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Basic information

Entry
Database: PDB / ID: 3kwv
TitleStructural basis for the unfolding of anthrax lethal factor by protective antigen oligomers
Components
  • Lethal factor
  • Protective antigen PA-63
KeywordsTOXIN/PROTEIN TRANSPORT / Bacillus anthracis / protective antigen / lethal factor / lethal toxin / octamer / protein transport / toxin / protein unfolding / protein translocation / Cleavage on pair of basic residues / Metal-binding / Secreted / Virulence / Hydrolase / Metalloprotease / Protease / TOXIN-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


anthrax lethal factor endopeptidase / positive regulation of apoptotic process in another organism / host cell cytosol / negative regulation of MAPK cascade / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / metalloendopeptidase activity / metallopeptidase activity / toxin activity ...anthrax lethal factor endopeptidase / positive regulation of apoptotic process in another organism / host cell cytosol / negative regulation of MAPK cascade / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / metalloendopeptidase activity / metallopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / identical protein binding / membrane / metal ion binding
Similarity search - Function
Protective antigen, heptamerisation domain / Immunoglobulin-like - #810 / Ubiquitin-like (UB roll) - #110 / Anthrax toxin lethal factor, central domain / Anthrax toxin lethal factor, middle domain / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Anthrax toxin, lethal/endema factor / : ...Protective antigen, heptamerisation domain / Immunoglobulin-like - #810 / Ubiquitin-like (UB roll) - #110 / Anthrax toxin lethal factor, central domain / Anthrax toxin lethal factor, middle domain / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Anthrax toxin, lethal/endema factor / : / Anthrax toxin lethal factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal 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 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Ubiquitin-like (UB roll) / Jelly Rolls / Roll / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protective antigen / Lethal factor
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å
AuthorsFeld, G.K. / Kintzer, A.F. / Krantz, B.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers.
Authors: Feld, G.K. / Thoren, K.L. / Kintzer, A.F. / Sterling, H.J. / Tang, I.I. / Greenberg, S.G. / Williams, E.R. / Krantz, B.A.
History
DepositionDec 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_seq_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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protective antigen PA-63
B: Protective antigen PA-63
C: Lethal factor
D: Protective antigen PA-63
E: Protective antigen PA-63
F: Lethal factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,35114
Polymers307,0306
Non-polymers3218
Water724
1
A: Protective antigen PA-63
B: Protective antigen PA-63
C: Lethal factor
hetero molecules

A: Protective antigen PA-63
B: Protective antigen PA-63
C: Lethal factor
hetero molecules

A: Protective antigen PA-63
B: Protective antigen PA-63
C: Lethal factor
hetero molecules

A: Protective antigen PA-63
B: Protective antigen PA-63
C: Lethal factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)614,70128
Polymers614,06012
Non-polymers64116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
2
D: Protective antigen PA-63
E: Protective antigen PA-63
F: Lethal factor
hetero molecules

D: Protective antigen PA-63
E: Protective antigen PA-63
F: Lethal factor
hetero molecules

D: Protective antigen PA-63
E: Protective antigen PA-63
F: Lethal factor
hetero molecules

D: Protective antigen PA-63
E: Protective antigen PA-63
F: Lethal factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)614,70128
Polymers614,06012
Non-polymers64116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Unit cell
Length a, b, c (Å)178.381, 178.381, 240.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
33
43
14
24
34
44
15
25
35
45
16
26
36
46
17
27
18
28
19
29

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resseq 174:240
211chain D and resseq 174:240
112chain B and resseq 174:240
212chain E and resseq 174:240
113chain A and resseq 241:274
213chain E and resseq 241:274
313chain B and resseq 241:274
413chain D and resseq 241:274
114chain A and resseq 286:339
214chain E and resseq 286:339
314chain B and resseq 286:339
414chain D and resseq 286:339
115chain A and resseq 343:442
215chain B and resseq 343:442
315chain E and resseq 343:442
415chain D and resseq 343:442
116chain A and resseq 446:575
216chain E and resseq 446:575
316chain B and resseq 446:575
416chain D and resseq 446:575
117chain A and resseq 576:715
217chain D and resseq 576:715
118chain B and resseq 576:715
218chain E and resseq 576:715
119chain C
219chain F

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

#1: Protein
Protective antigen PA-63 / PA / PA-83 / PA83 / Anthrax toxins translocating protein / Protective antigen PA-63 / PA63


Mass: 61484.336 Da / Num. of mol.: 4 / Fragment: UNP residues 197-764 / Mutation: V303P, H304G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: pagA / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P13423
#2: Protein Lethal factor / LF / Anthrax lethal toxin endopeptidase component


Mass: 30546.377 Da / Num. of mol.: 2
Fragment: protective antigen binding domain (UNP residues 34-296)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: lef / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P15917, anthrax lethal factor endopeptidase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 16% PEG 3000, 0.1M cacodylic acid, 0.2M magnesium chloride, 10 mM Tris-Cl, 75 mM sodium chloride, 10 mM adenosine-5'-triphosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 3.1→49.8 Å / Num. all: 70642 / Num. obs: 65167 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.4
Reflection shellResolution: 3.1→3.19 Å / Redundancy: 8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.2 / % possible all: 78

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HVD

3hvd


Resolution: 3.101→49.835 Å / SU ML: 0.39 / Isotropic thermal model: isotropic / σ(F): 0.14 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 1832 2.81 %
Rwork0.2491 --
obs0.25 65165 92.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.614 Å2 / ksol: 0.289 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.7082 Å2-0 Å20 Å2
2---3.7082 Å2-0 Å2
3---8.3746 Å2
Refinement stepCycle: LAST / Resolution: 3.101→49.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20337 0 8 4 20349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00520761
X-RAY DIFFRACTIONf_angle_d0.6128032
X-RAY DIFFRACTIONf_dihedral_angle_d11.0977824
X-RAY DIFFRACTIONf_chiral_restr0.0423196
X-RAY DIFFRACTIONf_plane_restr0.0023651
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A540X-RAY DIFFRACTIONPOSITIONAL
12D540X-RAY DIFFRACTIONPOSITIONAL0.01
21B540X-RAY DIFFRACTIONPOSITIONAL
22E540X-RAY DIFFRACTIONPOSITIONAL0.137
31A266X-RAY DIFFRACTIONPOSITIONAL
32E266X-RAY DIFFRACTIONPOSITIONAL0.01
33B266X-RAY DIFFRACTIONPOSITIONAL0.009
34D266X-RAY DIFFRACTIONPOSITIONAL0.01
41A248X-RAY DIFFRACTIONPOSITIONAL
42E248X-RAY DIFFRACTIONPOSITIONAL0.006
43B248X-RAY DIFFRACTIONPOSITIONAL0.006
44D241X-RAY DIFFRACTIONPOSITIONAL0.006
51A758X-RAY DIFFRACTIONPOSITIONAL
52B758X-RAY DIFFRACTIONPOSITIONAL0.114
53E758X-RAY DIFFRACTIONPOSITIONAL0.15
54D758X-RAY DIFFRACTIONPOSITIONAL0.105
61A1045X-RAY DIFFRACTIONPOSITIONAL
62E1045X-RAY DIFFRACTIONPOSITIONAL0.331
63B1045X-RAY DIFFRACTIONPOSITIONAL0.207
64D1045X-RAY DIFFRACTIONPOSITIONAL0.235
71A1133X-RAY DIFFRACTIONPOSITIONAL
72D1133X-RAY DIFFRACTIONPOSITIONAL0.202
81B1133X-RAY DIFFRACTIONPOSITIONAL
82E1133X-RAY DIFFRACTIONPOSITIONAL0.365
91C1816X-RAY DIFFRACTIONPOSITIONAL
92F1816X-RAY DIFFRACTIONPOSITIONAL0.055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1015-3.18530.35591190.28664096X-RAY DIFFRACTION78
3.1853-3.2790.34081240.29274282X-RAY DIFFRACTION83
3.279-3.38480.27721270.26264519X-RAY DIFFRACTION87
3.3848-3.50580.3161320.24714706X-RAY DIFFRACTION90
3.5058-3.64610.29511400.23524838X-RAY DIFFRACTION92
3.6461-3.8120.24731430.23344875X-RAY DIFFRACTION93
3.812-4.01290.30831410.23074803X-RAY DIFFRACTION92
4.0129-4.26420.25841400.22534924X-RAY DIFFRACTION94
4.2642-4.59320.23511450.20915071X-RAY DIFFRACTION96
4.5932-5.0550.25221540.20885146X-RAY DIFFRACTION97
5.055-5.78560.27651480.22695192X-RAY DIFFRACTION97
5.7856-7.28550.26611560.2525299X-RAY DIFFRACTION98
7.2855-49.84180.27311630.26865582X-RAY DIFFRACTION99

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