[English] 日本語
Yorodumi
- PDB-4efa: Crystal Structure of the Heterotrimeric EGChead Peripheral Stalk ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4efa
TitleCrystal Structure of the Heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase - second conformation
Components
  • V-type proton ATPase subunit C
  • V-type proton ATPase subunit E
  • V-type proton ATPase subunit G
KeywordsHYDROLASE / heterotrimer / peripheral stalk / vacuolar ATPase
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 / proton-transporting V-type ATPase complex / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex ...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 / proton-transporting V-type ATPase complex / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton transmembrane transport / proton-transporting ATPase activity, rotational mechanism / Golgi membrane / ATP hydrolysis activity / ATP binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2950 / ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2950 / ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / Alpha-Beta Plaits - #100 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
V-type proton ATPase subunit E / V-type proton ATPase subunit C / V-type proton ATPase subunit G
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8163 Å
AuthorsOot, R.A. / Huang, L.S. / Berry, E.A. / Wilkens, S.
CitationJournal: 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
DepositionMar 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: 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 1.3Sep 13, 2023Group: 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_initial_refinement_model / 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_ref_seq_dif.details / _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
C: V-type proton ATPase subunit C
G: V-type proton ATPase subunit G
E: V-type proton ATPase subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6977
Polymers54,3133
Non-polymers3844
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-113 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.537, 93.648, 116.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#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.: 1 / Fragment: 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: pMALc2e / 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.: 1
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: pMALc2e / 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.: 1
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: pMALc2e / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: P22203, H+-transporting two-sector ATPase
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / 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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 22, 2011
Diffraction measurementDetails: 1.00 degrees, 15.0 sec, detector distance 380.00 mm
Method: omega scans
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionAv R equivalents: 0.143 / Number: 198487
ReflectionResolution: 2.8→40 Å / Num. all: 14238 / Num. obs: 14187 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 35.089
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 2.306 / Rsym value: 0 / % possible all: 100
Cell measurementReflection used: 198487

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.82 Å38.66 Å
Translation2.82 Å38.66 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.0phasing
PHENIXdev_1012refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DL0

4dl0


Resolution: 2.8163→38.655 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 30.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2767 1418 10 %random using lattice symmetry
Rwork0.2295 ---
obs0.2345 14187 99.3 %-
all-14238 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.287 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 222.28 Å2 / Biso mean: 93.5261 Å2 / Biso min: 22.53 Å2
Baniso -1Baniso -2Baniso -3
1--6.3956 Å20 Å20 Å2
2--1.4884 Å2-0 Å2
3---4.9071 Å2
Refinement stepCycle: LAST / Resolution: 2.8163→38.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 20 24 3429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023433
X-RAY DIFFRACTIONf_angle_d0.4994606
X-RAY DIFFRACTIONf_chiral_restr0.035535
X-RAY DIFFRACTIONf_plane_restr0.002588
X-RAY DIFFRACTIONf_dihedral_angle_d7.8511353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8163-2.91690.37151350.33581209134497
2.9169-3.03370.34341420.299712801422100
3.0337-3.17170.35921380.294212401378100
3.1717-3.33880.33971410.275512761417100
3.3388-3.54790.29641400.266512571397100
3.5479-3.82160.27991390.23411255139499
3.8216-4.20570.28971400.22231273141399
4.2057-4.81330.23671440.182912931437100
4.8133-6.06050.25271460.216813121458100
6.0605-38.65870.24731530.2061374152799
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)
15.6385-0.08140.17376.2732.95752.22640.07310.07760.8719-0.58090.4371-0.3993-0.54030.7007-0.51510.3554-0.13730.06470.8351-0.21510.5409-107.073112.0629156.929
24.1943-1.3203-2.18855.67740.76182.34240.47950.2443-0.1795-0.4895-0.2378-0.38860.05220.4799-0.21590.43710.01710.00060.6996-0.16080.3726-94.385693.1442158.5256
33.5113-0.6646-2.39113.78362.24179.51460.3839-0.10220.09810.27130.5024-0.1802-0.12870.30880.62110.48-0.19730.08250.2648-0.06020.2761-97.0799103.9559161.5372
47.7832-1.1011-2.28769.18472.34437.37550.0717-0.1257-0.560.25410.2879-0.59890.340.4446-0.24390.2122-0.0206-0.07170.4095-0.04330.2632-97.364388.4772162.8563
57.55330.4285-1.72827.4716-2.33882.00010.10421.5409-0.4933-0.95380.10750.84130.9183-0.428-0.66010.5827-0.1489-0.41271.15-0.09370.8406-103.405890.2892151.7954
61.06150.0220.27095.28926.6038.240.1349-0.1573-0.1098-0.81820.2542-0.7028-0.33250.5039-0.2340.4539-0.02410.03690.7731-0.21150.5782-84.160158.69131.2477
70.11050.0637-0.06570.5885-1.0671.9453-0.00950.2170.06750.52010.8007-0.60180.84981.5896-0.85490.79080.3043-0.36070.998-0.22111.0301-83.2142-17.0127100.5418
80.50450.0336-0.04574.67463.68142.83410.18620.1253-0.20271.59450.2772-0.38421.23030.2963-0.43950.92870.1679-0.27710.8053-0.19410.5954-87.131536.4746125.9122
92.13271.3832-0.01341.2121-0.89813.4620.04040.7469-0.3634-0.21450.5276-0.53720.77450.4626-0.55750.940.3108-0.16760.7459-0.21840.7934-96.1882-28.588875.1828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 158:172 )C0
2X-RAY DIFFRACTION2chain 'C' and (resid 173:222 )C0
3X-RAY DIFFRACTION3chain 'C' and (resid 223:230 )C0
4X-RAY DIFFRACTION4chain 'C' and (resid 231:258 )C0
5X-RAY DIFFRACTION5chain 'C' and (resid 259:263 )C0
6X-RAY DIFFRACTION6chain 'G' and (resid 2:60 )G0
7X-RAY DIFFRACTION7chain 'G' and (resid 61:105 )G0
8X-RAY DIFFRACTION8chain 'E' and (resid 2:111 )E0
9X-RAY DIFFRACTION9chain 'E' and (resid 112:226 )E0

+
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://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

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