[English] 日本語
Yorodumi
- PDB-4rnd: Crystal Structure of the subunit DF-assembly of the eukaryotic V-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rnd
TitleCrystal Structure of the subunit DF-assembly of the eukaryotic V-ATPase.
Components
  • V-type proton ATPase subunit D
  • V-type proton ATPase subunit F
KeywordsHYDROLASE / alpha helical / Rossmann Fold / Regulatory / Coupling
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 / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / vacuolar acidification ...Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / vacuolar acidification / fungal-type vacuole membrane / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / membrane raft / Golgi membrane / membrane
Similarity search - Function
ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
V-type proton ATPase subunit D / V-type proton ATPase subunit F
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.18 Å
AuthorsBalakrishna, A.M. / Basak, S. / Gruber, G.
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of Subunits D and F in Complex Gives Insight into Energy Transmission of the Eukaryotic V-ATPase from Saccharomyces cerevisiae.
Authors: Balakrishna, A.M. / Basak, S. / Manimekalai, M.S. / Gruber, G.
#1: Journal: J.Biol.Chem. / Year: 2013
Title: Crystal and NMR structures give insights into the role and dynamics of subunit F of the eukaryotic V-ATPase from Saccharomyces cerevisiae.
Authors: Basak, S. / Lim, J. / Manimekalai, M.S. / Balakrishna, A.M. / Gruber, G.
History
DepositionOct 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Feb 28, 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 / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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 proton ATPase subunit D
B: V-type proton ATPase subunit F
C: V-type proton ATPase subunit D
D: V-type proton ATPase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7057
Polymers85,4284
Non-polymers2763
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15200 Å2
ΔGint-110 kcal/mol
Surface area28100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.063, 168.063, 128.629
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUARGARGAA37 - 20237 - 202
21GLUGLUARGARGCC37 - 20237 - 202
12ALAALALEULEUBB2 - 1152 - 115
22ALAALALEULEUDD2 - 1152 - 115

NCS ensembles :
ID
1
2

-
Components

#1: Protein V-type proton ATPase subunit D / V-ATPase subunit D / Vacuolar proton pump subunit D


Mass: 29235.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: SYGP-ORF11, VMA8, YEL051W / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32610
#2: Protein V-type proton ATPase subunit F / V-ATPase subunit F / V-ATPase 14 kDa subunit / Vacuolar proton pump subunit F


Mass: 13479.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: VMA7, YGR020C / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39111
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.14 Å3/Da / Density % sol: 79.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic dehydrate, 1.2 M Ammonium citrate monobasic, ph 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2014
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: Double Crystal Si(111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.18→30 Å / Num. all: 38345 / Num. obs: 33061 / % possible obs: 80.08 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.1
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.2 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.18→29.63 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.895 / SU B: 20.993 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23201 1010 3 %RANDOM
Rwork0.20365 ---
obs0.20448 33061 97.83 %-
all-38345 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.757 Å2
Baniso -1Baniso -2Baniso -3
1--7.23 Å2-0 Å2-0 Å2
2---7.23 Å2-0 Å2
3---14.46 Å2
Refinement stepCycle: LAST / Resolution: 3.18→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 18 59 4741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194753
X-RAY DIFFRACTIONr_bond_other_d0.0040.024637
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.9636405
X-RAY DIFFRACTIONr_angle_other_deg0.946310636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8545576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69324.049247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94615884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9861546
X-RAY DIFFRACTIONr_chiral_restr0.060.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025355
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021099
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A80250.17
12C80250.17
21B60480.15
22D60480.15
LS refinement shellResolution: 3.177→3.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 46 -
Rwork0.3 1879 -
obs--75.52 %
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)
12.28661.40910.04450.91620.04670.0219-0.0240.0311-0.21320.05180.0295-0.11890.0153-0.0056-0.00560.1634-0.0687-0.04660.23630.03630.1454-19.880267.58759.7277
21.27330.91990.83422.47581.07421.06290.1536-0.2535-0.07620.4124-0.11030.0610.1542-0.0761-0.04340.2927-0.1465-0.00340.2370.06490.0305-11.258176.933321.8969
33.13850.967-0.15690.3486-0.09510.1116-0.03530.249-0.02160.05240.0721-0.0318-0.007-0.0599-0.03680.17-0.0511-0.01920.17180.03310.1382-54.827453.27889.5829
42.2117-0.58840.07071.5551-0.10631.0174-0.08860.22810.2562-0.07210.1323-0.0431-0.1812-0.0541-0.04370.1658-0.094-0.04470.18780.11830.1099-69.624457.13982.6872
500000000000000-00.16000.1600.16000
600000000000000-00.16000.1600.16000
700000000000000-00.16000.1600.16000
800000000000000-00.16000.1600.16000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 204
2X-RAY DIFFRACTION2B1 - 118
3X-RAY DIFFRACTION3C37 - 203
4X-RAY DIFFRACTION4D2 - 116
5X-RAY DIFFRACTION5A401 - 423
6X-RAY DIFFRACTION5B301 - 312
7X-RAY DIFFRACTION5C401 - 417
8X-RAY DIFFRACTION5D201 - 210
9X-RAY DIFFRACTION6A301
10X-RAY DIFFRACTION7C301
11X-RAY DIFFRACTION8B201

+
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