-RAY DIFFRACTION	100
3.3262-3.4335	0.3695	138	0.2787	2696	X-RAY DIFFRACTION	100
3.4335-3.5561	0.3166	161	0.2641	2672	X-RAY DIFFRACTION	100
3.5561-3.6984	0.3037	138	0.2563	2688	X-RAY DIFFRACTION	100
3.6984-3.8666	0.3137	152	0.246	2664	X-RAY DIFFRACTION	100
3.8666-4.0702	0.3105	146	0.2406	2684	X-RAY DIFFRACTION	99
4.0702-4.3249	0.3068	152	0.228	2673	X-RAY DIFFRACTION	99
4.3249-4.6583	0.2481	154	0.1934	2682	X-RAY DIFFRACTION	99
4.6583-5.1262	0.2531	150	0.1963	2660	X-RAY DIFFRACTION	99
5.1262-5.8657	0.2999	141	0.2399	2668	X-RAY DIFFRACTION	98
5.8657-7.3818	0.3061	151	0.2472	2647	X-RAY DIFFRACTION	98
7.3818-38.733	0.1881	142	0.1905	2587	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	0.001	-0.0013	0.0016	0.001	0.0001	-0.0016	-0.012	-0.0134	-0.0081	0.0028	0.0087	0.0034	-0.0154	0.0237	0	0.5342	-0.0342	0.0001	0.5252	0.1	0.7415	3.9917	-3.6135	35.4544
2	-0.0016	0.0031	-0.0036	0.0001	-0.0031	-0.0015	-0.0031	0.0021	-0.0145	-0.029	-0.0334	-0.0045	0.0043	-0.0014	-0	0.4979	-0.0851	0.1285	0.3349	0.0696	0.6416	-10.0315	-13.7774	26.1774
3	0.0089	-0.003	-0.0037	-0.0003	-0.0008	-0.0058	-0.0307	0.0217	-0.0487	-0.0178	-0.035	0.0105	-0.0041	0.0134	-0	0.4377	-0.004	-0.0387	0.4492	0.139	0.7655	0.6868	0.9709	26.4187
4	0.0007	0.0006	0.0006	0.0007	0.0002	-0.0001	0.001	-0.0081	0.0057	-0.0034	-0	-0.0099	-0.0062	0.0006	0	0.5948	0.0167	-0.0433	0.4752	0.1875	0.633	-5.3826	26.0843	14.8066
5	0.0049	-0.006	-0.0041	-0.0001	0.0028	0.0008	-0.0021	0.0094	-0.0006	0.0133	0.0003	0.0289	0.0463	-0.0134	-0	0.6241	0.1757	-0.0312	1.0735	0.0193	0.8084	-57.6461	16.8513	20.4427
6	0.009	-0.0027	0.0022	0.0001	-0.0013	0.0026	-0.0038	-0.0028	-0.0033	0.0029	-0.007	-0.0057	0.0015	0.0106	0	0.9574	0.067	0.0046	1.0419	0.02	0.9276	-53.0929	16.9196	26.4686
7	0.0219	-0.0036	0.0122	0.0061	0.0014	0.0063	-0.0092	0.0099	0.0428	-0.0125	0.0223	0.0343	0.0122	-0.0184	0	0.5685	0.3397	0.0251	1.1659	0.0495	0.658	-48.3649	19.6288	24.0012
8	0.015	-0.0318	-0.0297	0.002	-0.036	-0.0043	-0.0344	-0.195	-0.0913	0.0113	0.0286	-0.3136	-0.1496	-0.475	-0	-0.5166	1.1251	-0.2225	-0.7905	0.2265	0.3707	-23.0397	18.8075	19.4805
9	0.0044	0.0029	0.0086	0.0001	0.0009	-0.0068	-0.0096	0.0113	0.0054	-0.0109	0.0373	-0.0566	0.0654	-0.0461	-0	0.603	-0.0873	-0.1326	0.7072	0.0061	0.685	-44.4281	4.8635	0.0026
10	0.0029	0.0158	0.0011	0.0257	0.0023	0.0095	-0.0374	0.151	-0.1104	-0.068	0.0189	-0.1531	0.077	-0.1581	0	0.8346	-0.0051	-0.0259	0.6781	-0.0544	0.6082	-28.386	1.3113	-6.6667
11	-0.0065	-0.0055	0.0104	0.0271	-0.0013	0.0085	0.0319	-0.0039	0.0439	-0.0668	0.0077	-0.3115	-0.0509	-0.0757	0	-0.0103	0.7023	-0.4583	0.3226	0.2891	-0.2352	-36.051	26.699	-4.9126
12	0.0036	-0.0032	-0.001	0.001	0.0013	0.0004	-0.0026	0.0128	0.0016	0.0038	0.0146	-0.0019	-0.0123	-0.011	-0	0.8038	0.3806	-0.0528	0.9587	0.0764	0.7536	-45.4291	34.0324	2.4314
13	-0.0008	-0.0021	-0.0032	0.0017	-0.0021	-0.0026	-0.0214	-0.0065	0.0144	-0.003	0.0006	-0.002	-0.0143	-0.0123	0	0.502	0.0565	0.1272	0.5056	0.0707	0.6739	-6.487	0.0233	27.5526
14	-0.0019	-0.0016	0.0014	0.0024	-0.0024	-0.0004	-0.0001	0.0082	0.0022	-0.0058	-0.0266	-0.0055	-0.0107	0.0024	-0	0.4834	0.0228	-0.0011	0.4147	0.1648	0.7383	-7.7947	1.279	28.1869
15	0.0108	-0.002	0.0065	0.0012	-0.0004	-0.0032	-0.0503	0.0091	0.0489	0.015	-0.0207	0.0001	0.0296	0.0192	-0	0.4962	-0.0235	-0.0027	0.3234	0.138	0.6892	-1.0197	-19.5724	31.7573
16	0.0006	0.0002	0.0001	0.0011	-0.0001	0.0001	-0.0032	0.0085	-0.0005	0.0072	-0.0004	-0.0001	-0.005	-0.0007	0	0.6584	-0.0507	-0.0093	0.552	0.0483	0.6146	-12.7865	-40.5364	42.1129
17	0.0118	0.0016	0.0092	0.0141	-0.0012	0.0081	-0.0386	0.0557	0.0473	-0.0413	-0.139	0.0498	-0.0179	-0.0778	0	0.3852	-0.4638	-0.034	0.6751	-0.1315	0.3902	-62.8248	-27.5425	22.4213
18	0.0065	-0.0028	-0.0002	0.0001	0.0164	-0.0183	0.1501	0.0046	-0.0045	-0.0262	-0.0635	-0.0323	0.0558	-0.1226	-0	0.1794	-1.0339	-0.0607	-0.044	-0.1553	0.2793	-41.1591	-34.5463	25.9639
19	-0.0051	0.0084	0.0016	0.0055	0.006	-0.003	0.0598	-0.0034	0.0456	-0.0944	-0.0786	-0.0824	0.1217	0.005	-0	0.4076	-0.6786	0.0231	-0.2537	0.0634	0.4097	-19.4658	-29.8308	36.3011
20	0.0026	-0.0057	-0.0261	0.0094	0.0462	0.0019	-0.0589	0.0305	0.0476	0.0499	-0.0085	-0.0994	-0.0282	-0.1456	0	0.3708	-0.4017	0.0698	0.3368	-0.2494	0.51	-42.1836	-14.7047	45.6551
21	0.0018	0.0011	-0.0009	0.0008	0.0003	-0.0001	-0.0111	0.0134	-0.0295	-0.018	-0.0281	0.0237	-0.0278	-0.0088	0	0.624	-0.1684	0.0476	0.5231	-0.0945	0.7599	-20.2835	-0.9883	44.6057
22	-0.0009	0.0035	-0.0017	0.0072	0.0062	0.0008	0.0035	-0.0419	-0.0115	-0.0051	0.0337	0.0088	-0.0087	-0.0213	-0	0.677	-0.211	0.1106	0.6306	-0.2116	0.6374	-40.1189	-8.7623	63.8281
23	0.0016	0.0005	-0.0064	0.0034	-0.0069	-0.0001	-0.0463	-0.0381	0.0294	0.0137	-0.0292	-0.0454	0.0073	-0.0256	0	0.7138	-0.6684	0.1766	0.923	-0.1559	0.7366	-42.8896	-24.5364	57.4598
24	0.007	0.0238	-0.004	0.0011	-0.0115	-0.002	-0.0196	-0.0658	-0.0704	-0.0469	-0.0446	0.0274	0.0373	0.0049	0	0.6372	-1.1266	0.0161	0.9003	-0.0972	0.578	-49.7592	-40.041	50.0427

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid -3:8)
2	X-RAY DIFFRACTION	2	(chain A and resid 9:39)
3	X-RAY DIFFRACTION	3	(chain A and resid 40:62)
4	X-RAY DIFFRACTION	4	(chain A and resid 63:76)
5	X-RAY DIFFRACTION	5	(chain B and resid 2:116)
6	X-RAY DIFFRACTION	6	(chain B and resid 135:142)
7	X-RAY DIFFRACTION	7	(chain B and resid 143:236)
8	X-RAY DIFFRACTION	8	(chain B and resid 237:426)
9	X-RAY DIFFRACTION	9	(chain B and resid 427:484)
10	X-RAY DIFFRACTION	10	(chain B and resid 485:613)
11	X-RAY DIFFRACTION	11	(chain B and resid 614:696)
12	X-RAY DIFFRACTION	12	(chain B and resid 697:722)
13	X-RAY DIFFRACTION	13	(chain C and resid 2:17)
14	X-RAY DIFFRACTION	14	(chain C and resid 18:42)
15	X-RAY DIFFRACTION	15	(chain C and resid 43:66)
16	X-RAY DIFFRACTION	16	(chain C and resid 67:76)
17	X-RAY DIFFRACTION	17	(chain D and resid 2:171)
18	X-RAY DIFFRACTION	18	(chain D and resid 172:306)
19	X-RAY DIFFRACTION	19	(chain D and resid 307:403)
20	X-RAY DIFFRACTION	20	(chain D and resid 404:501)
21	X-RAY DIFFRACTION	21	(chain D and resid 502:543)
22	X-RAY DIFFRACTION	22	(chain D and resid 544:568)
23	X-RAY DIFFRACTION	23	(chain D and resid 573:632)
24	X-RAY DIFFRACTION	24	(chain D and resid 636:722)

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

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Jul 12, 2017. Major update of PDB

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Yorodumi