[English] 日本語
Yorodumi
- PDB-2db4: Crystal structure of rotor ring with DCCD of the V- ATPase from E... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2db4
TitleCrystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae
ComponentsV-Type Sodium ATPase Subunit K
KeywordsHYDROLASE / NtpK / V-ATPase / Na(+)-ATPase / DCCD / Proteolipid / Enterococcus hirae / 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
DICYCLOHEXYLUREA / 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: 2.4 Å
AuthorsMurata, T. / Yamato, I. / Kakinuma, Y. / Shirouzu, M. / Walker, J.E. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of the rotor ring modified with N,N'-dicyclohexylcarbodiimide of the Na+-transporting vacuolar ATPase.
Authors: Mizutani, K. / Yamamoto, M. / Suzuki, K. / Yamato, I. / Kakinuma, Y. / Shirouzu, M. / Walker, J.E. / Yokoyama, S. / Iwata, S. / Murata, T.
History
DepositionDec 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Sep 28, 2011Group: Database references
Revision 1.4May 23, 2012Group: Non-polymer description
Revision 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: V-Type Sodium ATPase Subunit K
B: V-Type Sodium ATPase Subunit K
C: V-Type Sodium ATPase Subunit K
D: V-Type Sodium ATPase Subunit K
E: V-Type Sodium ATPase Subunit K
F: V-Type Sodium ATPase Subunit K
G: V-Type Sodium ATPase Subunit K
H: V-Type Sodium ATPase Subunit K
I: V-Type Sodium ATPase Subunit K
J: V-Type Sodium ATPase Subunit K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,33860
Polymers160,43910
Non-polymers21,89950
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61630 Å2
ΔGint-649 kcal/mol
Surface area43610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.214, 125.229, 211.577
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 label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METALAAA1 - 1561 - 156
211METALABB1 - 1561 - 156
311METALAGG1 - 1561 - 156
411METALADD1 - 1561 - 156
511METALAEE1 - 1561 - 156
611METALAHH1 - 1561 - 156
112METPROAA1 - 491 - 49
212METPROCC1 - 491 - 49
312METPROFF1 - 491 - 49
422LYSALAAA51 - 15651 - 156
522LYSALACC51 - 15651 - 156
622LYSALAFF51 - 15651 - 156
113METTYRAA1 - 41 - 4
213METTYRII1 - 41 - 4
323VALGLNAA13 - 4813 - 48
423VALGLNII13 - 4813 - 48
533ALAPHEAA55 - 7755 - 77
633ALAPHEII55 - 7755 - 77
743VALPROAA86 - 12586 - 125
843VALPROII86 - 12586 - 125
953HISLEUAA127 - 154127 - 154
1053HISLEUII127 - 154127 - 154
1163NALHGAK - V557 - 5591
1263NALHGIS - LA8157 - 81591
114VALILEAA13 - 7813 - 78
214VALILEJJ13 - 7813 - 78
324GLYALAAA89 - 15689 - 156
424GLYALAJJ89 - 15689 - 156

NCS ensembles :
ID
1
2
3
4

-
Components

-
Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
V-Type Sodium ATPase 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

-
Non-polymers , 5 types, 295 molecules

#2: Chemical
ChemComp-DCW / DICYCLOHEXYLUREA


Mass: 224.342 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C13H24N2O
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: 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
#5: Chemical
ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.9 Å3/Da / Density % sol: 74.89 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 32% PEG 400, 240mM Sodium citrate, 100mM Tris-HCl (pH 7.5), 4% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→107.83 Å / Num. all: 125160 / Num. obs: 124723 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 57.321 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.462 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 1.8 / Num. unique all: 8579

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→107.83 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.919 / SU B: 10.704 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.8 / ESU R: 0.242 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23094 6272 5 %RANDOM
Rwork0.22499 ---
obs0.22529 118450 99.65 %-
all-124797 --
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: 57.321 Å2
Baniso -1Baniso -2Baniso -3
1--3.32 Å20 Å20 Å2
2--2.75 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.4→107.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11270 0 1134 245 12649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02212839
X-RAY DIFFRACTIONr_angle_refined_deg1.1992.05517091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.70551550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.30225.652368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.521151995
X-RAY DIFFRACTIONr_chiral_restr0.0890.22006
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028622
X-RAY DIFFRACTIONr_nbd_refined0.1940.27257
X-RAY DIFFRACTIONr_nbtor_refined0.30.28905
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2517
X-RAY DIFFRACTIONr_metal_ion_refined0.0190.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.27
X-RAY DIFFRACTIONr_mcbond_it0.4031.57660
X-RAY DIFFRACTIONr_mcangle_it0.742212229
X-RAY DIFFRACTIONr_scbond_it0.94335209
X-RAY DIFFRACTIONr_scangle_it1.6244.54862
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1251tight positional0.020.05
12B1251tight positional0.020.05
13G1251tight positional0.020.05
14D1251tight positional0.020.05
15E1251tight positional0.020.05
16H1251tight positional0.020.05
21A1242tight positional0.020.05
22C1242tight positional0.020.05
23F1242tight positional0.020.05
31A1054tight positional0.040.05
41A1082tight positional0.030.05
11A1251tight thermal0.080.5
12B1251tight thermal0.050.5
13G1251tight thermal0.050.5
14D1251tight thermal0.040.5
15E1251tight thermal0.040.5
16H1251tight thermal0.060.5
21A1242tight thermal0.070.5
22C1242tight thermal0.050.5
23F1242tight thermal0.050.5
31A1054tight thermal0.110.5
41A1082tight thermal0.170.5
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 509 -
Rwork0.281 8579 -
obs--99.11 %
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)
12.5598-0.55270.14911.03730.3141.58220.230.04590.4561-0.07170.0247-0.1574-0.37880.2511-0.2547-0.0256-0.06850.0931-0.1639-0.06550.038836.230658.701121.2007
22.1223-0.4038-0.06741.06870.15321.44290.1871-0.1590.36090.16780.0219-0.102-0.36610.3441-0.20890.0525-0.10280.0939-0.0909-0.19390.025734.250361.129738.846
31.1735-0.4877-0.7651.3236-0.12471.32550.1718-0.42510.15810.3484-0.0072-0.0826-0.24940.4516-0.16470.0928-0.0880.05030.0708-0.225-0.026532.323752.720354.5862
42.7613-0.507-0.48871.6370.14270.98520.0256-0.70920.12840.48310.0692-0.1179-0.0120.4588-0.09470.1408-0.0112-0.00790.2179-0.0651-0.07531.118936.655562.4186
52.9388-0.4421-0.60491.54280.2580.96770.004-0.61680.05640.47840.0386-0.12910.17370.4337-0.04260.12820.07280.01190.14680.1416-0.076931.121819.022459.2715
62.1830.1869-0.85540.99620.13431.2345-0.0543-0.3562-0.16080.23070.0055-0.07880.2960.37110.04880.05670.1090.0496-0.03830.2087-0.020532.36086.577246.3721
72.11790.7354-0.49240.9102-0.21821.3343-0.0249-0.2243-0.42150.0606-0.0586-0.05780.30490.22620.0836-0.03950.09110.0533-0.15630.11670.009534.3654.015228.7323
82.6360.55150.44780.79010.01071.4332-0.01360.016-0.4225-0.0553-0.0253-0.04150.19990.1780.0388-0.12320.05220.0291-0.16740.0229-0.100236.407612.437113.0571
93.5002-0.04210.54150.3547-0.20410.7260.04180.0779-0.121-0.0943-0.0103-0.0143-0.02520.0853-0.0315-0.18660.00690.0149-0.1262-0.0029-0.209737.609328.49715.281
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

+
About Yorodumi

-
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://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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more