[English] 日本語
Yorodumi
- PDB-3w9t: pore-forming CEL-III -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3w9t
Titlepore-forming CEL-III
ComponentsHemolytic lectin CEL-III
KeywordsTOXIN / Hemolytic lectin / Pore forming toxin
Function / homology
Function and homology information


positive regulation of erythrocyte aggregation / melibiose binding / lactose binding / cell killing / N-acetylgalactosamine binding / disruption of plasma membrane integrity in another organism / fucose binding / galactose binding / hemolysis in another organism / protein homooligomerization ...positive regulation of erythrocyte aggregation / melibiose binding / lactose binding / cell killing / N-acetylgalactosamine binding / disruption of plasma membrane integrity in another organism / fucose binding / galactose binding / hemolysis in another organism / protein homooligomerization / : / antibacterial humoral response / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding / magnesium ion binding / extracellular space
Similarity search - Function
hemolytic lectin cel-iii, domain 3 / Hemolytic lectin CEL-III, C-terminal domain / Hemolytic lectin CEL-III, C-terminal domain superfamily / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...hemolytic lectin cel-iii, domain 3 / Hemolytic lectin CEL-III, C-terminal domain / Hemolytic lectin CEL-III, C-terminal domain superfamily / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
lactulose / Galactose/N-acetylgalactosamine-binding lectin CEL-III
Similarity search - Component
Biological speciesCucumaria echinata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.9 Å
AuthorsUnno, H. / Goda, S. / Hatakeyama, T.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Hemolytic lectin CEL-III heptamer reveals its transmembrane pore-formation mechanism
Authors: Unno, H. / Goda, S. / Hatakeyama, T.
History
DepositionApr 16, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Other
Revision 2.0Jul 25, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Non-polymer description / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_nat / pdbx_distant_solvent_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_fragment / _entity.pdbx_mutation / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 3.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 4.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemolytic lectin CEL-III
C: Hemolytic lectin CEL-III
G: Hemolytic lectin CEL-III
B: Hemolytic lectin CEL-III
F: Hemolytic lectin CEL-III
E: Hemolytic lectin CEL-III
D: Hemolytic lectin CEL-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,934102
Polymers332,1657
Non-polymers14,76995
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36080 Å2
ΔGint-101 kcal/mol
Surface area124050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.800, 228.650, 133.020
Angle α, β, γ (deg.)90.00, 127.13, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.715623, -0.681754, 0.15197), (0.682308, 0.635745, -0.360949), (0.149465, 0.361994, 0.92012)71.19553, -54.07935, -40.51479
3given(0.678702, 0.722479, 0.131865), (-0.720887, 0.621072, 0.307557), (0.140306, -0.303799, 0.942348)-8.93051, 101.91695, 3.64025
4given(0.006637, 0.874369, 0.485217), (-0.889714, -0.216333, 0.402006), (0.45647, -0.434372, 0.776502)55.22257, 172.51936, -25.34215
5given(-0.562523, 0.386421, 0.730922), (-0.408928, -0.898388, 0.160243), (0.718572, -0.208754, 0.663382)148.05255, 160.72713, -66.96054
6given(-0.543318, -0.395233, 0.740673), (0.382098, -0.901991, -0.201028), (0.747534, 0.173787, 0.641086)192.59212, 74.26899, -94.74038
7given(-0.010275, -0.875096, 0.483841), (0.874593, -0.242431, -0.419897), (0.484748, 0.418849, 0.767844)165.11728, -19.32623, -79.9135

-
Components

#1: Protein
Hemolytic lectin CEL-III


Mass: 47452.164 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Cucumaria echinata (invertebrata) / References: UniProt: Q868M7*PLUS
#2: Polysaccharide...
beta-D-galactopyranose-(1-4)-beta-D-fructofuranose / lactulose /


Type: oligosaccharide, Oligosaccharide / Class: Water retention / Mass: 342.297 Da / Num. of mol.: 37
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: lactulose
DescriptorTypeProgram
DGalpb1-4DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 4.01 Å3/Da / Density % sol: 69.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: 30% PEG400, 0.1M CdCl2, 0.1M sodium acetate, 10mM CaCl2, 0.1M lactulose, pH 4.2, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2010
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.9→53.5 Å / Num. obs: 113863 / % possible obs: 98.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIXmodel building
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIR / Resolution: 2.9→48.2 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.895 / SU B: 37.412 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R: 1.039 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27305 5691 5 %RANDOM
Rwork0.23942 ---
obs0.24108 107985 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.149 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20.1 Å2
2--0.39 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23191 0 909 75 24175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224590
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9833546
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.65153017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.53625.4821162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.109153836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.85415126
X-RAY DIFFRACTIONr_chiral_restr0.1340.23812
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118368
X-RAY DIFFRACTIONr_gen_planes_other
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 420 -
Rwork0.339 7991 -
obs--99.14 %
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)
10.3767-0.4276-0.12850.75940.15710.3207-0.1173-0.03770.09450.16320.1254-0.00320.0948-0.0952-0.00810.15890.09190.03530.27350.00440.106783.3228105.9592-14.6935
20.33270.0288-0.20820.2799-0.08830.3092-0.05920.0121-0.1527-0.0268-0.00520.0620.1365-0.16240.06430.2179-0.12170.090.28010.03930.149263.503933.6309-5.4994
30.80530.14720.05870.72230.37120.3595-0.12530.00380.3946-0.21510.0610.1487-0.11910.01750.06430.28260.0023-0.03260.13930.02710.215121.2997103.2956-32.6771
40.3954-0.25850.02440.38580.0530.1665-0.1538-0.0434-0.17260.04150.08680.20420.08-0.00590.0670.1856-0.00980.1060.26140.09420.165657.456775.2413-2.7634
50.94540.3261-0.11340.59440.24110.2088-0.25680.05220.0782-0.21650.22130.0646-0.00590.03950.03550.4533-0.03450.08210.37520.03270.0524142.700568.4932-42.0606
60.8101-0.0995-0.10350.35020.02420.0884-0.03270.0975-0.1468-0.0622-0.02650.02190.09670.07860.05920.33460.08810.0990.3376-0.0050.06131.847328.1256-37.226
70.23490.1665-0.08210.504-0.02540.2574-0.01860.0083-0.0877-0.0639-0.0633-0.09560.23470.03060.08190.30050.00160.07880.09990.00040.051296.508912.8579-21.073
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 432
2X-RAY DIFFRACTION1A1001 - 1013
3X-RAY DIFFRACTION2C1 - 432
4X-RAY DIFFRACTION2C1001 - 1013
5X-RAY DIFFRACTION3G1 - 432
6X-RAY DIFFRACTION3G501 - 513
7X-RAY DIFFRACTION4B1 - 432
8X-RAY DIFFRACTION4B501 - 514
9X-RAY DIFFRACTION5F1 - 432
10X-RAY DIFFRACTION5F501 - 513
11X-RAY DIFFRACTION6E1 - 432
12X-RAY DIFFRACTION6E501 - 514
13X-RAY DIFFRACTION7D1 - 432
14X-RAY DIFFRACTION7D501 - 513

+
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