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- PDB-8s5r: Structure of the Chlamydia pneumoniae effector SemD -

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Basic information

Entry
Database: PDB / ID: 8s5r
TitleStructure of the Chlamydia pneumoniae effector SemD
ComponentsEffector SemD
KeywordsENDOCYTOSIS / effector effector protein
Function / homologyUncharacterized protein
Function and homology information
Biological speciesChlamydia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKocher, F. / Applegate, V. / Reiners, J. / Port, A. / Spona, D. / Haensch, S. / Smits, S.H. / Hegemann, J. / Moelleken, K.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)417919780 Germany
German Research Foundation (DFG)267205415 Germany
CitationJournal: Nat Commun / Year: 2024
Title: The Chlamydia pneumoniae effector SemD exploits its host's endocytic machinery by structural and functional mimicry.
Authors: Kocher, F. / Applegate, V. / Reiners, J. / Port, A. / Spona, D. / Hansch, S. / Mirzaiebadizi, A. / Ahmadian, M.R. / Smits, S.H.J. / Hegemann, J.H. / Molleken, K.
History
DepositionFeb 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Effector SemD
A: Effector SemD


Theoretical massNumber of molelcules
Total (without water)68,6632
Polymers68,6632
Non-polymers00
Water3,891216
1
B: Effector SemD


Theoretical massNumber of molelcules
Total (without water)34,3321
Polymers34,3321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Effector SemD


Theoretical massNumber of molelcules
Total (without water)34,3321
Polymers34,3321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.999, 51.957, 58.628
Angle α, β, γ (deg.)88.333, 105.892, 117.433
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 12 through 43 or resid 45 through 156 or resid 158 through 247))
d_2ens_1(chain "B" and (resid 12 through 43 or resid 45...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUASNASNAB12 - 4387 - 118
d_12GLYGLYTHRTHRAB45 - 156120 - 231
d_13ASPASPALAALAAB158 - 247233 - 322
d_21LEULEUASNASNBA12 - 4387 - 118
d_22GLYGLYGLYGLYBA45 - 148120 - 223
d_23SERSERTHRTHRBA151 - 156226 - 231
d_24ASPASPALAALABA158 - 247233 - 322

NCS oper: (Code: givenMatrix: (0.551977439338, 0.826944613355, 0.107161153899), (0.823340270627, -0.560843187638, 0.0869811338344), (0.132029183232, 0.0402184699273, -0.990429588336)Vector: -28. ...NCS oper: (Code: given
Matrix: (0.551977439338, 0.826944613355, 0.107161153899), (0.823340270627, -0.560843187638, 0.0869811338344), (0.132029183232, 0.0402184699273, -0.990429588336)
Vector: -28.6460167275, 54.554218117, 3.17935490557)

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Components

#1: Protein Effector SemD


Mass: 34331.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia (bacteria)
Gene: CP_0070, CPn_0677, BN1224_CV15_C_01450, BN1224_GiD_A_07040, BN1224_H12_EK_00710, BN1224_MUL2216_F_02260, BN1224_Panola_J_01100, BN1224_PB1_B_06920, BN1224_U1271_C_05340, BN1224_Wien2_G_03310, ...Gene: CP_0070, CPn_0677, BN1224_CV15_C_01450, BN1224_GiD_A_07040, BN1224_H12_EK_00710, BN1224_MUL2216_F_02260, BN1224_Panola_J_01100, BN1224_PB1_B_06920, BN1224_U1271_C_05340, BN1224_Wien2_G_03310, BN1224_YK41_BR_01220, CWL029c_D_02120
Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z7M7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Citric acid (pH 2.5), 20% (w/v) PEG 6000 (pH 4)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.916771 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916771 Å / Relative weight: 1
ReflectionResolution: 2.1→45.82 Å / Num. obs: 51456 / % possible obs: 97.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.34 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.61
Reflection shellResolution: 2.1→2.175 Å / Mean I/σ(I) obs: 2.56 / Num. unique obs: 2675 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.82 Å / SU ML: 0.2786 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.3166
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2776 2838 5.52 %
Rwork0.2182 48618 -
obs0.2214 51456 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3543 0 0 216 3759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113621
X-RAY DIFFRACTIONf_angle_d1.19294914
X-RAY DIFFRACTIONf_chiral_restr0.0809565
X-RAY DIFFRACTIONf_plane_restr0.0102643
X-RAY DIFFRACTIONf_dihedral_angle_d4.4614495
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.26105376419 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.32951460.27922518X-RAY DIFFRACTION95.62
2.14-2.180.30221480.27272441X-RAY DIFFRACTION95.89
2.18-2.220.35661450.26862489X-RAY DIFFRACTION95.64
2.22-2.260.44541390.33192348X-RAY DIFFRACTION89.72
2.26-2.310.31751370.28532403X-RAY DIFFRACTION94.85
2.31-2.370.29111400.25672444X-RAY DIFFRACTION91.89
2.37-2.420.28671410.24752402X-RAY DIFFRACTION94.39
2.42-2.490.31921460.23662509X-RAY DIFFRACTION94.48
2.49-2.560.30651470.23942472X-RAY DIFFRACTION95.79
2.56-2.650.29951470.2362471X-RAY DIFFRACTION95.76
2.65-2.740.34261440.23252470X-RAY DIFFRACTION95.19
2.74-2.850.30361330.24082392X-RAY DIFFRACTION93.45
2.85-2.980.32811360.23552445X-RAY DIFFRACTION94.4
2.98-3.140.2671490.24692488X-RAY DIFFRACTION94.11
3.14-3.330.30361440.21992372X-RAY DIFFRACTION92.43
3.33-3.590.29131410.20542385X-RAY DIFFRACTION92.53
3.59-3.950.25691340.1932360X-RAY DIFFRACTION89.78
3.95-4.520.24221370.16942315X-RAY DIFFRACTION90.15
4.52-5.70.23591430.18712448X-RAY DIFFRACTION93.74
5.7-100.20291410.19292446X-RAY DIFFRACTION94.42

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