[English] 日本語
Yorodumi
- PDB-3vwi: High resolution crystal structure of FraC in the monomeric form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vwi
TitleHigh resolution crystal structure of FraC in the monomeric form
ComponentsFragaceatoxin C
KeywordsTOXIN / beta-sandwich / amphipathic alpha-helix / actinoporin / pore-forming toxin / citolysin / Membrane lipids / secreted protein / LIPID RAFT
Function / homology
Function and homology information


nematocyst / pore complex assembly / cytolysis in another organism / other organism cell membrane / pore complex / monoatomic cation transport / channel activity / toxin activity / lipid binding / extracellular region / identical protein binding
Similarity search - Function
Sea anemone actinoporin-like / : / Sea anemone cytotoxic protein / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta
Similarity search - Domain/homology
AMMONIUM ION / DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesActinia fragacea (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsTanaka, K. / Morante, K. / Caaveiro, J.M.M. / Gonzalez-Manas, J.M. / Tsumoto, K.
Citation
Journal: Nat Commun / Year: 2015
Title: Structural basis for self-assembly of a cytolytic pore lined by protein and lipid
Authors: Tanaka, K. / Caaveiro, J.M.M. / Morante, K. / Gonzalez-Manas, J.M. / Tsumoto, K.
#1: Journal: Structure / Year: 2011
Title: Structural insights into the oligomerization and architecture of eukaryotic membrane pore-forming toxins
Authors: Mechaly, A.E. / Bellomio, A. / Gil-Carton, D. / Morante, K. / Valle, M. / Gonzalez-Manas, J.M. / Guerin, D.M.
History
DepositionAug 23, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 8, 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
A: Fragaceatoxin C
B: Fragaceatoxin C
C: Fragaceatoxin C
D: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,20618
Polymers79,5104
Non-polymers69614
Water13,007722
1
A: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9313
Polymers19,8771
Non-polymers532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2647
Polymers19,8771
Non-polymers3876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9664
Polymers19,8771
Non-polymers893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0444
Polymers19,8771
Non-polymers1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.170, 44.290, 114.710
Angle α, β, γ (deg.)90.000, 92.800, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Fragaceatoxin C / fraC


Mass: 19877.498 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinia fragacea (sea anemone) / Gene: FraC / Plasmid: pGEM-T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B9W5G6

-
Non-polymers , 5 types, 736 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.46 Å3/Da / Density % sol: 50.05 % / Mosaicity: 0.6 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% Jeffamine, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2012
Details: Collimating and focusing mirrors: Rhodium coated silicon single crystals
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→114.573 Å / Num. all: 80105 / Num. obs: 80105 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.792.90.3480.2912.62676091900.1880.3480.2913.375.1
1.79-1.93.30.2510.2123.536105109870.1320.2510.2125.193.4
1.9-2.033.50.1660.1415.236650105770.0860.1660.1417.795.6
2.03-2.193.50.1240.1056.93514499980.0650.1240.1051096.9
2.19-2.43.60.0970.0838.63296092700.0510.0970.08312.597.5
2.4-2.693.60.0820.079.73057784350.0420.0820.0714.897.9
2.69-3.13.70.0660.05610.82792875100.0340.0660.05618.698.6
3.1-3.83.70.0540.04612.22391563800.0280.0540.04623.998.6
3.8-5.383.70.0550.04712.21842049910.0280.0550.04729.498.9
5.38-36.6813.60.0680.0589.3992727670.0350.0680.05829.897.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LIM

3lim


Resolution: 1.7→114.57 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1959 / WRfactor Rwork: 0.1564 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8962 / SU B: 3.604 / SU ML: 0.061 / SU R Cruickshank DPI: 0.096 / SU Rfree: 0.0989 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 3182 4 %RANDOM
Rwork0.1533 ---
all0.1549 80105 --
obs0.1549 80105 93.29 %-
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 max: 60.27 Å2 / Biso mean: 19.4017 Å2 / Biso min: 8.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å2-0.03 Å2
2--0.32 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.7→114.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 32 722 6290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.025882
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.938010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9615767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.21622.768271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60415961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8911544
X-RAY DIFFRACTIONr_chiral_restr0.1590.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024560
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 175 -
Rwork0.202 3976 -
all-4151 -
obs--65.83 %
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)
11.6170.1685-0.21931.2184-0.14341.6955-0.007-0.1533-0.05220.087-0.0156-0.020.0064-0.00910.02260.01550.00240.00240.02450.01120.006826.91890.145612.0713
22.7428-0.4888-0.27140.8313-0.16781.30490.03620.05280.187-0.0309-0.0764-0.0343-0.00030.06620.04020.0130.00230.00290.00930.00620.015613.837818.6943-9.2654
31.28230.30550.31711.55860.46921.9887-0.009-0.0786-0.05290.11630.0053-0.04270.031-0.00070.00370.02830.0019-0.00260.0264-0.00690.007814.42047.9559-45.1453
43.1791-0.41930.11720.85520.16481.19590.04940.1434-0.2262-0.0462-0.09420.03910.0043-0.05730.04480.02680.003-0.00210.0183-0.01740.024927.5623-10.7163-66.4412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 179
2X-RAY DIFFRACTION2B3 - 179
3X-RAY DIFFRACTION3C3 - 179
4X-RAY DIFFRACTION4D3 - 179

+
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