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- PDB-1t6b: Crystal structure of B. anthracis Protective Antigen complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1t6b
TitleCrystal structure of B. anthracis Protective Antigen complexed with human Anthrax toxin receptor
Components
  • Anthrax toxin receptor 2
  • Protective Antigen
KeywordsMEMBRANE PROTEIN/TOXIN / Bacillus Anthracis / Anthrax toxin / X-ray crystallography / MEMBRANE PROTEIN-TOXIN COMPLEX
Function / homology
Function and homology information


positive regulation of apoptotic process in another organism / host cell cytosol / Uptake and function of anthrax toxins / negative regulation of MAPK cascade / host cell endosome membrane / protein homooligomerization / transmembrane signaling receptor activity / toxin activity / endosome membrane / endoplasmic reticulum membrane ...positive regulation of apoptotic process in another organism / host cell cytosol / Uptake and function of anthrax toxins / negative regulation of MAPK cascade / host cell endosome membrane / protein homooligomerization / transmembrane signaling receptor activity / toxin activity / endosome membrane / endoplasmic reticulum membrane / host cell plasma membrane / cell surface / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Anthrax toxin receptor / Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / Protective antigen, heptamerisation domain / Immunoglobulin-like - #810 / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / Ubiquitin-like (UB roll) - #110 ...Anthrax toxin receptor / Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / Protective antigen, heptamerisation domain / Immunoglobulin-like - #810 / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / Ubiquitin-like (UB roll) - #110 / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / von Willebrand factor, type A domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Ubiquitin-like (UB roll) / Jelly Rolls / Roll / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Protective antigen / Anthrax toxin receptor 2
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSantelli, E. / Bankston, L.A. / Leppla, S.H. / Liddington, R.C.
CitationJournal: Nature / Year: 2004
Title: Crystal structure of a complex between anthrax toxin and its host cell receptor
Authors: Santelli, E. / Bankston, L.A. / Leppla, S.H. / Liddington, R.C.
History
DepositionMay 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Protective Antigen
Y: Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7758
Polymers103,3992
Non-polymers3756
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-28 kcal/mol
Surface area37610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.160, 94.118, 135.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules XY

#1: Protein Protective Antigen


Mass: 82768.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Production host: Bacillus anthracis (anthrax bacterium) / Strain (production host): BH445 / References: UniProt: P13423
#2: Protein Anthrax toxin receptor 2 / Capillary morphogenesis protein-2 / CMG-2


Mass: 20630.566 Da / Num. of mol.: 1 / Fragment: A/I domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANTXR2,CMG2 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P58335

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Non-polymers , 5 types, 145 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.6 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 9
Details: CHES buffer, PEG400, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.892 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.892 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 39975 / Num. obs: 39917 / Observed criterion σ(I): -4 / Redundancy: 5.3 % / Rsym value: 0.176 / Net I/σ(I): 11.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.00991 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.967 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26572 1990 5 %RANDOM
Rwork0.20717 ---
obs0.21009 37620 99.74 %-
all-39610 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.665 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2---1.55 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6695 0 18 139 6852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226823
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9559231
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2355841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025110
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.22918
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7941.54212
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54626838
X-RAY DIFFRACTIONr_scbond_it2.46532611
X-RAY DIFFRACTIONr_scangle_it4.1664.52393
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 160
Rwork0.274 2699
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)
12.4458-1.1112-1.63761.80091.51323.2231-0.0392-0.3550.1080.22060.09510.10210.1860.1057-0.05590.153-0.01440.04040.1622-0.00150.12639.218234.006278.4508
20.4655-0.08710.59480.6633-0.10512.5529-0.04930.0263-0.0048-0.0827-0.00620.0577-0.10080.00960.05550.1354-0.0109-0.00460.08670.01810.184840.124732.424931.6542
31.4323-0.0736-0.06792.38690.68542.3547-0.007-0.11980.10440.01910.009-0.09770.11550.0397-0.0020.12670.0283-0.00660.09420.00970.122350.685312.269951.1809
41.97770.4971.14841.61010.43092.4516-0.0071-0.0354-0.06150.0350.03260.1260.1423-0.0354-0.02550.12010.0222-0.00440.05930.00260.106229.55063.601621.1869
53.7182-0.04680.72734.41490.19822.6391-0.18390.35940.0778-0.22340.15380.03050.02560.12940.030.0827-0.0419-0.08330.14710.03250.084721.09247.9669-8.664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1XA16 - 25816 - 258
2X-RAY DIFFRACTION2XA259 - 487259 - 487
3X-RAY DIFFRACTION3XA488 - 595488 - 595
4X-RAY DIFFRACTION4XA596 - 735596 - 735
5X-RAY DIFFRACTION5YB41 - 21012 - 181

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