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- PDB-6hjd: Cholera toxin classical B-pentamer in complex with Lewis-x -

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Basic information

Entry
Database: PDB / ID: 6hjd
TitleCholera toxin classical B-pentamer in complex with Lewis-x
ComponentsCholera toxin B subunit
KeywordsTOXIN / cholera toxin / lectin / complex / Lewis-x / 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
Lewis X antigen, beta anomer / Lewis X antigen, alpha anomer / alpha-L-fucopyranose / Cholera toxin B / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 3, 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: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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_alt_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 / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _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_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_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 2.1Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,66539
Polymers116,23310
Non-polymers6,43329
Water12,034668
1
A: Cholera toxin B subunit
B: Cholera toxin B subunit
C: Cholera toxin B subunit
D: Cholera toxin B subunit
E: Cholera toxin B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,61719
Polymers58,1165
Non-polymers3,50114
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18290 Å2
ΔGint-43 kcal/mol
Surface area21690 Å2
MethodPISA
2
F: Cholera toxin B subunit
G: Cholera toxin B subunit
H: Cholera toxin B subunit
I: Cholera toxin B subunit
J: Cholera toxin B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,04820
Polymers58,1165
Non-polymers2,93215
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16730 Å2
ΔGint-63 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.965, 108.291, 115.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Cholera toxin B subunit


Mass: 11623.267 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ctxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6R7L2, UniProt: P01556*PLUS

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Sugars , 3 types, 9 molecules

#2: Polysaccharide
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Lewis X antigen / alpha anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis X antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose / Lewis X antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis X antigen, beta anomer
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 688 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 163.172 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Bicine-Tris, 8% PEG1000, 8% PEG3350, 8% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977021 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977021 Å / Relative weight: 1
ReflectionResolution: 1.54→82.97 Å / Num. obs: 153937 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.984 / Rrim(I) all: 0.117 / Net I/σ(I): 8.9
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7547 / CC1/2: 0.535 / Rrim(I) all: 0.907 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PHENIXrefinement
Cootmodel building
xia2data reduction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ELB

5elb


Resolution: 1.54→79.16 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.154 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.091 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22355 7676 5 %RANDOM
Rwork0.19255 ---
obs0.19411 146128 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.474 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---1.17 Å20 Å2
3---1.27 Å2
Refinement stepCycle: 1 / Resolution: 1.54→79.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8140 0 419 668 9227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0149422
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178656
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.6912876
X-RAY DIFFRACTIONr_angle_other_deg1.0081.65920488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.5895.2271214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0124.014436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.225151700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.361530
X-RAY DIFFRACTIONr_chiral_restr0.0870.21451
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210698
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021598
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_it0.7551.0864371
X-RAY DIFFRACTIONr_mcbond_other0.7551.0854370
X-RAY DIFFRACTIONr_mcangle_it1.2051.6215521
X-RAY DIFFRACTIONr_mcangle_other1.2051.6225522
X-RAY DIFFRACTIONr_scbond_it1.0741.3165051
X-RAY DIFFRACTIONr_scbond_other1.0731.3165051
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6621.9287297
X-RAY DIFFRACTIONr_long_range_B_refined3.63814.310507
X-RAY DIFFRACTIONr_long_range_B_other3.63814.30310508
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 515 -
Rwork0.309 10731 -
obs--99.82 %
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)
11.4117-0.67510.13591.71460.02810.9516-0.029-0.13770.02540.2030.0571-0.12150.04260.0787-0.0280.06140.0051-0.0250.0612-0.01230.0137-3.7616-23.932442.3617
21.0092-0.5883-0.38621.08810.19121.5897-0.0362-0.0180.0371-0.00770.0372-0.1536-0.02580.0656-0.0010.020.0003-0.01140.0254-0.0010.04034.8756-37.890927.9141
30.8709-0.77710.45931.0158-0.59112.1914-0.00220.11670.055-0.123-0.0156-0.10670.01440.08170.01770.0531-0.03220.02240.0488-0.01150.0151-3.6832-33.3028.2148
40.7752-0.393-0.04021.91530.24611.42180.01710.07810.1155-0.12610.009-0.003-0.0854-0.0449-0.02610.0189-0.0153-0.00340.05460.02180.0213-17.5801-16.473710.5128
50.74670.18790.27341.29570.27381.2932-0.0058-0.0630.05420.07470.01190.07920.0178-0.0504-0.00610.00490.00030.00240.0278-0.0060.0341-17.5968-10.733331.6434
60.9656-0.2733-0.32461.27250.33991.6987-0.008-0.1343-0.07030.2510.0014-0.01460.0832-0.01320.00660.1235-0.0224-0.00660.07090.02210.0088-28.7824-50.960247.3022
71.6281-0.54830.38921.2536-0.14481.354-0.0182-0.1710.0590.12830.02440.1735-0.065-0.1789-0.00620.0911-0.01120.02680.0786-0.00960.0377-43.0562-35.427441.4246
81.1496-0.10420.13921.4461-0.10621.29590.01040.06420.0175-0.0741-0.01040.1488-0.0176-0.089300.0218-0.008-0.01320.05270.00590.018-46.084-37.004319.8123
91.1806-0.2208-0.00622.44830.25750.9662-0.02480.1099-0.1002-0.23180.01060.03890.09160.00660.01420.0581-0.0167-0.00530.06750.00190.0121-33.8397-53.439412.2823
100.829-0.08150.25971.7142-0.22131.82950.0251-0.029-0.12310.120.0125-0.08720.18930.0622-0.03760.05020.0042-0.00430.0530.00180.0375-23.1636-62.210529.2134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION2B1 - 103
3X-RAY DIFFRACTION3C1 - 103
4X-RAY DIFFRACTION4D1 - 103
5X-RAY DIFFRACTION5E1 - 103
6X-RAY DIFFRACTION6F1 - 103
7X-RAY DIFFRACTION7G1 - 103
8X-RAY DIFFRACTION8H1 - 103
9X-RAY DIFFRACTION9I1 - 103
10X-RAY DIFFRACTION10J1 - 103

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