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- PDB-4p5h: Structure of Clostridium perfringens Enterotoxin with a peptide d... -

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Open data


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Basic information

Entry
Database: PDB / ID: 4p5h
TitleStructure of Clostridium perfringens Enterotoxin with a peptide derived from a modified version of ECL-2 of Claudin 2
Components
  • Claudin-2
  • Heat-labile enterotoxin B chain
KeywordsToxin/CELL Adhesion / TOXIN-CELL ADHESION COMPLEX / BETA PORE-FORMING TOXIN / RECEPTOR BINDING
Function / homology
Function and homology information


calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / bicellular tight junction assembly / bicellular tight junction / cell-cell junction / toxin activity / membrane => GO:0016020 / cell adhesion / structural molecule activity / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Claudin-2 / Jelly Rolls - #1050 / Proaerolysin; Chain A, domain 3 - #20 / Claudin / Claudin, conserved site / Claudin family signature. / Proaerolysin; Chain A, domain 3 / Clostridium enterotoxin / Clostridium enterotoxin / PMP-22/EMP/MP20/Claudin family ...Claudin-2 / Jelly Rolls - #1050 / Proaerolysin; Chain A, domain 3 - #20 / Claudin / Claudin, conserved site / Claudin family signature. / Proaerolysin; Chain A, domain 3 / Clostridium enterotoxin / Clostridium enterotoxin / PMP-22/EMP/MP20/Claudin family / PMP-22/EMP/MP20/Claudin superfamily / Beta Complex / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Claudin-2 / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å
AuthorsNaylor, C.E. / Yelland, T.S. / Basak, A.K.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)G0700051 United Kingdom
Wellcome TrustWT089618MA United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI19844-30 United States
Citation
Journal: J.Mol.Biol. / Year: 2014
Title: Structure of a C. perfringens Enterotoxin Mutant in Complex with a Modified Claudin-2 Extracellular Loop 2.
Authors: Yelland, T.S. / Naylor, C.E. / Bagoban, T. / Savva, C.G. / Moss, D.S. / McClane, B.A. / Blasig, I.E. / Popoff, M. / Basak, A.K.
#1: Journal: J.Mol.Biol. / Year: 2011
Title: Structure of the food-poisoning Clostridium perfringens enterotoxin reveals similarity to the aerolysin-like pore-forming toxins.
Authors: Briggs, D.C. / Naylor, C.E. / Smedley, J.G. / Lukoyanova, N. / Robertson, S. / Moss, D.S. / McClane, B.A. / Basak, A.K.
History
DepositionMar 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
SupersessionAug 6, 2014ID: 3ZJ3
Revision 1.2Aug 6, 2014Group: Other
Revision 1.3Oct 1, 2014Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Claudin-2
2: Claudin-2
3: Claudin-2
4: Claudin-2
A: Heat-labile enterotoxin B chain
B: Heat-labile enterotoxin B chain
C: Heat-labile enterotoxin B chain
D: Heat-labile enterotoxin B chain
E: Heat-labile enterotoxin B chain
F: Heat-labile enterotoxin B chain
G: Heat-labile enterotoxin B chain
H: Heat-labile enterotoxin B chain
I: Heat-labile enterotoxin B chain
J: Heat-labile enterotoxin B chain
K: Heat-labile enterotoxin B chain
L: Heat-labile enterotoxin B chain
M: Heat-labile enterotoxin B chain
N: Heat-labile enterotoxin B chain
O: Heat-labile enterotoxin B chain
P: Claudin-2
Q: Claudin-2
R: Claudin-2
S: Claudin-2
T: Claudin-2
U: Claudin-2
V: Claudin-2
W: Claudin-2
X: Claudin-2
Y: Claudin-2
Z: Claudin-2


Theoretical massNumber of molelcules
Total (without water)508,54130
Polymers508,54130
Non-polymers00
Water00
1
1: Claudin-2
J: Heat-labile enterotoxin B chain
K: Heat-labile enterotoxin B chain
L: Heat-labile enterotoxin B chain
Y: Claudin-2
Z: Claudin-2


Theoretical massNumber of molelcules
Total (without water)101,7086
Polymers101,7086
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-38 kcal/mol
Surface area38580 Å2
MethodPISA
2
2: Claudin-2
3: Claudin-2
4: Claudin-2
M: Heat-labile enterotoxin B chain
N: Heat-labile enterotoxin B chain
O: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)101,7086
Polymers101,7086
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-30 kcal/mol
Surface area38780 Å2
MethodPISA
3
A: Heat-labile enterotoxin B chain
B: Heat-labile enterotoxin B chain
C: Heat-labile enterotoxin B chain
P: Claudin-2
Q: Claudin-2
R: Claudin-2


Theoretical massNumber of molelcules
Total (without water)101,7086
Polymers101,7086
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-35 kcal/mol
Surface area38810 Å2
MethodPISA
4
D: Heat-labile enterotoxin B chain
E: Heat-labile enterotoxin B chain
F: Heat-labile enterotoxin B chain
S: Claudin-2
T: Claudin-2
U: Claudin-2


Theoretical massNumber of molelcules
Total (without water)101,7086
Polymers101,7086
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-38 kcal/mol
Surface area39000 Å2
MethodPISA
5
G: Heat-labile enterotoxin B chain
H: Heat-labile enterotoxin B chain
I: Heat-labile enterotoxin B chain
V: Claudin-2
W: Claudin-2
X: Claudin-2


Theoretical massNumber of molelcules
Total (without water)101,7086
Polymers101,7086
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-37 kcal/mol
Surface area38870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)369.600, 100.260, 265.360
Angle α, β, γ (deg.)90.00, 119.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide
Claudin-2


Mass: 2378.766 Da / Num. of mol.: 15 / Fragment: ECL2 (UNP residues 141-160) / Mutation: S149N, S155A / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: O88552
#2: Protein
Heat-labile enterotoxin B chain


Mass: 31523.965 Da / Num. of mol.: 15 / Fragment: UNP residues 38-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: 8-6 / Gene: cpe / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P01558

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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: 4 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 22 % MPD, 0.2 M AMACE, 0.1 M NACITRATE, PH 5.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8726 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 25, 2011
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.38→49.38 Å / Num. obs: 96906 / % possible obs: 80.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 84.89 Å2 / Rmerge(I) obs: 0.252 / Net I/σ(I): 4.2
Reflection shellResolution: 3.38→3.56 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 1.1 / % possible all: 48.6

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZIX

3zix


Resolution: 3.38→48.98 Å / Cor.coef. Fo:Fc: 0.7915 / Cor.coef. Fo:Fc free: 0.7677 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.495
RfactorNum. reflection% reflectionSelection details
Rfree0.24 4849 5.01 %RANDOM
Rwork0.2044 ---
obs0.2062 96758 80.82 %-
Displacement parametersBiso mean: 117.95 Å2
Baniso -1Baniso -2Baniso -3
1-37.2619 Å20 Å25.1601 Å2
2---105.5859 Å20 Å2
3---68.324 Å2
Refine analyzeLuzzati coordinate error obs: 0.771 Å
Refinement stepCycle: 1 / Resolution: 3.38→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34326 0 0 0 34326
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0135061HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3747827HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11825SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes975HARMONIC2
X-RAY DIFFRACTIONt_gen_planes5116HARMONIC5
X-RAY DIFFRACTIONt_it35061HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion22.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4800SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact39105SEMIHARMONIC4
LS refinement shellResolution: 3.38→3.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2964 170 5.17 %
Rwork0.253 3116 -
all0.2552 3286 -
obs--80.82 %
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)
13.6254-1.66691.14481.46570.20121.30950.02350.5547-0.41890.0640.21250.05520.2206-0.083-0.236-0.0135-0.07260.00070.2233-0.17850.222637.848-36.679428.8353
22.2294-1.8884-0.46893.12710.4121.73190.0204-0.1321-0.00960.2331-0.0507-0.18860.54760.25890.03030.32660.2075-0.1226-0.0955-0.05580.117570.4908-53.622642.7285
32.5358-1.6691-0.1275.93312.3013.03940.1980.13270.1104-0.26250.07390.36860.20330.7043-0.27190.10610.03790.00550.304-0.1535-0.048571.1319-38.336921.4956
45.11773.14420.66664.20380.37141.9550.04210.17220.28160.01690.00240.0862-0.45350.665-0.04450.0318-0.20750.1080.3040.05580.257976.9459-0.831330.4542
52.81721.45370.1880.4786-0.41493.9715-0.2860.2512-0.0426-0.07280.22180.066-0.15890.65470.06420.0252-0.20750.08860.3040.05580.273854.5929-8.574619.3895
62.4184-1.0336-0.83612.4595-0.89936.5373-0.19060.2595-0.11690.0341-0.0131-0.05020.1880.13340.2037-0.1747-0.06970.0259-0.0761-0.11150.120327.7314-19.609345.5349
71.7885-0.7645-0.80071.26470.23782.2722-0.21320.08650.2425-0.01210.1607-0.1253-0.02470.50440.05250.1196-0.20750.09520.3040.05580.360540.6268-29.1153-73.5455
87.81041.3575-0.21541.5706-0.33431.3458-0.1897-0.04010.2145-0.1139-0.14310.15110.0346-0.00630.3329-0.06350.01790.0404-0.0293-0.10210.241110.3688-26.434-48.7888
93.3159-1.5231.98853.3983-0.9271.19050.1767-0.03170.14780.1531-0.18370.1774-0.0365-0.21740.0070.0818-0.11570.2093-0.0266-0.10370.189914.0944-47.5752-63.2898
100.2154-0.112-0.67415.4688-1.80831.692-0.0762-0.3764-0.06330.35130.0388-0.39910.63770.2480.03740.330.09140.0637-0.3040.10350.003737.1461-73.972-45.3786
111.51651.73730.64342.9931.85032.61690.1005-0.35010.0765-0.0708-0.0749-0.49560.18910.4264-0.02560.13010.16350.18180.16420.02060.196944.3666-62.2848-67.399
128.16022.42851.82372.48571.61512.39420.05010.13850.5902-0.1844-0.1795-0.1582-0.26750.70760.12940.0796-0.20750.03170.3040.05580.394463.6013-28.6386-61.1753
133.27431.54881.33692.49030.75963.69380.1534-0.10030.0943-0.2451-0.235-0.12260.30760.18190.0816-0.06750.08360.0723-0.304-0.12560.034169.1552-37.609472.0546
141.5115-0.7252-0.14773.1713-0.44141.4456-0.09570.20020.28060.0642-0.29210.0725-0.09390.74320.3878-0.1232-0.1717-0.05680.304-0.00640.294499.7433-13.741377.9703
150.9285-0.11120.05620.07920.40261.6435-0.13510.37850.37190.0882-0.0354-0.1385-0.13210.33140.17050.0071-0.18550.04550.26470.01760.302779.4285-6.456963.2102
16-0.1292-0.17970.07513.41240.69370.1292-0.2584-0.03080.26710.0362-0.0818-0.3203-0.10850.03550.34020.0309-0.0474-0.1185-0.304-0.04020.088651.100210.945783.9014
172.3609-1.48112.4495.4843-3.26132.422-0.0066-0.1648-0.0767-0.09260.08670.047-0.06360.1833-0.0801-0.1067-0.0640.09-0.3039-0.19020.140346.9803-11.820271.8166
180.64541.2105-0.19082.76-1.04911.88810.07870.05930.34010.392-0.1473-0.18490.2835-0.43180.0686-0.0829-0.12170.0957-0.304-0.0932-0.018856.2918-42.709294.1762
196.19681.74930.10442.83071.27751.338-0.2915-0.29750.09-0.11260.3884-0.1390.64230.4558-0.09690.35250.20750.06780.1883-0.0558-0.07840.483-55.5641-17.7479
205.799-1.37191.46221.91372.526210.8319-0.0607-0.02860.2774-0.0216-0.2161-0.24870.42780.61150.27680.17260.20750.07640.304-0.05580.435477.2012-43.4672-10.4823
214.9417-1.8469-2.84571.02532.29516.15750.25050.18690.121-0.0176-0.0117-0.19470.07790.5501-0.23880.02-0.08250.03690.304-0.16140.328762.1319-31.2755-27.8245
224.41451.0593-0.3883.42462.3059-1.7704-0.19570.26960.2763-0.20570.00440.1858-0.68090.08210.19140.2271-0.1835-0.08620.26110.01410.230341.0839-3.2226-10.6523
230.6270.90431.05883.1982-2.83753.0617-0.2721-0.24020.2435-0.07570.2073-0.0429-0.14690.28080.0648-0.0759-0.1259-0.01310.304-0.0860.290929.5501-23.7291-21.7793
241.79620.7638-1.74792.2134-1.07212.4960.0221-0.3123-0.21240.014-0.04060.0380.62710.10920.01850.0487-0.1479-0.06030.0827-0.04760.04925.1733-53.52263.2774
254.1603-0.09280.8810.77180.49260.8636-0.0782-0.3302-0.1326-0.1489-0.044-0.1720.0852-0.16590.1222-0.0309-0.12930.0514-0.304-0.08020.260964.6787-23.8925120.477
263.1775-1.08720.26011.8805-0.99323.24320.0399-0.23640.21470.16050.15-0.21740.22560.2583-0.1899-0.13750.0222-0.039-0.304-0.16260.2592102.5648-27.3807130.2622
270.8206-0.2441-1.0923.0750.86761.66520.04550.30920.38150.23330.1512-0.05650.02760.189-0.1967-0.0685-0.09420.0077-0.0077-0.1410.274194.8499-11.7996110.8145
282.00782.56862.37744.05540.93532.07130.0304-0.40750.1698-0.0176-0.17550.5877-0.73260.01930.14510.15-0.20650.0637-0.24770.0540.427686.477824.5564122.9045
291.43730.34010.29352.2581-1.59993.1290.0331-0.2549-0.0287-0.1136-0.0030.3377-0.11150.3416-0.0301-0.0186-0.0865-0.0252-0.304-0.15380.358468.13199.0306112.6245
301.77361.8601-2.637301.05083.81030.1155-0.2603-0.04170.2586-0.1898-0.0480.365-0.63880.0743-0.0236-0.10930.04610.1043-0.11470.274150.4813-13.3778139.6085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|34 - 193 }
2X-RAY DIFFRACTION2{ A|194 - 319 }
3X-RAY DIFFRACTION3{ B|34 - 193 }
4X-RAY DIFFRACTION4{ B|194 - 319 }
5X-RAY DIFFRACTION5{ C|34 - 193 }
6X-RAY DIFFRACTION6{ C|194 - 319 }
7X-RAY DIFFRACTION7{ D|34 - 193 }
8X-RAY DIFFRACTION8{ D|194 - 319 }
9X-RAY DIFFRACTION9{ E|34 - 193 }
10X-RAY DIFFRACTION10{ E|194 - 319 }
11X-RAY DIFFRACTION11{ F|34 - 193 }
12X-RAY DIFFRACTION12{ F|194 - 319 }
13X-RAY DIFFRACTION13{ G|34 - 193 }
14X-RAY DIFFRACTION14{ G|194 - 319 }
15X-RAY DIFFRACTION15{ H|34 - 193 }
16X-RAY DIFFRACTION16{ H|194 - 319 }
17X-RAY DIFFRACTION17{ I|34 - 193 }
18X-RAY DIFFRACTION18{ I|194 - 319 }
19X-RAY DIFFRACTION19{ J|34 - 193 }
20X-RAY DIFFRACTION20{ J|194 - 319 }
21X-RAY DIFFRACTION21{ K|34 - 193 }
22X-RAY DIFFRACTION22{ K|194 - 319 }
23X-RAY DIFFRACTION23{ L|34 - 193 }
24X-RAY DIFFRACTION24{ L|194 - 319 }
25X-RAY DIFFRACTION25{ M|34 - 193 }
26X-RAY DIFFRACTION26{ M|194 - 319 }
27X-RAY DIFFRACTION27{ N|34 - 193 }
28X-RAY DIFFRACTION28{ N|194 - 319 }
29X-RAY DIFFRACTION29{ O|34 - 193 }
30X-RAY DIFFRACTION30{ O|194 - 319 }

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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

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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

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