[English] 日本語
Yorodumi
- PDB-6hmw: Cholera toxin classical B-pentamer in complex with fucose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hmw
TitleCholera toxin classical B-pentamer in complex with fucose
ComponentsCholera enterotoxin B-subunit
KeywordsTOXIN / cholera toxin / lectin / complex / fucose / protein-carbohydrate interactions / X-ray crystal structure
Function / homology
Function and homology information


host cell surface binding / galactose binding / catalytic complex / positive regulation of tyrosine phosphorylation of STAT protein / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-L-fucopyranose / Cholera enterotoxin subunit B / Cholera enterotoxin B-subunit
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKrengel, U. / Heim, J.B.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway247730 Norway
CitationJournal: Sci Rep / Year: 2019
Title: Crystal structures of cholera toxin in complex with fucosylated receptors point to importance of secondary binding site.
Authors: Heim, J.B. / Hodnik, V. / Heggelund, J.E. / Anderluh, G. / Krengel, U.
History
DepositionSep 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_alt_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cholera enterotoxin B-subunit
B: Cholera enterotoxin B-subunit
C: Cholera enterotoxin B-subunit
D: Cholera enterotoxin B-subunit
E: Cholera enterotoxin B-subunit
F: Cholera enterotoxin B-subunit
G: Cholera enterotoxin B-subunit
H: Cholera enterotoxin B-subunit
I: Cholera enterotoxin B-subunit
J: Cholera enterotoxin B-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,89246
Polymers116,23310
Non-polymers4,65936
Water4,702261
1
A: Cholera enterotoxin B-subunit
B: Cholera enterotoxin B-subunit
C: Cholera enterotoxin B-subunit
D: Cholera enterotoxin B-subunit
E: Cholera enterotoxin B-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,62634
Polymers58,1165
Non-polymers3,51029
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15850 Å2
ΔGint-67 kcal/mol
Surface area21840 Å2
MethodPISA
2
F: Cholera enterotoxin B-subunit
G: Cholera enterotoxin B-subunit
H: Cholera enterotoxin B-subunit
I: Cholera enterotoxin B-subunit
J: Cholera enterotoxin B-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,26512
Polymers58,1165
Non-polymers1,1497
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15720 Å2
ΔGint-77 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.785, 100.543, 93.012
Angle α, β, γ (deg.)90.00, 117.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-326-

HOH

-
Components

#1: Protein
Cholera enterotoxin B-subunit / Cholera enterotoxin subunit B / Cholera toxin B protein (CTB) / Cholera toxin B subunit / Cholera ...Cholera enterotoxin subunit B / Cholera toxin B protein (CTB) / Cholera toxin B subunit / Cholera toxin beta subunit / Cholera toxin subunit B / Cholerae toxin B subunit / CtxB


Mass: 11623.267 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: ctxB, C9J66_18955, EN12_07055, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57193, UniProt: P01556*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Sugar
ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 0.1 M Bicine-Tris, 10% PEG1000, 10% PEG3350, 10% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.979531 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979531 Å / Relative weight: 1
ReflectionResolution: 1.95→47.42 Å / Num. all: 184186 / Num. obs: 67464 / % possible obs: 97.7 % / Redundancy: 2.7 % / Rrim(I) all: 0.149 / Net I/σ(I): 6.2
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 4577 / CC1/2: 0.41 / Rrim(I) all: 1.251 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ELB

5elb


Resolution: 1.95→47.42 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.253 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23743 3442 5.1 %RANDOM
Rwork0.18661 ---
obs0.18921 64017 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.418 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.16 Å2
2--0.2 Å20 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.95→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8131 0 290 261 8682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0148654
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177925
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.70811713
X-RAY DIFFRACTIONr_angle_other_deg0.9291.68318643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.14551042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62524.138406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.458151561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.2131532
X-RAY DIFFRACTIONr_chiral_restr0.0730.21305
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029247
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021445
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_it0.9561.7854141
X-RAY DIFFRACTIONr_mcbond_other0.9561.7854139
X-RAY DIFFRACTIONr_mcangle_it1.522.6695165
X-RAY DIFFRACTIONr_mcangle_other1.522.6695166
X-RAY DIFFRACTIONr_scbond_it1.051.9644513
X-RAY DIFFRACTIONr_scbond_other1.051.9644513
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6562.8986540
X-RAY DIFFRACTIONr_long_range_B_refined3.43222.1299505
X-RAY DIFFRACTIONr_long_range_B_other3.43222.1299505
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 231 -
Rwork0.298 4783 -
obs--98.22 %
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)
11.43310.3120.16691.9809-0.98541.6990.0912-0.0476-0.09890.0674-0.06090.18630.0812-0.2017-0.03020.03480.0167-0.00020.1276-0.03430.0393-6.952532.344622.9058
22.27710.16520.80260.66860.01612.80780.0295-0.1812-0.01240.185-0.02290.04770.1011-0.1018-0.00660.0601-0.01190.01160.08510.01190.03172.473126.768941.9299
32.17891.27280.18622.0164-0.24081.53250.0538-0.18360.18710.1189-0.10060.0249-0.153-0.010.04680.0290.0251-0.00320.1144-0.02040.021919.831540.025144.4735
40.61230.05540.53921.6385-1.15532.1867-0.03070.03170.21180.0417-0.0725-0.143-0.28840.02050.10320.10170.02520.02750.09070.0130.147620.840153.186126.9929
52.12890.52440.21791.5259-0.22351.3924-0.03110.10970.1205-0.1105-0.04-0.0095-0.10180.00780.07110.08130.0615-0.0010.090.0080.01014.542148.20613.8819
62.96540.76821.08861.10340.15842.49730.0550.38030.139-0.2149-0.0651-0.2174-0.20020.31440.01010.17640.07970.07030.23030.08410.096839.576330.06945.7946
71.6199-0.0050.1792.1075-0.26411.5780.06240.09090.1058-0.0610.0255-0.14680.05470.1382-0.0880.02850.04770.00870.1324-0.00660.027842.999219.084624.0651
82.44760.3121-0.02021.4026-0.17531.3560.0576-0.0036-0.21320.0748-0.02120.13370.1767-0.0982-0.03640.080.03940.00580.0812-0.00340.04427.57974.179326.6139
91.49620.38680.54952.0334-0.58112.34110.13150.3631-0.3856-0.3493-0.12820.18620.2236-0.044-0.00330.13080.084-0.06780.2168-0.13140.190114.41545.08249.4614
102.68260.4547-0.48791.2353-0.34761.64140.07870.50690.0221-0.3244-0.0008-0.0660.00240.0023-0.0780.19020.1540.00420.312-0.00430.023621.730421.1706-3.536
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION2B1 - 104
3X-RAY DIFFRACTION3C1 - 104
4X-RAY DIFFRACTION4D1 - 104
5X-RAY DIFFRACTION5E1 - 104
6X-RAY DIFFRACTION6F1 - 104
7X-RAY DIFFRACTION7G1 - 103
8X-RAY DIFFRACTION8H1 - 103
9X-RAY DIFFRACTION9I1 - 103
10X-RAY DIFFRACTION10J1 - 103

+
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