PDB-4dl0: Crystal Structure of the heterotrimeric EGChead Peripheral Stalk ...

ID or keywords:

Entry

Database: PDB / ID: 4dl0

Title

Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase

Components

(V-type proton ATPase subunit ...) x 3

Keywords

HYDROLASE / coiled-coil / heterotrimer / peripheral stalk / stator complex / ion transport / Vacuolar ATPase / vacuolar membrane

Function / homology

Function and homology information

Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD,

MOLECULAR REPLACEMENT /

SAD /

molecular replacement / Resolution: 2.905 Å

Authors

Oot, R.A. / Huang, L.S. / Berry, E.A. / Wilkens, S.

Citation

Journal: Structure / Year: 2012
Title: Crystal Structure of the Yeast Vacuolar ATPase Heterotrimeric EGC(head) Peripheral Stalk Complex.
Authors: Oot, R.A. / Huang, L.S. / Berry, E.A. / Wilkens, S.

History

Deposition	Feb 5, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 10, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2012	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4dl0.cif.gz	367 KB	Display	PDBx/mmCIF format
PDB format	pdb4dl0.ent.gz	302.8 KB	Display	PDB format
PDBx/mmJSON format	4dl0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4dl0_validation.pdf.gz	504.9 KB	Display	wwPDB validaton report
Full document	4dl0_full_validation.pdf.gz	511.5 KB	Display
Data in XML	4dl0_validation.xml.gz	31 KB	Display
Data in CIF	4dl0_validation.cif.gz	41.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dl/4dl0 ftp://data.pdbj.org/pub/pdb/validation_reports/dl/4dl0	HTTPS FTP

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Related structure data

Related structure data	4efaC C: citing same article (ref.)
Similar structure data	4efa-d 4pbx-d 4m4r-1 4m4r-2 4m4r-3 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
Related items in Molecule of the Month	#219 - Mar 2018 Vacuolar ATPase similarity (16) #131 - Nov 2010 Inteins similarity (4)

Deposited unit

I: V-type proton ATPase subunit C

K: V-type proton ATPase subunit G

J: V-type proton ATPase subunit E

C: V-type proton ATPase subunit C

G: V-type proton ATPase subunit G

E: V-type proton ATPase subunit E

hetero molecules

110 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

I: V-type proton ATPase subunit C

K: V-type proton ATPase subunit G

J: V-type proton ATPase subunit E

hetero molecules

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

2

C: V-type proton ATPase subunit C

G: V-type proton ATPase subunit G

E: V-type proton ATPase subunit E

hetero molecules

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

Unit cell

Length a, b, c (Å)	95.790, 105.611, 120.486
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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V-type proton ATPase subunit ... , 3 types, 6 molecules ICKGJE

#1: Protein	V-type proton ATPase subunit C / V-ATPase subunit C / V-ATPase 42 kDa subunit / Vacuolar proton pump subunit C Mass: 14586.475 Da / Num. of mol.: 2 / Fragment: C subunit head domain, UNP residues 158-277 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: VAT3, VATC, VMA5, YKL080W, YKL410 / Plasmid: pMal c2e / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 References: UniProt: P31412, H+-transporting two-sector ATPase
#2: Protein	V-type proton ATPase subunit G / V-ATPase subunit G / V-ATPase 13 kDa subunit / Vacuolar proton pump subunit G Mass: 13218.298 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: VMA10, YHR039BC, YHR039C-A, YHR039C-B / Plasmid: pMal c2e / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 References: UniProt: P48836, H+-transporting two-sector ATPase
#3: Protein	V-type proton ATPase subunit E / V-ATPase subunit E / V-ATPase 27 kDa subunit / Vacuolar proton pump subunit E Mass: 26508.393 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: O6241, VAT5, VMA4, YOR332W / Plasmid: pMal c2e / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 References: UniProt: P22203, H+-transporting two-sector ATPase

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Non-polymers , 3 types, 41 molecules

#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-PBM / TRIMETHYL LEAD ION Mass: 252.304 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₉Pb
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.81 Å³/Da / Density % sol: 56.15 %
Crystal grow	Temperature: 292 K / pH: 6 Details: 0.1 M Lithium Sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M Glycine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 21, 2011 / Details: MICROBEAM
Radiation	Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9767 Å / Relative weight: 1
Reflection	Resolution: 2.9→40 Å / Num. obs: 51697 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / R_merge(I) obs: 0.158 / Net I/σ(I): 5.3
Reflection shell	Resolution: 2.9→2.95 Å / Redundancy: 9.7 % / % possible all: 99.4

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Phasing

Phasing

Method
SAD
molecular replacement

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-117.883	-16.594	-117.094	PB	26.44	0.29
2	118.54	-17.514	41.903	PB	28.42	0.29
3	31.674	-12.135	-0.122	PB	20.78	0.21
4	-121.245	-2.495	-129.187	PB	21.79	0.19

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.91 Å	39.71 Å
Translation	2.91 Å	39.71 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.4.0	phasing
SOLVE		phasing
PHENIX	dev_989	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

SAD,

MOLECULAR REPLACEMENT / Resolution: 2.905→39.71 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.45 / σ(F): 1.34 / Phase error: 29.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2569	3740	7.25 %
R_work	0.2078	-	-
obs	0.2115	51603	99.23 %
all	-	51697	-

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.853 Å² / k_sol: 0.331 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.5516 Å²	-0 Å²	0 Å²
2-	-	-5.5855 Å²	-0 Å²
3-	-	-	12.1371 Å²

Refinement step

Cycle: LAST / Resolution: 2.905→39.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7062	0	42	31	7135

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7157
X-RAY DIFFRACTION	f_angle_d	0.635	9595
X-RAY DIFFRACTION	f_dihedral_angle_d	12.262	2827
X-RAY DIFFRACTION	f_chiral_restr	0.042	1112
X-RAY DIFFRACTION	f_plane_restr	0.002	1227

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 (%)
2.9051-2.9419	0.3903	126	0.3733	1614	X-RAY DIFFRACTION	91
2.9419-2.9806	0.42	138	0.3623	1724	X-RAY DIFFRACTION	98
2.9806-3.0214	0.362	148	0.3681	1767	X-RAY DIFFRACTION	98
3.0214-3.0645	0.3845	141	0.3305	1749	X-RAY DIFFRACTION	99
3.0645-3.1103	0.3641	135	0.3147	1794	X-RAY DIFFRACTION	99
3.1103-3.1589	0.3879	141	0.3025	1773	X-RAY DIFFRACTION	99
3.1589-3.2106	0.3973	130	0.3082	1761	X-RAY DIFFRACTION	99
3.2106-3.266	0.4069	138	0.2929	1792	X-RAY DIFFRACTION	99
3.266-3.3253	0.3304	135	0.2895	1781	X-RAY DIFFRACTION	100
3.3253-3.3892	0.3475	133	0.2667	1782	X-RAY DIFFRACTION	100
3.3892-3.4584	0.2613	139	0.2453	1784	X-RAY DIFFRACTION	100
3.4584-3.5335	0.2875	136	0.2283	1779	X-RAY DIFFRACTION	100
3.5335-3.6157	0.2836	136	0.234	1757	X-RAY DIFFRACTION	100
3.6157-3.706	0.2473	139	0.2218	1797	X-RAY DIFFRACTION	100
3.706-3.8062	0.253	142	0.1952	1791	X-RAY DIFFRACTION	100
3.8062-3.9181	0.2477	139	0.1987	1788	X-RAY DIFFRACTION	100
3.9181-4.0444	0.1949	139	0.1984	1800	X-RAY DIFFRACTION	100
4.0444-4.1888	0.2892	143	0.1682	1789	X-RAY DIFFRACTION	100
4.1888-4.3563	0.2149	139	0.1683	1788	X-RAY DIFFRACTION	100
4.3563-4.5543	0.1956	139	0.1558	1782	X-RAY DIFFRACTION	100
4.5543-4.7941	0.2087	144	0.1608	1787	X-RAY DIFFRACTION	100
4.7941-5.0938	0.2146	138	0.1635	1772	X-RAY DIFFRACTION	100
5.0938-5.4862	0.1857	139	0.1635	1804	X-RAY DIFFRACTION	100
5.4862-6.0366	0.2337	141	0.1963	1758	X-RAY DIFFRACTION	100
6.0366-6.9061	0.2835	145	0.2071	1788	X-RAY DIFFRACTION	100
6.9061-8.686	0.1882	138	0.1505	1798	X-RAY DIFFRACTION	100
8.686-39.7135	0.197	139	0.1549	1764	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	3.2766	1.7254	-1.6953	4.7743	4.7573	9.1179	0.0089	-1.026	0.0268	1.6025	0.6836	-2.2094	1.7335	0.7965	-0.9568	0.8228	0.0984	-0.2854	0.6504	0.0265	0.4851	74.0573	5.2995	54.7394
2	7.739	3.0577	1.8579	3.3833	-3.1591	7.4466	0.2683	-0.1464	-1.3447	-1.0308	-0.4839	-0.2071	0.0028	-0.1843	0.0069	0.6747	0.1762	-0.1338	0.6304	-0.26	0.7152	58.6426	-7.3199	42.3045
3	4.1091	-0.0132	-1.7056	6.3862	-0.6841	5.1998	0.0057	1.004	0.1919	-0.3049	0.3001	0.313	0.0578	0.0381	-0.273	0.5149	0.0963	-0.0605	0.7247	-0.0331	0.3251	45.0754	5.0995	36.9744
4	4.5942	5.1298	5.103	5.7812	5.7502	5.7164	0.0818	-2.708	0.3357	1.5687	-1.7108	0.8783	1.5504	-1.1879	1.6642	1.2645	-0.0859	0.2562	1.7119	0.0981	1.3204	46.4074	-0.3165	53.7256
5	6.5686	-0.1144	-5.1909	0.2447	0.0544	4.353	0.5024	-0.2923	1.5503	0.0298	0.2152	-0.1057	-0.2197	0.2192	-0.607	0.4581	0.0409	0.1193	0.3902	-0.0797	0.6029	4.2126	19.8512	69.5806
6	2.628	1.2499	-3.8506	2.4917	-0.5213	6.9884	0.6797	-0.005	1.204	-0.8037	-0.1173	0.1385	-0.7263	-0.2276	-0.3645	1.0226	0.3833	0.27	0.9786	0.2529	0.8588	-66.3467	22.2552	106.5349
7	8.0283	-0.054	-5.6725	0.2244	-0.0413	4.2518	0.3515	0.6405	0.6683	0.057	0.1273	0.0033	-0.1357	-0.4778	-0.4901	0.474	0.0562	0.0502	0.4513	0.0994	0.5104	-9.7941	16.1832	73.2397
8	3.5413	0.1792	0.2573	4.5499	-1.3667	5.5928	0.207	0.2308	0.1413	0.0272	-0.1099	0.1863	0.1277	-0.3789	-0.117	0.3862	0.0864	0.0659	0.5121	0.0246	0.4286	-74.6476	7.3596	125.9815
9	1.1082	-2.3472	1.9466	8.9785	-7.672	6.5582	-1.4935	0.1293	-0.1177	-1.0792	1.7291	1.1022	1.8366	-3.1935	-1.2685	1.1019	0.0078	-0.0497	1.0506	0.1436	0.3846	-74.589	6.6232	110.8116
10	6.0527	6.0754	6.9209	6.0875	6.9348	7.9036	-0.2597	-0.0272	0.7038	-0.5169	-0.2173	0.6227	-0.2847	-0.3228	0.4064	0.6044	0.0082	0.0274	0.5467	-0.0009	0.5405	-58.6269	-5.3663	123.8893
11	7.5796	0.619	-1.3481	6.2241	-0.5967	5.2773	0.0525	-0.3254	0.1932	0.0399	0.2333	-0.4047	-0.1173	0.1047	-0.2749	0.391	0.0073	-0.0225	0.3881	-0.0526	0.2531	-44.9898	7.0275	129.2868
12	5.5199	-4.0771	5.4283	8.5904	-4.4561	5.3856	-0.8493	1.1076	0.8149	-1.1087	-1.0828	0.2127	0.3266	-0.1679	1.8206	1.3289	0.217	0.2125	1.1368	-0.064	1.1053	-46.2655	1.9174	112.4024
13	6.2853	0.3833	-6.0307	-0.3828	-0.1345	4.9029	0.6555	0.7659	0.9001	-0.0482	-0.1323	-0.0253	-0.4363	-0.4203	-0.558	0.6245	0.0733	0.2142	0.7293	0.2755	0.9313	-4.4048	21.1924	95.7348
14	4.9382	-2.7343	-6.6231	6.0541	3.9139	8.9151	0.329	-0.0794	1.4116	0.065	0.2791	-0.1177	-0.4411	0.1636	-0.7931	0.4831	-0.1007	-0.0364	0.3486	-0.0185	0.4547	63.143	21.4825	59.7696
15	9.1051	-0.0083	-6.2578	-0.2343	0.1679	4.2172	0.4449	-0.2478	0.4032	0.0256	-0.0774	0.0416	-0.4306	0.1356	-0.3324	0.6307	0.0165	0.2058	0.6153	0.0877	0.7801	9.5206	16.9775	92.7017
16	4.0759	-1.2005	0.5804	4.8999	2.2664	2.1935	0.2413	0.7885	0.242	-0.2234	-0.2062	-0.3911	0.309	0.2896	-0.0305	0.4266	0.0864	0.038	0.624	0.0717	0.3704	74.3871	5.9188	39.7079

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'I' and (resid 153 through 162 )
2	X-RAY DIFFRACTION	2	chain 'I' and (resid 163 through 177 )
3	X-RAY DIFFRACTION	3	chain 'I' and (resid 178 through 258 )
4	X-RAY DIFFRACTION	4	chain 'I' and (resid 259 through 273 )
5	X-RAY DIFFRACTION	5	chain 'K' and (resid 2 through 78 )
6	X-RAY DIFFRACTION	6	chain 'K' and (resid 79 through 106 )
7	X-RAY DIFFRACTION	7	chain 'J' and (resid 2 through 111 )
8	X-RAY DIFFRACTION	8	chain 'J' and (resid 112 through 224 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 153 through 162 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 163 through 177 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 178 through 258 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 259 through 273 )
13	X-RAY DIFFRACTION	13	chain 'G' and (resid 2 through 73 )
14	X-RAY DIFFRACTION	14	chain 'G' and (resid 74 through 106 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 2 through 111 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 112 through 224 )

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V-type proton ATPase subunit ... , 3 types, 6 molecules ICKGJE

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Non-polymers , 3 types, 41 molecules

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-V-type proton ATPase subunit ... , 3 types, 6 molecules ICKGJE

-Non-polymers , 3 types, 41 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

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-Processing

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-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

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V-type proton ATPase subunit ... , 3 types, 6 molecules ICKGJE

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Non-polymers , 3 types, 41 molecules

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