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

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Entry
Database: PDB / ID: 1bcp
TitleBINARY COMPLEX OF PERTUSSIS TOXIN AND ATP
Components(PERTUSSIS TOXIN) x 5
KeywordsTOXIN / ADP-RIBOSYLTRANSFERASE / TRANSFERASE / WHOOPING COUGH
Function / homologyC-type lectin fold / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily / Pertussis toxin S5 subunit / Pertussis toxin S4 subunit / Aerolysin/Pertussis toxin (APT) domain / Pertussis toxin, subunit 2 and 3, C-terminal domain / Bordetella pertussis toxin A / Bordetella pertussis toxin B / Aerolysin/Pertussis toxin domain / Enterotoxin ...C-type lectin fold / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily / Pertussis toxin S5 subunit / Pertussis toxin S4 subunit / Aerolysin/Pertussis toxin (APT) domain / Pertussis toxin, subunit 2 and 3, C-terminal domain / Bordetella pertussis toxin A / Bordetella pertussis toxin B / Aerolysin/Pertussis toxin domain / Enterotoxin / Pertussis toxin, subunit S4 / Pertussis toxin, subunit S5 / Pertussis toxin, subunit 1 / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Transferases, Glycosyltransferases, Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / toxin activity / host cell plasma membrane / membrane / extracellular region / Pertussis toxin subunit 1 / Pertussis toxin subunit 2 / Pertussis toxin subunit 3 / Pertussis toxin subunit 5 / Pertussis toxin subunit 4
Function and homology information
Specimen sourceBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2.7 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 21, 1995 / Release: Jun 5, 1997
RevisionDateData content typeGroupProviderType
1.0Jun 5, 1997Structure modelrepositoryInitial release
1.1Mar 21, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Polyers210,35712
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
Polyers105,1796
Non-polymers5071
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)15910
ΔGint (kcal/M)-85
Surface area (Å2)34880
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
Polyers105,1796
Non-polymers5071
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)16040
ΔGint (kcal/M)-87
Surface area (Å2)34750
MethodPISA
Unit cell
γ
α
β
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-MP 21 21 21
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/peptide , 5 types, 12 molecules AGBHCIDEJKFL

#1: Protein/peptide PERTUSSIS TOXIN /


Mass: 26248.740 Da / Num. of mol.: 2 / Source: (natural) Bordetella pertussis (bacteria)
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).
Genus: Bordetella / Strain: 10536
References: UniProt: P04977, Transferases, Glycosyltransferases, Pentosyltransferases
#2: Protein/peptide PERTUSSIS TOXIN /


Mass: 21943.701 Da / Num. of mol.: 2 / Source: (natural) Bordetella pertussis (bacteria)
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).
Genus: Bordetella / Strain: 10536
References: UniProt: P04978, Transferases, Glycosyltransferases, Pentosyltransferases
#3: Protein/peptide PERTUSSIS TOXIN /


Mass: 21889.867 Da / Num. of mol.: 2 / Source: (natural) Bordetella pertussis (bacteria)
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).
Genus: Bordetella / Strain: 10536
References: UniProt: P04979, Transferases, Glycosyltransferases, Pentosyltransferases
#4: Protein/peptide
PERTUSSIS TOXIN /


Mass: 12072.426 Da / Num. of mol.: 4 / Source: (natural) Bordetella pertussis (bacteria)
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).
Genus: Bordetella / Strain: 10536
References: UniProt: P0A3R5, Transferases, Glycosyltransferases, Pentosyltransferases
#5: Protein/peptide PERTUSSIS TOXIN /


Mass: 10951.524 Da / Num. of mol.: 2 / Source: (natural) Bordetella pertussis (bacteria)
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).
Genus: Bordetella / 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 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Formula: H2O / Water

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Details

Compound detailsSUBUNIT S1 OF THE HOLOTOXIN MOLECULE (CHAINS A AND G) FORMS THE ENZYMATIC PART OF THE TOXIN. S1 ...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).
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 / Density percent 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 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
IDConcCommon 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 kelvins
SourceSource: SYNCHROTRON / Type: PHOTON FACTORY BEAMLINE BL-6A / Synchrotron site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Collection date: Nov 27, 1993
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 2.5 Å / Number obs: 62637 / Observed criterion sigma I: 0 / Rmerge I obs: 0.093 / Redundancy: 3 % / Percent possible obs: 64
Reflection
*PLUS
Number measured all: 195544
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.7 Å / Percent possible obs: 19.6

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Processing

Software
NameClassification
WEISdata collection
X-PLORrefinement
WEISdata reduction
RefineDetails: 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
Sigma F: 0
Displacement parametersB iso mean: 21.84 Å2
Least-squares processR factor R work: 0.232 / R factor obs: 0.232 / Highest resolution: 2.7 Å / Lowest resolution: 8 Å / Number reflection obs: 55031
Refine analyzeLuzzati sigma a obs: 0.46 Å
Refine hist #LASTHighest resolution: 2.7 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 14518 / Nucleic acid: 0 / Ligand: 62 / Solvent: 41 / Total: 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_deg2.0
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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