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- PDB-2cyd: Crystal structure of Lithium bound rotor ring of the V-ATPase fro... -

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Basic information

Entry
Database: PDB / ID: 2cyd
TitleCrystal structure of Lithium bound rotor ring of the V-ATPase from Enterococcus hirae
ComponentsV-type sodium ATP synthase subunit K
KeywordsHYDROLASE / NtpK / V-ATPase / Na(+)-ATPase / Lithium / Proteolipid / Enterococcus / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
lithium bound rotor ring of v- atpase / V-ATPase proteolipid subunit / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / : / V-type sodium ATPase subunit K
Similarity search - Component
Biological speciesEnterococcus hirae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMurata, T. / Yamato, I. / Kakinuma, Y. / Shirouzu, M. / Walker, J.E. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of Lithium bound rotor ring of the V-ATPase from Enterococcus hirae
Authors: Murata, T. / Yamato, I. / Kakinuma, Y. / Shirouzu, M. / Walker, J.E. / Yokoyama, S.
History
DepositionJul 6, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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.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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)175,96142
Polymers160,43910
Non-polymers15,52232
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61880 Å2
ΔGint-616 kcal/mol
Surface area42760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.648, 125.779, 210.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31G
41D
51E
61H
12A
22C
32F
42A
52C
62F
13A
23I
33A
43I
53A
63I
73A
83I
93A
103I
113A
123I
14A
24J
34A
44J

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETALAALAAA1 - 1561 - 156
211METMETALAALABB1 - 1561 - 156
311METMETALAALAGG1 - 1561 - 156
411METMETALAALADD1 - 1561 - 156
511METMETALAALAEE1 - 1561 - 156
611METMETALAALAHH1 - 1561 - 156
112METMETPROPROAA1 - 491 - 49
212METMETPROPROCC1 - 491 - 49
312METMETPROPROFF1 - 491 - 49
422LYSLYSALAALAAA51 - 15651 - 156
522LYSLYSALAALACC51 - 15651 - 156
622LYSLYSALAALAFF51 - 15651 - 156
113METMETTYRTYRAA1 - 41 - 4
213METMETTYRTYRII1 - 41 - 4
323VALVALGLNGLNAA13 - 4813 - 48
423VALVALGLNGLNII13 - 4813 - 48
533ALAALAPHEPHEAA55 - 7755 - 77
633ALAALAPHEPHEII55 - 7755 - 77
743VALVALPROPROAA86 - 12586 - 125
843VALVALPROPROII86 - 12586 - 125
953HISHISLEULEUAA127 - 154127 - 154
1053HISHISLEULEUII127 - 154127 - 154
1163ALAALAALAALAAA156156
1263ALAALAALAALAII156156
114VALVALILEILEAA13 - 7813 - 78
214VALVALILEILEJJ13 - 7813 - 78
324GLYGLYALAALAAA89 - 15689 - 156
424GLYGLYALAALAJJ89 - 15689 - 156

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
V-type sodium ATP synthase subunit K / Na+ / - translocating ATPase subunit K / Sodium ATPase proteolipid component


Mass: 16043.918 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus hirae (bacteria) / Production host: Enterococcus hirae (bacteria) / Strain (production host): 25D
References: UniProt: P43457, H+-transporting two-sector ATPase
#2: Chemical
ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Li
#3: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#4: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.9 Å3/Da / Density % sol: 74.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 400, Lithium chroride, Potassium citrate, Tris-HCl, Glycerol, Undecyl-maltoside, Dodecyl-maltoside, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→107.83 Å / Num. all: 78734 / Num. obs: 77244 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 1.9 / Num. unique all: 10723 / Rsym value: 0.706

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→107.8 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.913 / SU B: 15.666 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.9 / ESU R: 0.455 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21813 3890 5 %RANDOM
Rwork0.20811 ---
obs0.20861 73353 98.11 %-
all-77318 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.981 Å2
Baniso -1Baniso -2Baniso -3
1--4 Å20 Å20 Å2
2--2.38 Å20 Å2
3---1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.8→107.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11280 0 968 322 12570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02212671
X-RAY DIFFRACTIONr_angle_refined_deg1.1342.0416911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.20151550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.35425.767378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.449152015
X-RAY DIFFRACTIONr_chiral_restr0.0810.21986
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028572
X-RAY DIFFRACTIONr_nbd_refined0.2020.27419
X-RAY DIFFRACTIONr_nbtor_refined0.3010.29112
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2590
X-RAY DIFFRACTIONr_metal_ion_refined0.0210.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.26
X-RAY DIFFRACTIONr_mcbond_it0.5391.57798
X-RAY DIFFRACTIONr_mcangle_it0.947212221
X-RAY DIFFRACTIONr_scbond_it1.24335237
X-RAY DIFFRACTIONr_scangle_it2.2954.54690
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1245tight positional0.020.05
12B1245tight positional0.020.05
13G1245tight positional0.020.05
14D1245tight positional0.020.05
15E1245tight positional0.020.05
16H1245tight positional0.020.05
21A1236tight positional0.030.05
22C1236tight positional0.020.05
23F1236tight positional0.020.05
31A1048tight positional0.040.05
41A1076tight positional0.030.05
11A1245tight thermal0.060.5
12B1245tight thermal0.040.5
13G1245tight thermal0.040.5
14D1245tight thermal0.040.5
15E1245tight thermal0.040.5
16H1245tight thermal0.050.5
21A1236tight thermal0.060.5
22C1236tight thermal0.050.5
23F1236tight thermal0.050.5
31A1048tight thermal0.080.5
41A1076tight thermal0.10.5
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 283 -
Rwork0.286 5121 -
obs--94.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.2768-0.6326-0.12841.15170.42481.63470.27830.08870.5187-0.1282-0.0572-0.1364-0.2980.2008-0.2212-0.0217-0.06090.0981-0.1198-0.04680.010136.658758.799121.0308
22.6623-0.6297-0.29371.29970.19611.6220.1881-0.09670.33290.1297-0.0207-0.1353-0.33530.294-0.16730.0325-0.09980.0825-0.0987-0.14810.044134.487861.432238.5111
31.5506-0.2292-0.65591.3771-0.19371.32470.1626-0.43180.29720.3797-0.0304-0.1585-0.27430.3692-0.13220.0845-0.09280.03670.0616-0.19240.012332.31753.243754.2389
41.8979-0.2527-0.1522.18440.08230.98390.0827-0.47490.0920.561-0.014-0.1619-0.08890.3789-0.06870.1524-0.0171-0.01650.2001-0.0487-0.131930.966137.341762.2372
52.9109-0.0423-0.4281.73480.11771.16680.0598-0.54330.110.4905-0.0161-0.12270.15830.4039-0.04380.12390.066-0.01370.13640.1143-0.093730.948119.750659.3149
61.45850.4253-0.88651.26110.13081.45310.0654-0.3711-0.15680.3521-0.0607-0.10890.29270.3195-0.00470.04020.09480.0159-0.00030.1749-0.034532.28967.208746.6628
72.24060.1951-0.25211.0272-0.21351.5808-0.0003-0.1721-0.30960.1371-0.0515-0.11040.35130.21480.0519-0.02070.08660.0337-0.12990.1110.01534.49264.432429.1772
82.1340.22520.51160.821-0.19811.53640.08160.0119-0.3752-0.0392-0.0525-0.10790.26360.1348-0.0291-0.10230.05430.0275-0.1231-0.0057-0.101136.722812.613313.5244
91.6963-0.06810.27730.3616-0.19740.72560.06420.107-0.1199-0.1042-0.0419-0.0220.03550.0777-0.0223-0.16250.0110.035-0.0681-0.0051-0.183938.02128.51745.6051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1561 - 156
2X-RAY DIFFRACTION2BB1 - 1561 - 156
3X-RAY DIFFRACTION3CC1 - 1561 - 156
4X-RAY DIFFRACTION4DD1 - 1561 - 156
5X-RAY DIFFRACTION5EE1 - 1561 - 156
6X-RAY DIFFRACTION6FF1 - 1561 - 156
7X-RAY DIFFRACTION7GG1 - 1561 - 156
8X-RAY DIFFRACTION8HH1 - 1561 - 156
9X-RAY DIFFRACTION9II1 - 1561 - 156

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