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- PDB-1bcp: BINARY COMPLEX OF PERTUSSIS TOXIN AND ATP -

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Basic information

Entry
Database: PDB / ID: 1bcp
TitleBINARY COMPLEX OF PERTUSSIS TOXIN AND ATP
Components(PERTUSSIS TOXIN) x 5
KeywordsTOXIN / ADP-RIBOSYLTRANSFERASE / TRANSFERASE / WHOOPING COUGH
Function / homology
Function and homology information


symbiont-mediated activation of host MAPK cascade / symbiont-mediated activation of host G protein-coupled receptor signal transduction / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Pertussis Toxin; Chain B, domain 1 / Aerolysin/Pertussis toxin (APT), N-terminal domain / Bordetella pertussis toxin B / Pertussis toxin, subunit S4 / Pertussis toxin, subunit S5 / Pertussis toxin S4 subunit / Pertussis toxin S5 subunit / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Bordetella pertussis toxin A ...Pertussis Toxin; Chain B, domain 1 / Aerolysin/Pertussis toxin (APT), N-terminal domain / Bordetella pertussis toxin B / Pertussis toxin, subunit S4 / Pertussis toxin, subunit S5 / Pertussis toxin S4 subunit / Pertussis toxin S5 subunit / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Aerolysin/Pertussis toxin domain / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily / Aerolysin/Pertussis toxin (APT) domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / C-type lectin fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Pertussis toxin subunit 1 / Pertussis toxin subunit 2 / Pertussis toxin subunit 3 / Pertussis toxin subunit 5 / Pertussis toxin subunit 4
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsHazes, B. / Read, R.J.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of the pertussis toxin-ATP complex: a molecular sensor.
Authors: Hazes, B. / Boodhoo, A. / Cockle, S.A. / Read, R.J.
#1: Journal: Structure / Year: 1994
Title: The Crystal Structure of Pertussis Toxin
Authors: Stein, P.E. / Boodhoo, A. / Armstrong, G.D. / Cockle, S.A. / Klein, M.H. / Read, R.J.
#2: Journal: Nat.Struct.Biol. / Year: 1994
Title: Structure of a Pertussis Toxin-Sugar Complex as a Model for Receptor Binding
Authors: Stein, P.E. / Boodhoo, A. / Armstrong, G.D. / Heerze, L.D. / Cockle, S.A. / Klein, M.H. / Read, R.J.
#3: Journal: Nucleic Acids Res. / Year: 1989
Title: A Unique Sequence of the Bordetella Pertussis Toxin Operon
Authors: Loosmore, S.M. / Cunningham, J.D. / Bradley, W.R. / Yao, F.L. / Dekaban, G.A. / Klein, M.H.
History
DepositionNov 21, 1995Processing site: BNL
Revision 1.0Jun 5, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PERTUSSIS TOXIN
B: PERTUSSIS TOXIN
C: PERTUSSIS TOXIN
D: PERTUSSIS TOXIN
E: PERTUSSIS TOXIN
F: PERTUSSIS TOXIN
G: PERTUSSIS TOXIN
H: PERTUSSIS TOXIN
I: PERTUSSIS TOXIN
J: PERTUSSIS TOXIN
K: PERTUSSIS TOXIN
L: PERTUSSIS TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,37214
Polymers210,35712
Non-polymers1,0142
Water73941
1
A: PERTUSSIS TOXIN
B: PERTUSSIS TOXIN
C: PERTUSSIS TOXIN
D: PERTUSSIS TOXIN
E: PERTUSSIS TOXIN
F: PERTUSSIS TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6867
Polymers105,1796
Non-polymers5071
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15910 Å2
ΔGint-85 kcal/mol
Surface area34880 Å2
MethodPISA
2
G: PERTUSSIS TOXIN
H: PERTUSSIS TOXIN
I: PERTUSSIS TOXIN
J: PERTUSSIS TOXIN
K: PERTUSSIS TOXIN
L: PERTUSSIS TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6867
Polymers105,1796
Non-polymers5071
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16040 Å2
ΔGint-87 kcal/mol
Surface area34750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.800, 98.200, 194.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.91421, 0.372578, -0.159394), (0.377028, 0.637808, -0.671604), (-0.148562, -0.674082, -0.723562)
Vector: 17.781, 21.706, 62.029)
DetailsEACH OF THE TWO HOLOTOXIN MOLECULES IN THE ASYMMETRIC UNIT CONSISTS OF SIX SUBUNITS AND THEY HAVE BEEN ASSIGNED CHAIN INDICATORS A - F AND G - L, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS G - L WHEN APPLIED TO CHAINS A - F.

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Components

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Protein , 5 types, 12 molecules AGBHCIDEJKFL

#1: Protein PERTUSSIS TOXIN


Mass: 26248.740 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE PERTUSSIS TOXIN USED FOR THIS WORK WAS PURIFIED FROM B. PERTUSSIS STRAIN 10536 (LOOSMORE ET AL., NUCLEIC ACIDS RES., VOL. 17, 8365, 1989), WHICH DIFFERS AT TWO POSITIONS IN SUBUNIT S1 ...Details: THE PERTUSSIS TOXIN USED FOR THIS WORK WAS PURIFIED FROM B. PERTUSSIS STRAIN 10536 (LOOSMORE ET AL., NUCLEIC ACIDS RES., VOL. 17, 8365, 1989), WHICH DIFFERS AT TWO POSITIONS IN SUBUNIT S1 (ASP 34 GLU AND ILE 198 VAL) FROM THE SEQUENCE THAT WAS FIRST REPORTED FOR THE PROTEIN (NICOSIA ET AL., PNAS VOL 83, 4631 - 4635, 1986).
Source: (natural) Bordetella pertussis (bacteria) / Strain: 10536
References: UniProt: P04977, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein PERTUSSIS TOXIN


Mass: 21943.701 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE PERTUSSIS TOXIN USED FOR THIS WORK WAS PURIFIED FROM B. PERTUSSIS STRAIN 10536 (LOOSMORE ET AL., NUCLEIC ACIDS RES., VOL. 17, 8365, 1989), WHICH DIFFERS AT TWO POSITIONS IN SUBUNIT S1 ...Details: THE PERTUSSIS TOXIN USED FOR THIS WORK WAS PURIFIED FROM B. PERTUSSIS STRAIN 10536 (LOOSMORE ET AL., NUCLEIC ACIDS RES., VOL. 17, 8365, 1989), WHICH DIFFERS AT TWO POSITIONS IN SUBUNIT S1 (ASP 34 GLU AND ILE 198 VAL) FROM THE SEQUENCE THAT WAS FIRST REPORTED FOR THE PROTEIN (NICOSIA ET AL., PNAS VOL 83, 4631 - 4635, 1986).
Source: (natural) Bordetella pertussis (bacteria) / Strain: 10536
References: UniProt: P04978, Transferases; Glycosyltransferases; Pentosyltransferases
#3: Protein PERTUSSIS TOXIN


Mass: 21889.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE PERTUSSIS TOXIN USED FOR THIS WORK WAS PURIFIED FROM B. PERTUSSIS STRAIN 10536 (LOOSMORE ET AL., NUCLEIC ACIDS RES., VOL. 17, 8365, 1989), WHICH DIFFERS AT TWO POSITIONS IN SUBUNIT S1 ...Details: THE PERTUSSIS TOXIN USED FOR THIS WORK WAS PURIFIED FROM B. PERTUSSIS STRAIN 10536 (LOOSMORE ET AL., NUCLEIC ACIDS RES., VOL. 17, 8365, 1989), WHICH DIFFERS AT TWO POSITIONS IN SUBUNIT S1 (ASP 34 GLU AND ILE 198 VAL) FROM THE SEQUENCE THAT WAS FIRST REPORTED FOR THE PROTEIN (NICOSIA ET AL., PNAS VOL 83, 4631 - 4635, 1986).
Source: (natural) Bordetella pertussis (bacteria) / Strain: 10536
References: UniProt: P04979, Transferases; Glycosyltransferases; Pentosyltransferases
#4: Protein
PERTUSSIS TOXIN


Mass: 12072.426 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: THE PERTUSSIS TOXIN USED FOR THIS WORK WAS PURIFIED FROM B. PERTUSSIS STRAIN 10536 (LOOSMORE ET AL., NUCLEIC ACIDS RES., VOL. 17, 8365, 1989), WHICH DIFFERS AT TWO POSITIONS IN SUBUNIT S1 ...Details: THE PERTUSSIS TOXIN USED FOR THIS WORK WAS PURIFIED FROM B. PERTUSSIS STRAIN 10536 (LOOSMORE ET AL., NUCLEIC ACIDS RES., VOL. 17, 8365, 1989), WHICH DIFFERS AT TWO POSITIONS IN SUBUNIT S1 (ASP 34 GLU AND ILE 198 VAL) FROM THE SEQUENCE THAT WAS FIRST REPORTED FOR THE PROTEIN (NICOSIA ET AL., PNAS VOL 83, 4631 - 4635, 1986).
Source: (natural) Bordetella pertussis (bacteria) / Strain: 10536
References: UniProt: P0A3R5, Transferases; Glycosyltransferases; Pentosyltransferases
#5: Protein PERTUSSIS TOXIN


Mass: 10951.524 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE PERTUSSIS TOXIN USED FOR THIS WORK WAS PURIFIED FROM B. PERTUSSIS STRAIN 10536 (LOOSMORE ET AL., NUCLEIC ACIDS RES., VOL. 17, 8365, 1989), WHICH DIFFERS AT TWO POSITIONS IN SUBUNIT S1 ...Details: THE PERTUSSIS TOXIN USED FOR THIS WORK WAS PURIFIED FROM B. PERTUSSIS STRAIN 10536 (LOOSMORE ET AL., NUCLEIC ACIDS RES., VOL. 17, 8365, 1989), WHICH DIFFERS AT TWO POSITIONS IN SUBUNIT S1 (ASP 34 GLU AND ILE 198 VAL) FROM THE SEQUENCE THAT WAS FIRST REPORTED FOR THE PROTEIN (NICOSIA ET AL., PNAS VOL 83, 4631 - 4635, 1986).
Source: (natural) Bordetella pertussis (bacteria) / Strain: 10536
References: UniProt: P04981, Transferases; Glycosyltransferases; Pentosyltransferases

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Non-polymers , 2 types, 43 molecules

#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsSUBUNIT S1 OF THE HOLOTOXIN MOLECULE (CHAINS A AND G) FORMS THE ENZYMATIC PART OF THE TOXIN. S1 ADP- ...SUBUNIT S1 OF THE HOLOTOXIN MOLECULE (CHAINS A AND G) FORMS THE ENZYMATIC PART OF THE TOXIN. S1 ADP-RIBOSYLATES THE ALPHA SUBUNIT OF TRIMERIC G-PROTEINS AT A CYSTEINE RESIDUE THE REMAINING FIVE SUBUNITS S2, S3, 2 COPIES OF S4, AND S5 (CHAINS B-F AND H-L) FORM THE CELL-BINDING PART OF THE TOXIN. THE STRUCTURE OF A COMPLEX OF PERTUSSIS TOXIN AND A CARBOHYDRATE WITH A TERMINAL SIALIC ACID GROUP IS DESCRIBED IN REF 2 (GIVEN ABOVE).
Has protein modificationY
Nonpolymer detailsATP 1 IS BOUND TO HOLOTOXIN MOLECULE 1 (CHAINS A-F). ATP 2 IS BOUND TO HOLOTOXIN MOLECULE 2 (CHAINS ...ATP 1 IS BOUND TO HOLOTOXIN MOLECULE 1 (CHAINS A-F). ATP 2 IS BOUND TO HOLOTOXIN MOLECULE 2 (CHAINS G-L). WATER MOLECULES 3 TO 27 BIND TO HOLOTOXIN MOLECULE 1. WATER MOLECULES 28 TO 43 BIND TO HOLOTOXIN MOLECULE 2.
Sequence detailsTHE PERTUSSIS TOXIN USED FOR THIS WORK WAS PURIFIED FROM B. PERTUSSIS STRAIN 10536 (LOOSMORE ET AL. ...THE PERTUSSIS TOXIN USED FOR THIS WORK WAS PURIFIED FROM B. PERTUSSIS STRAIN 10536 (LOOSMORE ET AL., NUCLEIC ACIDS RES., VOL. 17, 8365, 1989), WHICH DIFFERS AT TWO POSITIONS IN SUBUNIT S1 (ASP 34 GLU AND ILE 198 VAL) FROM THE SEQUENCE THAT WAS FIRST REPORTED FOR THE PROTEIN (NICOSIA ET AL., PNAS VOL 83, 4631 - 4635, 1986).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.9 %
Description: DATA COLLECTION STATISTICS ARE GIVEN FOR ALL DATA UP TO 2.5 ANGSTROMS. HOWEVER, DUE TO RADIATION DAMAGE THE HIGH RESOLUTION DATA IS VERY INCOMPLETE AND THEREFORE ONLY DATA TO 2.7 ...Description: DATA COLLECTION STATISTICS ARE GIVEN FOR ALL DATA UP TO 2.5 ANGSTROMS. HOWEVER, DUE TO RADIATION DAMAGE THE HIGH RESOLUTION DATA IS VERY INCOMPLETE AND THEREFORE ONLY DATA TO 2.7 ANGSTROM HAVE BEEN USED FOR REFINEMENT. THE DATA UP TO THIS RESOLUTION IS 67.3 % COMPLETE WITH A COMPLETENESS OF 19.6 % IN THE HIGHEST RESOLUTION SHELL
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Stein, P.E., (1994) Structure (London), 2, 45.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mMsodium potassium phosphate1reservoir
20.25 M1reservoirKCl
30.02 %1reservoirNaN3
40.3-0.5 M1reservoirKCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 27, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 62637 / % possible obs: 64 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.093
Reflection
*PLUS
Num. measured all: 195544
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.7 Å / % possible obs: 19.6 %

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Processing

Software
NameClassification
WEISdata collection
X-PLORrefinement
WEISdata reduction
RefinementResolution: 2.7→8 Å / σ(F): 0
Details: THERE ARE MISSING RESIDUES AT THE N-TERMINI OF SUBUNITS S1, S2, S3, AND S5. IN ADDITION, NO COORDINATES ARE PRESENT FOR RESIDUES 211 - 220 IN SUBUNIT S1 (CHAINS A AND G). DATA COLLECTION ...Details: THERE ARE MISSING RESIDUES AT THE N-TERMINI OF SUBUNITS S1, S2, S3, AND S5. IN ADDITION, NO COORDINATES ARE PRESENT FOR RESIDUES 211 - 220 IN SUBUNIT S1 (CHAINS A AND G). DATA COLLECTION STATISTICS ARE GIVEN FOR ALL DATA UP TO 2.5 ANGSTROMS. HOWEVER, DUE TO RADIATION DAMAGE THE HIGH RESOLUTION DATA IS VERY INCOMPLETE AND THEREFORE ONLY DATA TO 2.7 ANGSTROM HAVE BEEN USED FOR REFINEMENT. THE DATA UP TO THIS RESOLUTION IS 67.3 % COMPLETE WITH A COMPLETENESS OF 19.6 % IN THE HIGHEST RESOLUTION SHELL
RfactorNum. reflection
Rwork0.232 -
obs0.232 55031
Displacement parametersBiso mean: 21.84 Å2
Refine analyzeLuzzati sigma a obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14518 0 62 41 14621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.25
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it0.5
X-RAY DIFFRACTIONx_scangle_it

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