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- PDB-2f2l: Crystal structure of tracheal cytotoxin (TCT) bound to the ectodo... -

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Basic information

Entry
Database: PDB / ID: 2f2l
TitleCrystal structure of tracheal cytotoxin (TCT) bound to the ectodomain complex of peptidoglycan recognition proteins LCa (PGRP-LCa) and LCx (PGRP-LCx)
Components
  • Peptidoglycan recognition protein-LC isoform LCx
  • Peptidoglycan-recognition protein-LC isoform LCa
KeywordsMEMBRANE PROTEIN / IMMUNE SYSTEM / TOXIN / Protein-peptidoglycan complex
Function / homology
Function and homology information


regulation of melanization defense response / Peptidoglycans (PGN) bind to a peptidoglycan recognition protein receptor, PGRP-LC/LE / Peptidoglycan bound PGRP-LC/LE oligomerises / Assembly of the PGN:PGRP-LC/LE receptor 'signalling complex' / Activated IkappaB kinase (IKK) complex, Phospho IRD5:KEY dimer, phosphorylates REL in the PGN:PGRP-LC/LE receptor 'signalling complex' / REL binds to DREDD in the PGN:PGRP-LC/LE receptor 'signalling complex' / Phosphorylated REL is cleaved by and dissociates from DREDD / peptidoglycan recognition protein signaling pathway / positive regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria / positive regulation of antibacterial peptide biosynthetic process ...regulation of melanization defense response / Peptidoglycans (PGN) bind to a peptidoglycan recognition protein receptor, PGRP-LC/LE / Peptidoglycan bound PGRP-LC/LE oligomerises / Assembly of the PGN:PGRP-LC/LE receptor 'signalling complex' / Activated IkappaB kinase (IKK) complex, Phospho IRD5:KEY dimer, phosphorylates REL in the PGN:PGRP-LC/LE receptor 'signalling complex' / REL binds to DREDD in the PGN:PGRP-LC/LE receptor 'signalling complex' / Phosphorylated REL is cleaved by and dissociates from DREDD / peptidoglycan recognition protein signaling pathway / positive regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria / positive regulation of antibacterial peptide biosynthetic process / regulation of humoral immune response / lipopolysaccharide immune receptor activity / peptidoglycan immune receptor activity / apicolateral plasma membrane / peptidoglycan binding / detection of bacterium / response to bacterium / regulation of synaptic plasticity / presynapse / antibacterial humoral response / cytoplasmic vesicle / defense response to Gram-negative bacterium / defense response to virus / defense response to Gram-positive bacterium / immune response / innate immune response / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Peptidoglycan recognition protein family domain, metazoa/bacteria / Peptidoglycan recognition protein / Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. / Lysozyme-like / Peptidoglycan recognition protein-like / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 2-acetylamino-2-deoxy-alpha-L-idopyranose / Chem-MLD / : / Peptidoglycan-recognition protein LC
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChang, C.I. / Deisenhofer, J.
CitationJournal: Science / Year: 2006
Title: Structure of tracheal cytotoxin in complex with a heterodimeric pattern-recognition receptor.
Authors: Chang, C.I. / Chelliah, Y. / Borek, D. / Mengin-Lecreulx, D. / Deisenhofer, J.
History
DepositionNov 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 5, 2011Group: Derived calculations
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan-recognition protein-LC isoform LCa
X: Peptidoglycan recognition protein-LC isoform LCx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5398
Polymers37,7902
Non-polymers1,7496
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-25 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.123, 79.695, 114.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AX

#1: Protein Peptidoglycan-recognition protein-LC isoform LCa / Immune response deficient 7 protein


Mass: 18717.281 Da / Num. of mol.: 1 / Fragment: Extracellular domain (residues 355-520)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cell line (production host): Hi-5 insect cells / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9GNK5
#2: Protein Peptidoglycan recognition protein-LC isoform LCx


Mass: 19072.721 Da / Num. of mol.: 1 / Fragment: Extracellular domain (residues 335-500)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cell line (production host): Hi-5 insect cells / Production host: Spodoptera frugiperda (fall armyworm) / References: GenBank: 20271150, UniProt: Q9GNK5*PLUS

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Sugars , 2 types, 2 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-HSQ / 2-acetylamino-2-deoxy-alpha-L-idopyranose / N-acetyl-alpha-L-idosamine / 2-acetylamino-2-deoxy-alpha-L-idose / 2-acetylamino-2-deoxy-L-idose / 2-acetylamino-2-deoxy-idose / 2-(acetylamino)-2-deoxy-alpha-L-idopyranose


Type: L-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
LIdopNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-L-idopyranosamineCOMMON NAMEGMML 1.0
a-L-IdopNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
IdoNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 199 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MLD / GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA / 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE(BETA1-4)-2-ACETAMIDO-1,6-ANHYDRO-3-O-[(R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSE-L-ALANYL-GAMMA-D-GLUTAMYL-MESO-DIAMINOPIMELYL-D-ALANINE


Mass: 921.899 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H59N7O20
#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4.2
Details: 20% polyethylene glycol 1500, 5% ethylene glycol, and 100 mM phosphate-citrate, pH 4.2, EVAPORATION, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 22, 2005
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 24185 / Num. obs: 23701 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1S2J and 1Z6I

1s2j

1z6i


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.604 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21378 1148 5.1 %RANDOM
Rwork0.1663 ---
all0.16872 22645 --
obs0.16872 21203 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2---2.05 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 115 195 2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222867
X-RAY DIFFRACTIONr_bond_other_d0.0010.022537
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9873893
X-RAY DIFFRACTIONr_angle_other_deg0.7983.0045827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92823.333129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69415467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8631521
X-RAY DIFFRACTIONr_chiral_restr0.0790.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
X-RAY DIFFRACTIONr_nbd_refined0.1930.2499
X-RAY DIFFRACTIONr_nbd_other0.1810.22504
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21382
X-RAY DIFFRACTIONr_nbtor_other0.0840.21614
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2164
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.28
X-RAY DIFFRACTIONr_mcbond_it0.5241.52155
X-RAY DIFFRACTIONr_mcbond_other0.1111.5695
X-RAY DIFFRACTIONr_mcangle_it0.67422692
X-RAY DIFFRACTIONr_scbond_it1.41731424
X-RAY DIFFRACTIONr_scangle_it2.2264.51201
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 89 -
Rwork0.185 1431 -
obs--92.57 %

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