PDB-2g3k: Crystal structure of the C-terminal domain of Vps28

ID or keywords:

Entry

Database: PDB / ID: 2g3k

Title

Crystal structure of the C-terminal domain of Vps28

Components

Vacuolar protein sorting-associated protein VPS28

Vacuole

Keywords

TRANSPORT PROTEIN / 4 helix bundle

Function / homology

Function and homology information

ESCRT I complex / ATP export / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to membrane / late endosome membrane /

endosome / protein-containing complex binding /

cytosol
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.05 Å

Authors

Pineda-Molina, E. / Belrhali, H. / Piefer, A.J. / Akula, I. / Bates, P. / Weissenhorn, W.

Citation

Journal: Traffic / Year: 2006
Title: The crystal structure of the C-terminal domain of Vps28 reveals a conserved surface required for Vps20 recruitment.
Authors: Pineda-Molina, E. / Belrhali, H. / Piefer, A.J. / Akula, I. / Bates, P. / Weissenhorn, W.

History

Deposition	Feb 20, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 27, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2g3k.cif.gz	137 KB	Display	PDBx/mmCIF format
PDB format	pdb2g3k.ent.gz	117.6 KB	Display	PDB format
PDBx/mmJSON format	2g3k.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g3/2g3k ftp://data.pdbj.org/pub/pdb/validation_reports/g3/2g3k	HTTPS FTP

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Related structure data

Similar structure data	3tqm-3 4wwr-1 2jf1-d 6h88-d 5t7r-d 4wwr-2 1os3-d 4cxl-1 6hnf-d 2bp3-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Vacuolar protein sorting-associated protein VPS28

B: Vacuolar protein sorting-associated protein VPS28

C: Vacuolar protein sorting-associated protein VPS28

D: Vacuolar protein sorting-associated protein VPS28

E: Vacuolar protein sorting-associated protein VPS28

F: Vacuolar protein sorting-associated protein VPS28

G: Vacuolar protein sorting-associated protein VPS28

76.7 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Vacuolar protein sorting-associated protein VPS28

defined by author
11 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Vacuolar protein sorting-associated protein VPS28

defined by author&software
11 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Vacuolar protein sorting-associated protein VPS28

defined by author&software
11 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Vacuolar protein sorting-associated protein VPS28

defined by author&software
11 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Vacuolar protein sorting-associated protein VPS28

defined by author&software
11 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Vacuolar protein sorting-associated protein VPS28

defined by author&software
11 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: Vacuolar protein sorting-associated protein VPS28

defined by author&software
11 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

A: Vacuolar protein sorting-associated protein VPS28

B: Vacuolar protein sorting-associated protein VPS28

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

9

A: Vacuolar protein sorting-associated protein VPS28

B: Vacuolar protein sorting-associated protein VPS28

F: Vacuolar protein sorting-associated protein VPS28

defined by software
32.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

10

C: Vacuolar protein sorting-associated protein VPS28

G: Vacuolar protein sorting-associated protein VPS28

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

11

A: Vacuolar protein sorting-associated protein VPS28

F: Vacuolar protein sorting-associated protein VPS28

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

Unit cell

Length a, b, c (Å)	117.579, 117.579, 294.116
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-ID	Component-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PHE	LYS	A	A	148 - 151	1 - 4
2	1	PHE	LYS	B	B	148 - 151	1 - 4
3	1	PHE	LYS	C	C	148 - 151	1 - 4
4	1	PHE	LYS	D	D	148 - 151	1 - 4
5	1	PHE	LYS	E	E	148 - 151	1 - 4
6	1	PHE	LYS	F	F	148 - 151	1 - 4
7	1	PHE	LYS	G	G	148 - 151	1 - 4
8	2	TYR	LYS	A	A	152 - 168	5 - 21
9	2	TYR	LYS	B	B	152 - 168	5 - 21
10	2	TYR	LYS	C	C	152 - 168	5 - 21
11	2	TYR	LYS	D	D	152 - 168	5 - 21
12	2	TYR	LYS	E	E	152 - 168	5 - 21
13	2	TYR	LYS	F	F	152 - 168	5 - 21
14	2	TYR	LYS	G	G	152 - 168	5 - 21
15	3	LEU	LYS	A	A	169 - 174	22 - 27
16	3	LEU	LYS	B	B	169 - 174	22 - 27
17	3	LEU	LYS	C	C	169 - 174	22 - 27
18	3	LEU	LYS	D	D	169 - 174	22 - 27
19	3	LEU	LYS	E	E	169 - 174	22 - 27
20	3	LEU	LYS	F	F	169 - 174	22 - 27
21	3	LEU	LYS	G	G	169 - 174	22 - 27
22	4	ASP	ARG	A	A	175 - 190	28 - 43
23	4	ASP	ARG	B	B	175 - 190	28 - 43
24	4	ASP	ARG	C	C	175 - 190	28 - 43
25	4	ASP	ARG	D	D	175 - 190	28 - 43
26	4	ASP	ARG	E	E	175 - 190	28 - 43
27	4	ASP	ARG	F	F	175 - 190	28 - 43
28	4	ASP	ARG	G	G	175 - 190	28 - 43
29	5	VAL	ARG	A	A	191 - 199	44 - 52
30	5	VAL	ARG	B	B	191 - 199	44 - 52
31	5	VAL	ARG	C	C	191 - 199	44 - 52
32	5	VAL	ARG	D	D	191 - 199	44 - 52
33	5	VAL	ARG	E	E	191 - 199	44 - 52
34	5	VAL	ARG	F	F	191 - 199	44 - 52
35	5	VAL	ARG	G	G	191 - 199	44 - 52
36	6	SER	ASN	A	A	200 - 210	53 - 63
37	6	SER	ASN	B	B	200 - 210	53 - 63
38	6	SER	ASN	C	C	200 - 210	53 - 63
39	6	SER	ASN	D	D	200 - 210	53 - 63
40	6	SER	ASN	E	E	200 - 210	53 - 63
41	6	SER	ASN	F	F	200 - 210	53 - 63
42	6	SER	ASN	G	G	200 - 210	53 - 63
43	7	LYS	THR	A	A	211 - 221	64 - 74
44	7	LYS	THR	B	B	211 - 221	64 - 74
45	7	LYS	THR	C	C	211 - 221	64 - 74
46	7	LYS	THR	D	D	211 - 221	64 - 74
47	7	LYS	THR	E	E	211 - 221	64 - 74
48	7	LYS	THR	F	F	211 - 221	64 - 74
49	7	LYS	THR	G	G	211 - 221	64 - 74
50	8	GLN	ALA	A	A	222 - 239	75 - 92
51	8	GLN	ALA	B	B	222 - 239	75 - 92
52	8	GLN	ALA	C	C	222 - 239	75 - 92
53	8	GLN	ALA	D	D	222 - 239	75 - 92
54	8	GLN	ALA	E	E	222 - 239	75 - 92
55	8	GLN	ALA	F	F	222 - 239	75 - 92
56	8	GLN	ALA	G	G	222 - 239	75 - 92
57	9	LEU	LEU	A	A	240 - 241	93 - 94
58	9	LEU	LEU	B	B	240 - 241	93 - 94
59	9	LEU	LEU	C	C	240 - 241	93 - 94
60	9	LEU	LEU	D	D	240 - 241	93 - 94
61	9	LEU	LEU	E	E	240 - 241	93 - 94
62	9	LEU	LEU	F	F	240 - 241	93 - 94
63	9	LEU	LEU	G	G	240 - 241	93 - 94

Details

The biological assembly is a monomer. They are 7 monomers in the asymmetric unit (labeled A to G).

#1: Protein	Vacuolar protein sorting-associated protein VPS28 / Vacuole Mass: 10952.433 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VPS28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus / References: UniProt: Q02767
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.84 Å³/Da / Density % sol: 67.98 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ESRF	BM14	1	0.97797
SYNCHROTRON	ESRF	ID14-1	2	0.933

Detector

Type	ID	Detector	Date	Details
MARRESEARCH	1	CCD	Oct 10, 2004	Collimating mirror+channel cut Si(111) monochromator + focussing toroidal mirror.
ADSC QUANTUM 4	2	CCD	Jan 1, 2005	diamond monochromator-germanium 220 vertically foucssing mirror - horizontally focussing multilayer mirror.

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Channel Cut Si111 crystal	SINGLE WAVELENGTH	M	x-ray	1
2	diamond crystal	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97797	1
2	0.933	1

Reflection

Resolution: 3.05→20 Å / Num. all: 24827 / Num. obs: 23615 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

Reflection shell

Resolution: 3.05→3.21 Å / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
SHELXS		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.05→19.94 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.883 / SU B: 41.072 / SU ML: 0.336 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.991 / ESU R Free: 0.419
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27269	1205	5.1 %	RANDOM
R_work	0.21299	-	-	-
all	0.21599	23684	-	-
obs	0.21599	22301	99.25 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 73.974 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.11 Å²	-0.05 Å²	0 Å²
2-	-	-0.11 Å²	0 Å²
3-	-	-	0.16 Å²

Refinement step

Cycle: LAST / Resolution: 3.05→19.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5390	0	0	56	5446

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	5453
X-RAY DIFFRACTION	r_angle_refined_deg	1.749	1.975	7385
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.998	5	651
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.328	24.474	266
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	23.397	15	1001
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.324	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.126	0.2	875
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4032
X-RAY DIFFRACTION	r_nbd_refined	0.258	0.2	2725
X-RAY DIFFRACTION	r_nbtor_refined	0.326	0.2	3821
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.197	0.2	195
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.243	0.2	73
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.345	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	0.727	1.5	3357
X-RAY DIFFRACTION	r_mcangle_it	1.069	2	5292
X-RAY DIFFRACTION	r_scbond_it	1.674	3	2345
X-RAY DIFFRACTION	r_scangle_it	2.729	4.5	2093

Refine LS restraints NCS

Ens-ID: 1 / Number: 767 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	loose positional	0.7	5
2	B	loose positional	0.77	5
3	C	loose positional	0.74	5
4	D	loose positional	0.79	5
5	E	loose positional	0.61	5
6	F	loose positional	0.61	5
7	G	loose positional	0.64	5
1	A	loose thermal	6.76	10
2	B	loose thermal	4.11	10
3	C	loose thermal	13.31	10
4	D	loose thermal	4.05	10
5	E	loose thermal	8.67	10
6	F	loose thermal	2.65	10
7	G	loose thermal	6.18	10

LS refinement shell

Resolution: 3.05→3.128 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.42	89	-
R_work	0.332	1573	-
obs	-	-	98.87 %

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	5.4565	2.4749	-2.0931	3.0776	-0.2806	5.0697	0.0191	0.0076	-0.3252	-0.0276	-0.1506	0.1867	-0.0032	-0.4526	0.1314	-1.2672	0.1	-0.0028	-1.1417	-0.1332	-1.2516	111.9918	66.9546	3.0047
2	10.7059	-0.3136	-0.1263	8.6534	4.1203	7.206	0.4297	0.3212	0.3867	-0.9893	-0.8851	0.1414	-1.0068	-0.506	0.4555	-0.9391	0.1273	-0.0429	-1.2321	-0.2752	-1.3419	112.3504	84.7136	13.2481
3	5.4926	-0.3163	-2.1202	1.8137	0.5616	0.926	-0.1494	0.1358	-0.11	0.1724	0.0751	0.0826	-0.1801	-0.0055	0.0743	-0.9514	0.0022	-0.0679	-1.1213	-0.0363	-1.2326	131.57	55.7715	12.8898
4	7.6885	-2.8475	-6.1404	5.4161	1.9454	11.4952	-0.0713	-0.5597	0.8743	-0.4552	-1.0381	0.071	-1.8369	1.5402	1.1094	-1.1663	-0.3643	-0.0965	-0.5467	0.073	-1.2391	91.7255	62.5324	-11.2124
5	6.6974	-2.1957	1.9082	7.544	-0.6353	7.8226	0.025	1.9713	-0.2118	-0.2786	-0.5424	-1.0022	0.0303	1.1451	0.5173	-1.7783	0.0122	0.0574	-0.3107	0.1579	-1.3494	109.5091	44.4672	-13.7209
6	8.7666	-13.9521	0.6497	22.4098	-2.2447	7.1985	0.6177	0.1451	-0.6982	-1.1444	-0.3646	0.4534	-0.0509	0.2248	-0.2531	-1.5884	-0.0486	-0.06	-1.0655	-0.1488	-1.4766	129.6669	59.2215	-13.7429
7	9.4395	6.3965	5.6557	10.4759	2.5934	11.6454	0.5136	-0.7823	0.5743	1.4087	-0.6245	1.5234	0.769	0.3695	0.1109	-1.6995	0.155	0.1964	-0.9686	-0.1634	-1.0389	90.8012	35.4685	0.4249

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	148 - 241	1 - 94
2	X-RAY DIFFRACTION	2	B	B	148 - 241	1 - 94
3	X-RAY DIFFRACTION	3	C	C	148 - 241	1 - 94
4	X-RAY DIFFRACTION	4	D	D	148 - 241	1 - 94
5	X-RAY DIFFRACTION	5	E	E	148 - 241	1 - 94
6	X-RAY DIFFRACTION	6	F	F	148 - 241	1 - 94
7	X-RAY DIFFRACTION	7	G	G	148 - 241	1 - 94

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