PDB-2bl2: The membrane rotor of the V-type ATPase from Enterococcus hirae

ID or keywords:

Entry

Database: PDB / ID: 2bl2

Title

The membrane rotor of the V-type ATPase from Enterococcus hirae

Components

V-TYPE SODIUM ATP SYNTHASE SUBUNIT K

Keywords

HYDROLASE / V-TYPE ATPASE / K-RING / MEMBRANE ROTOR / SODIUM TRANSPORTER / HYDROGEN ION TRANSPORT / TRANSMEMBRANE

Function / homology

Function and homology information

proton-transporting V-type ATPase, V0 domain / sodium ion transport / proton-transporting ATPase activity, rotational mechanism / identical protein binding / plasma membrane
Similarity search - Function

Biological species

ENTEROCOCCUS HIRAE (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 2.1 Å

Authors

Murata, T. / Yamato, I. / Kakinuma, Y. / Leslie, A.G.W. / Walker, J.E.

Citation

Journal: Science / Year: 2005
Title: Structure of the Rotor of the Vacuolar-Type Na- ATPase from Enterococcus Hirae
Authors: Murata, T. / Yamato, I. / Kakinuma, Y. / Leslie, A.G.W. / Walker, J.E.

History

Deposition	Feb 25, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 5, 2005	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.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.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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2bl2.cif.gz	340.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2bl2.ent.gz	277.5 KB	Display	PDB format
PDBx/mmJSON format	2bl2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2bl2_validation.pdf.gz	10.2 MB	Display	wwPDB validaton report
Full document	2bl2_full_validation.pdf.gz	10.3 MB	Display
Data in XML	2bl2_validation.xml.gz	76.6 KB	Display
Data in CIF	2bl2_validation.cif.gz	92 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bl/2bl2 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/2bl2	HTTPS FTP

-
Related structure data

Similar structure data	2db4-d 2cyd-d 3h1c-1 3fz3-d 3ehk-d 4y4m-d 9581 2d5f-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#219 - Mar 2018 Vacuolar ATPase similarity (4) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #59 - Nov 2004 Photosystem II similarity (1) #66 - Jun 2005 Carotenoid Oxygenase similarity (1) #72 - Dec 2005 ATP Synthase similarity (3)

Deposited unit

A: V-TYPE SODIUM ATP SYNTHASE SUBUNIT K

B: V-TYPE SODIUM ATP SYNTHASE SUBUNIT K

C: V-TYPE SODIUM ATP SYNTHASE SUBUNIT K

D: V-TYPE SODIUM ATP SYNTHASE SUBUNIT K

E: V-TYPE SODIUM ATP SYNTHASE SUBUNIT K

F: V-TYPE SODIUM ATP SYNTHASE SUBUNIT K

G: V-TYPE SODIUM ATP SYNTHASE SUBUNIT K

H: V-TYPE SODIUM ATP SYNTHASE SUBUNIT K

I: V-TYPE SODIUM ATP SYNTHASE SUBUNIT K

J: V-TYPE SODIUM ATP SYNTHASE SUBUNIT K

hetero molecules

208 kDa, 10 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)	120.136, 125.604, 210.866
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	Details
1	1	A
2	1	B
3	1	D
4	1	E
5	1	G
6	1	H
1	2	A
2	2	C
1	3	A
2	3	F
1	4	A
2	4	I
1	5	A
2	5	J

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1 - 159
2	1	1	1	B	1 - 159
3	1	1	1	D	1 - 159
4	1	1	1	E	1 - 159
5	1	1	1	G	1 - 159
6	1	1	1	H	1 - 159
1	1	2	1	A	1 - 49
2	1	2	1	C	1 - 49
1	2	2	1	A	51 - 159
2	2	2	1	C	51 - 159
1	1	3	1	A	1 - 49
2	1	3	1	F	1 - 49
1	2	3	1	A	51 - 159
2	2	3	1	F	51 - 159
1	1	4	1	A	1 - 4
2	1	4	1	I	1 - 4
1	2	4	1	A	13 - 47
2	2	4	1	I	13 - 47
1	3	4	1	A	55 - 77
2	3	4	1	I	55 - 77
1	4	4	1	A	86 - 125
2	4	4	1	I	86 - 125
1	5	4	1	A	127 - 154
2	5	4	1	I	127 - 154
1	6	4	1	A	157 - 159
2	6	4	1	I	157 - 159
1	1	5	1	A	13 - 78
2	1	5	1	J	13 - 78
1	2	5	1	A	89 - 159
2	2	5	1	J	89 - 159

NCS ensembles :

ID
1
2
3
4
5

#1: Protein	V-TYPE SODIUM ATP SYNTHASE SUBUNIT K / NTPK RING / NA(+)-TRANSLOCATING ATPASE SUBUNIT K / SODIUM ATPASE PROTEOLIPID COMPONENT Mass: 16043.918 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) ENTEROCOCCUS HIRAE (bacteria) References: UniProt: P43457, H+-transporting two-sector ATPase
#2: Chemical	... ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE Mass: 722.970 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C₃₈H₇₅O₁₀P / Comment: phospholipid*YM
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Chemical	... ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE Mass: 496.589 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C₂₃H₄₄O₁₁ / Comment: detergent*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H₂O
Compound details	FUNCTION: INVOLVEMENT IN ATP-DRIVEN SODIUM EXTRUSION

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 4.25 Å³/Da / Density % sol: 70.84 %
Crystal grow	pH: 8 Details: 32% PEG 400, 220MM NA CITRATE, 0.32MM DODECYLMALTOSIDE, 1.2MM UNDECYLMALTOSIDE, pH 8.00

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792
Detector	Type: ADSC CCD / Detector: CCD / Date: Nov 23, 2003
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.1→61.3 Å / Num. obs: 184567 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / R_merge(I) obs: 0.09 / Net I/σ(I): 9.1
Reflection shell	Resolution: 2.1→2.21 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 1.8 / % possible all: 97.5

-
Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
SHARP		phasing
SHELXD		phasing
REFMAC	5.1.24	refinement

Refinement

Method to determine structure:

MIRAS / Resolution: 2.1→61 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.943 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LIPIDS WITH RESIDUE NUMBERS 160,161 AND 162 FOR CHAINS A TO J ARE VERY DISORDERED, AND MAY IN FACT BE DETERGENT MOLECULES. DETERGENTS WITH ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2	5580	3 %	RANDOM
R_work	0.19	-	-	-
obs	0.191	178986	99.3 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 33.82 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.93 Å²	0 Å²	0 Å²
2-	-	2.07 Å²	0 Å²
3-	-	-	0.86 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11280	0	1478	348	13106

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	13181
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.955	2.06	17311
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.114	5	1550
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	1986
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	8572
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.181	0.2	7264
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.106	0.2	540
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.125	0.2	23
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.107	0.2	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.832	3	7694
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.455	5	12231
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.657	5	5487
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.703	8	5080
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1245	tight positional	0.01	0.05
1	2	B	1245	tight positional	0.01	0.05
1	3	D	1245	tight positional	0.01	0.05
1	4	E	1245	tight positional	0.01	0.05
1	5	G	1245	tight positional	0.01	0.05
1	6	H	1245	tight positional	0.01	0.05
2	1	A	1236	tight positional	0.01	0.05
3	1	A	1236	tight positional	0.02	0.05
4	1	A	1039	tight positional	0.03	0.05
5	1	A	1076	tight positional	0.02	0.05
1	1	A	1245	tight thermal	0.57	5
1	2	B	1245	tight thermal	0.68	5
1	3	D	1245	tight thermal	0.65	5
1	4	E	1245	tight thermal	0.64	5
1	5	G	1245	tight thermal	0.72	5
1	6	H	1245	tight thermal	0.88	5
2	1	A	1236	tight thermal	0.6	5
3	1	A	1236	tight thermal	0.65	5
4	1	A	1039	tight thermal	0.74	5
5	1	A	1076	tight thermal	0.71	5

LS refinement shell

Resolution: 2.1→2.15 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.265	383
R_work	0.277	12783

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	1.9051	-0.5296	0.0082	0.8262	0.3186	1.3949	0.1852	0.0775	0.4163	-0.0525	0.0035	-0.0955	-0.3403	0.1956	-0.1887	0.2089	-0.0532	0.1116	0.0755	-0.0515	0.2487	36.7404	58.714	21.1111
2	2.0198	-0.5461	-0.21	0.8876	0.108	1.3037	0.1882	-0.135	0.3607	0.1673	0.0006	-0.0839	-0.3341	0.3014	-0.1887	0.2688	-0.1041	0.1063	0.1274	-0.163	0.2776	34.6116	61.3134	38.6539
3	1.7291	-0.5649	-0.5356	1.3016	-0.1835	1.1235	0.1429	-0.3833	0.2547	0.3855	-0.0092	-0.062	-0.2312	0.3895	-0.1337	0.3099	-0.0832	0.0569	0.2794	-0.1837	0.2007	32.5024	53.0736	54.4158
4	1.977	-0.2567	-0.3239	1.604	0.0272	0.9577	0.0579	-0.4979	0.1012	0.491	0.0112	-0.0677	-0.0525	0.4162	-0.0692	0.3506	-0.0141	0.0097	0.3968	-0.061	0.1237	31.1815	37.1432	62.3763
5	2.5217	0.0987	-0.407	1.3534	0.1435	0.934	-0.0391	-0.4588	0.0206	0.4424	0.0455	-0.0534	0.1593	0.3948	-0.0064	0.3368	0.0674	0.0109	0.3372	0.0965	0.1332	31.1673	19.5391	59.382
6	1.4988	0.2551	-0.7109	0.9348	0.0927	1.1459	-0.0889	-0.3614	-0.1275	0.2694	0.02	-0.0506	0.2841	0.2919	0.0689	0.2778	0.1017	0.036	0.1928	0.1521	0.1959	32.4829	7.0194	46.6663
7	1.8208	0.4844	-0.3056	0.8441	-0.0967	1.2067	-0.0645	-0.1875	-0.324	0.0785	-0.0108	-0.0529	0.2886	0.1779	0.0753	0.2113	0.0784	0.0471	0.0795	0.096	0.2034	34.64	4.2853	29.1294
8	1.9604	0.2873	0.3824	0.699	-0.1282	1.1771	0.0102	-0.0058	-0.3343	-0.0602	-0.0224	-0.055	0.1841	0.1274	0.0121	0.1197	0.0451	0.0236	0.0721	0.012	0.1222	36.8353	12.5157	13.4405
9	2.4982	0.0448	0.3571	0.4201	-0.1475	0.5665	0.0455	0.0868	-0.1012	-0.0816	-0.0201	-0.0186	-0.0002	0.0733	-0.0254	0.0731	0.0133	0.0216	0.1155	-0.0056	0.0413	38.1112	28.4671	5.5305
10	1.3938	-0.2968	0.075	0.6072	0.1132	0.8311	0.1016	0.0655	0.249	-0.0935	-0.0043	-0.047	-0.176	0.0621	-0.0974	0.1201	-0.0062	0.0594	0.1102	0.0078	0.1061	38.0967	46.1378	8.4345

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 156
2	X-RAY DIFFRACTION	2	B	1 - 156
3	X-RAY DIFFRACTION	3	C	1 - 156
4	X-RAY DIFFRACTION	4	D	1 - 156
5	X-RAY DIFFRACTION	5	E	1 - 156
6	X-RAY DIFFRACTION	6	F	1 - 156
7	X-RAY DIFFRACTION	7	G	1 - 156
8	X-RAY DIFFRACTION	8	H	1 - 156
9	X-RAY DIFFRACTION	9	I	1 - 156
10	X-RAY DIFFRACTION	10	J	1 - 156

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi