PDB-2qp9: Crystal Structure of S.cerevisiae Vps4

ID or keywords:

Entry

Database: PDB / ID: 2qp9

Title

Crystal Structure of S.cerevisiae Vps4

Components

Vacuolar protein sorting-associated protein 4

Keywords

PROTEIN TRANSPORT / ATPase domain / beta domain / C-terminal helix / ATP-binding / Endosome / Nucleotide-binding / Transport / Vacuole

Function / homology

Function and homology information

ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / multivesicular body sorting pathway ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.9 Å

Authors

Xiao, J. / Xu, Z.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: Structural characterization of the ATPase reaction cycle of endosomal AAA protein Vps4.
Authors: Xiao, J. / Xia, H. / Yoshino-Koh, K. / Zhou, J. / Xu, Z.

History

Deposition	Jul 23, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Oct 20, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Feb 21, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	2qp9_validation.pdf.gz	438.4 KB	Display	wwPDB validaton report
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Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qp/2qp9 ftp://data.pdbj.org/pub/pdb/validation_reports/qp/2qp9	HTTPS FTP

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Related structure data

Related structure data	2qpaC C: citing same article (ref.)
Similar structure data	4nhy-2 5omi-d 5k82-2 3eih-2 4url-2 6o59-d 2rko-d 4pcl-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	#80 - Aug 2006 AAA+ Proteases similarity (6) #166 - Oct 2013 Proteasome similarity (4) #167 - Nov 2013 SNARE Proteins similarity (4) #161 - May 2013 Ricin similarity (1)

Deposited unit

X: Vacuolar protein sorting-associated protein 4

hetero molecules

39.1 kDa, 1 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)	86.553, 86.553, 236.061
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	Vacuolar protein sorting-associated protein 4 / Protein END13 / DOA4-independent degradation protein 6 / Vacuolar protein-targeting protein 10 Mass: 38777.504 Da / Num. of mol.: 1 / Fragment: residues: 83-437 / Mutation: E233Q, C317S, C376S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10 / Plasmid: pSJ3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P52917
#2: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 3.29 Å³/Da / Density % sol: 62.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: Sodium Acetate, CdSO4, pH 6.5, temperature 293K, VAPOR DIFFUSION

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Data collection

Diffraction

ID	Crystal-ID
1	1
2	1
1,2	1

Diffraction source

Source	Site	Beamline	ID
SYNCHROTRON	APS	23-ID-D	1
SYNCHROTRON	APS	23-ID-D	2

Detector

ID	Detector
1	CCD
2	CCD

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	MAD	M	x-ray	1

Radiation wavelength

Relative weight: 1

Reflection

Redundancy: 13.3 % / Av σ(I) over netI: 13 / Number: 125756 / R_merge(I) obs: 0.081 / Χ²: 1.56 / D res high: 3.2 Å / D res low: 50 Å / Num. obs: 9425 / % possible obs: 99.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.89	50	98.4	1	0.062	3.479	12
5.47	6.89	99.8	1	0.074	2.507	13.4
4.78	5.47	99.9	1	0.074	1.89	13.7
4.34	4.78	99.9	1	0.08	1.519	13.9
4.03	4.34	100	1	0.089	1.096	14.1
3.79	4.03	100	1	0.116	1.042	14.1
3.6	3.79	99.9	1	0.185	0.983	14.2
3.45	3.6	100	1	0.278	1.007	14.2
3.31	3.45	100	1	0.434	0.971	13.4
3.2	3.31	97.8	1	0.505	0.91	10.3

Reflection

Resolution: 2.9→50 Å / Num. obs: 12599 / % possible obs: 98.1 % / Redundancy: 13.2 % / R_merge(I) obs: 0.063 / Net I/σ(I): 37.5

Reflection shell

Resolution: 2.9→3 Å / R_merge(I) obs: 0.606 / Mean I/σ(I) obs: 3.8 / % possible all: 99.2

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 3.2 Å / D res low: 39.98 Å / FOM acentric: 0.507 / FOM centric: 0.345 / Reflection acentric: 7091 / Reflection centric: 2131

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	3.2	39.98	7073	2096
ISO_2	0.788	0.737	3.2	39.98	7043	2090
ISO_3	0.82	0.77	3.2	39.98	7034	2090
ANO_1	0.492	0	3.2	39.98	7012	0
ANO_2	0.692	0	3.2	39.98	7012	0
ANO_3	0.711	0	3.2	39.98	6992	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Reflection acentric	Reflection centric
ISO_1	13.51-39.98	0	0	42	61
ISO_1	9.84-13.51	0	0	114	97
ISO_1	8.12-9.84	0	0	161	106
ISO_1	7.07-8.12	0	0	212	105
ISO_1	6.34-7.07	0	0	238	103
ISO_1	5.8-6.34	0	0	262	108
ISO_1	5.38-5.8	0	0	293	101
ISO_1	5.04-5.38	0	0	323	97
ISO_1	4.75-5.04	0	0	348	107
ISO_1	4.51-4.75	0	0	363	99
ISO_1	4.3-4.51	0	0	387	107
ISO_1	4.12-4.3	0	0	403	109
ISO_1	3.96-4.12	0	0	428	105
ISO_1	3.82-3.96	0	0	458	118
ISO_1	3.69-3.82	0	0	467	109
ISO_1	3.57-3.69	0	0	481	119
ISO_1	3.47-3.57	0	0	504	111
ISO_1	3.37-3.47	0	0	516	104
ISO_1	3.28-3.37	0	0	538	118
ISO_1	3.2-3.28	0	0	535	112
ANO_1	13.51-39.98	0.256	0	42	0
ANO_1	9.84-13.51	0.289	0	114	0
ANO_1	8.12-9.84	0.315	0	161	0
ANO_1	7.07-8.12	0.266	0	212	0
ANO_1	6.34-7.07	0.289	0	238	0
ANO_1	5.8-6.34	0.326	0	262	0
ANO_1	5.38-5.8	0.381	0	293	0
ANO_1	5.04-5.38	0.384	0	323	0
ANO_1	4.75-5.04	0.479	0	348	0
ANO_1	4.51-4.75	0.517	0	363	0
ANO_1	4.3-4.51	0.58	0	387	0
ANO_1	4.12-4.3	0.643	0	403	0
ANO_1	3.96-4.12	0.719	0	428	0
ANO_1	3.82-3.96	0.737	0	458	0
ANO_1	3.69-3.82	0.839	0	467	0
ANO_1	3.57-3.69	0.876	0	481	0
ANO_1	3.47-3.57	0.937	0	504	0
ANO_1	3.37-3.47	0.965	0	516	0
ANO_1	3.28-3.37	0.974	0	538	0
ANO_1	3.2-3.28	0.993	0	474	0
ISO_2	13.51-39.98	0.518	0.457	42	61
ISO_2	9.84-13.51	0.628	0.636	114	96
ISO_2	8.12-9.84	0.694	0.704	161	106
ISO_2	7.07-8.12	0.736	0.663	212	105
ISO_2	6.34-7.07	0.713	0.705	238	103
ISO_2	5.8-6.34	0.706	0.67	262	108
ISO_2	5.38-5.8	0.736	0.719	293	101
ISO_2	5.04-5.38	0.786	0.726	323	97
ISO_2	4.75-5.04	0.874	0.839	348	107
ISO_2	4.51-4.75	0.879	0.893	363	99
ISO_2	4.3-4.51	0.889	0.83	387	107
ISO_2	4.12-4.3	0.869	0.85	403	108
ISO_2	3.96-4.12	0.85	0.93	428	105
ISO_2	3.82-3.96	0.848	0.833	458	118
ISO_2	3.69-3.82	0.864	0.8	467	109
ISO_2	3.57-3.69	0.83	0.873	481	119
ISO_2	3.47-3.57	0.798	0.817	504	111
ISO_2	3.37-3.47	0.807	0.839	516	104
ISO_2	3.28-3.37	0.828	0.891	538	118
ISO_2	3.2-3.28	0.906	0.985	505	108
ANO_2	13.51-39.98	0.284	0	51	0
ANO_2	9.84-13.51	0.375	0	114	0
ANO_2	8.12-9.84	0.363	0	161	0
ANO_2	7.07-8.12	0.293	0	212	0
ANO_2	6.34-7.07	0.339	0	238	0
ANO_2	5.8-6.34	0.338	0	262	0
ANO_2	5.38-5.8	0.442	0	293	0
ANO_2	5.04-5.38	0.446	0	323	0
ANO_2	4.75-5.04	0.59	0	348	0
ANO_2	4.51-4.75	0.656	0	363	0
ANO_2	4.3-4.51	0.749	0	387	0
ANO_2	4.12-4.3	0.772	0	403	0
ANO_2	3.96-4.12	0.866	0	428	0
ANO_2	3.82-3.96	0.885	0	458	0
ANO_2	3.69-3.82	0.94	0	467	0
ANO_2	3.57-3.69	0.957	0	481	0
ANO_2	3.47-3.57	0.981	0	504	0
ANO_2	3.37-3.47	0.987	0	516	0
ANO_2	3.28-3.37	0.994	0	532	0
ANO_2	3.2-3.28	0.998	0	471	0
ISO_3	13.51-39.98	0.582	0.529	42	61
ISO_3	9.84-13.51	0.716	0.655	114	97
ISO_3	8.12-9.84	0.761	0.79	161	106
ISO_3	7.07-8.12	0.758	0.734	212	105
ISO_3	6.34-7.07	0.848	0.779	238	103
ISO_3	5.8-6.34	0.902	0.97	262	108
ISO_3	5.38-5.8	0.891	0.907	293	101
ISO_3	5.04-5.38	0.887	0.87	323	97
ISO_3	4.75-5.04	0.824	0.844	348	107
ISO_3	4.51-4.75	0.862	0.796	363	99
ISO_3	4.3-4.51	0.84	0.811	387	107
ISO_3	4.12-4.3	0.874	0.902	403	108
ISO_3	3.96-4.12	0.859	0.909	428	105
ISO_3	3.82-3.96	0.879	0.845	458	118
ISO_3	3.69-3.82	0.877	0.89	466	109
ISO_3	3.57-3.69	0.866	0.909	481	119
ISO_3	3.47-3.57	0.871	0.846	504	111
ISO_3	3.37-3.47	0.874	0.849	516	104
ISO_3	3.28-3.37	0.905	1.026	536	118
ISO_3	3.2-3.28	0.944	0.975	499	107
ANO_3	13.51-39.98	0.277	0	51	0
ANO_3	9.84-13.51	0.379	0	114	0
ANO_3	8.12-9.84	0.382	0	161	0
ANO_3	7.07-8.12	0.302	0	212	0
ANO_3	6.34-7.07	0.327	0	238	0
ANO_3	5.8-6.34	0.387	0	262	0
ANO_3	5.38-5.8	0.451	0	293	0
ANO_3	5.04-5.38	0.471	0	323	0
ANO_3	4.75-5.04	0.644	0	348	0
ANO_3	4.51-4.75	0.681	0	363	0
ANO_3	4.3-4.51	0.736	0	387	0
ANO_3	4.12-4.3	0.844	0	403	0
ANO_3	3.96-4.12	0.841	0	428	0
ANO_3	3.82-3.96	0.922	0	458	0
ANO_3	3.69-3.82	0.947	0	466	0
ANO_3	3.57-3.69	0.967	0	481	0
ANO_3	3.47-3.57	0.979	0	504	0
ANO_3	3.37-3.47	0.988	0	516	0
ANO_3	3.28-3.37	0.992	0	530	0
ANO_3	3.2-3.28	0.997	0	454	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-49.911	43.898	35.088	SE	160.89	2.22
2	-40.765	41.86	17.042	SE	121.58	2.35
3	-37.514	66.612	3.435	SE	117.81	1.78
4	-33.248	72.019	19.096	SE	136.47	2.12
5	-53.552	33.278	53.672	SE	166.2	1.87
6	-48.849	29.769	21.568	SE	187.85	2.37

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
13.51-39.98	0.932	0.712	51	94
9.84-13.51	0.913	0.675	114	97
8.12-9.84	0.856	0.629	161	106
7.07-8.12	0.853	0.617	212	105
6.34-7.07	0.835	0.546	238	103
5.8-6.34	0.837	0.505	262	108
5.38-5.8	0.793	0.423	293	101
5.04-5.38	0.782	0.449	323	97
4.75-5.04	0.701	0.398	348	107
4.51-4.75	0.679	0.333	363	99
4.3-4.51	0.626	0.365	387	107
4.12-4.3	0.58	0.266	403	109
3.96-4.12	0.538	0.252	428	105
3.82-3.96	0.498	0.231	458	118
3.69-3.82	0.41	0.127	467	109
3.57-3.69	0.365	0.162	481	119
3.47-3.57	0.279	0.113	504	111
3.37-3.47	0.226	0.091	516	104
3.28-3.37	0.182	0.094	538	118
3.2-3.28	0.141	0.091	544	114

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
REFMAC		refinement
PDB_EXTRACT	3	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 2.9→10 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.895 / SU B: 36.159 / SU ML: 0.333 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.707 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28819	576	5.1 %	RANDOM
R_work	0.25842	-	-	-
obs	0.25996	10792	95.1 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 58.579 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.69 Å²	1.34 Å²	0 Å²
2-	-	2.69 Å²	0 Å²
3-	-	-	-4.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→10 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2067	0	7	0	2074

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	2106
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.137	1.969	2868
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.045	5	283
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.004	24.4	75
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.48	15	306
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.824	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	341
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1580
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	954
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.303	0.2	1454
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.105	0.2	53
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.2	0.2	2
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.372	0.2	29
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.131	0.2	3
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.073	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.515	1.5	1462
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.945	2	2244
X-RAY DIFFRACTION	r_scbond_it	1.052	3	726
X-RAY DIFFRACTION	r_scangle_it	1.645	4.5	624
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.9→2.969 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.42	28	-
R_work	0.318	621	-
obs	-	-	81.64 %

Refinement TLS params.

Method: refined / Origin x: -40.873 Å / Origin y: 49.539 Å / Origin z: 17.075 Å

	11	12	13	21	22	23	31	32	33
T	0.2791 Å²	-0.1487 Å²	-0.0378 Å²	-	0.0063 Å²	-0.1219 Å²	-	-	0.2235 Å²
L	2.4044 °²	1.3263 °²	-1.2691 °²	-	2.5212 °²	-1.3443 °²	-	-	4.2527 °²
S	-0.1985 Å °	0.1998 Å °	0.0442 Å °	-0.3556 Å °	0.1421 Å °	0.1105 Å °	0.5084 Å °	-0.3062 Å °	0.0564 Å °

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