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- PDB-4hji: Structure of the CooA pilin subunit from enterotoxigenic Escheric... -

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Basic information

Entry
Database: PDB / ID: 4hji
TitleStructure of the CooA pilin subunit from enterotoxigenic Escherichia coli
ComponentsCS1 fimbrial subunit A
KeywordsCELL ADHESION / CS1 pilus / COLONIZATION FACTOR / pilin / chaperone-usher family / BACTERIAL SURFACE
Function / homologyCFA/I fimbrial subunit E, pilin domain / Fimbrial major subunit, CS1-type / CS1 type fimbrial major subunit / pilus / Immunoglobulin-like / Sandwich / Mainly Beta / IMIDAZOLE / CS1 fimbrial subunit A
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKolappan, S. / Zong, Z. / Craig, L.
CitationJournal: J Bacteriol / Year: 2013
Title: The structure of the CS1 pilus of enterotoxigenic Escherichia coli reveals structural polymorphism.
Authors: Vitold E Galkin / Subramaniapillai Kolappan / Dixon Ng / ZuSheng Zong / Juliana Li / Xiong Yu / Edward H Egelman / Lisa Craig /
Abstract: Enterotoxigenic Escherichia coli (ETEC) is a bacterial pathogen that causes diarrhea in children and travelers in developing countries. ETEC adheres to host epithelial cells in the small intestine ...Enterotoxigenic Escherichia coli (ETEC) is a bacterial pathogen that causes diarrhea in children and travelers in developing countries. ETEC adheres to host epithelial cells in the small intestine via a variety of different pili. The CS1 pilus is a prototype for a family of related pili, including the CFA/I pili, present on ETEC and other Gram-negative bacterial pathogens. These pili are assembled by an outer membrane usher protein that catalyzes subunit polymerization via donor strand complementation, in which the N terminus of each incoming pilin subunit fits into a hydrophobic groove in the terminal subunit, completing a β-sheet in the Ig fold. Here we determined a crystal structure of the CS1 major pilin subunit, CooA, to a 1.6-Å resolution. CooA is a globular protein with an Ig fold and is similar in structure to the CFA/I major pilin CfaB. We determined three distinct negative-stain electron microscopic reconstructions of the CS1 pilus and generated pseudoatomic-resolution pilus structures using the CooA crystal structure. CS1 pili adopt multiple structural states with differences in subunit orientations and packing. We propose that the structural perturbations are accommodated by flexibility in the N-terminal donor strand of CooA and by plasticity in interactions between exposed flexible loops on adjacent subunits. Our results suggest that CS1 and other pili of this class are extensible filaments that can be stretched in response to mechanical stress encountered during colonization.
History
DepositionOct 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Feb 18, 2015Group: Derived calculations
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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.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 / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CS1 fimbrial subunit A
B: CS1 fimbrial subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5834
Polymers36,4912
Non-polymers922
Water2,810156
1
A: CS1 fimbrial subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3142
Polymers18,2451
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CS1 fimbrial subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2682
Polymers18,2451
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.990, 46.870, 51.270
Angle α, β, γ (deg.)83.72, 89.95, 74.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CS1 fimbrial subunit A / CS1 pilin


Mass: 18245.250 Da / Num. of mol.: 2 / Fragment: CS1 PILIN, COOA-DSE: unp residues 35-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: LMC10 / Gene: csoA, cooA / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABW7
#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.89 Å3/Da / Density % sol: 34.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 M SODIUM CITRATE, 100 MM IMIDAZOLE , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.07 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 8, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 131428 / Num. obs: 33503 / % possible obs: 92.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 24.47 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 34.1
Reflection shellResolution: 1.6→1.69 Å / % possible all: 92.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F83

3f83


Resolution: 1.6→19.67 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.108 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25057 1676 5 %RANDOM
Rwork0.22214 ---
obs0.22356 31826 94.94 %-
all-35943 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.257 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0.79 Å20.22 Å2
2--1.73 Å2-1.15 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 6 156 2374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192337
X-RAY DIFFRACTIONr_bond_other_d0.0010.022250
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9623212
X-RAY DIFFRACTIONr_angle_other_deg1.89135207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7795325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68627.40377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81115380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.23152
X-RAY DIFFRACTIONr_chiral_restr0.1290.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21184
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2120
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5631.51585
X-RAY DIFFRACTIONr_mcbond_other0.1271.5637
X-RAY DIFFRACTIONr_mcangle_it1.05422612
X-RAY DIFFRACTIONr_scbond_it1.7413756
X-RAY DIFFRACTIONr_scangle_it2.8644.5600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 118 -
Rwork0.274 2225 -
obs--90.85 %
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)
11.4186-0.16910.10231.2359-0.08632.10250.03250.0633-0.0292-0.028-0.02430.0189-0.2152-0.0615-0.00820.11820.01630.02720.00940.02880.22793.14482.4351-15.1446
21.44210.2274-0.06641.28520.23483.21380.0617-0.08710.01610.0264-0.03060.00960.1556-0.0162-0.03110.11530.01030.01340.01030.02510.22353.1955-17.5715-0.3097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 165
2X-RAY DIFFRACTION2B13 - 165

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