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- PDB-8s5t: Structure of SemD in complex -

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Basic information

Entry
Database: PDB / ID: 8s5t
TitleStructure of SemD in complex
Components
  • Effector SemD
  • Neural Wiskott-Aldrich syndrome protein
KeywordsENDOCYTOSIS / effector protein
Function / homology
Function and homology information


regulation of Rho protein signal transduction / phagocytosis / actin filament organization / small GTPase binding / regulation of cell shape / cytoskeleton / plasma membrane / cytoplasm
Similarity search - Function
CDC42 small effector protein / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. ...CDC42 small effector protein / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / PH-like domain superfamily
Similarity search - Domain/homology
Neural Wiskott-Aldrich syndrome protein / Uncharacterized protein
Similarity search - Component
Biological speciesChlamydia (bacteria)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKocher, F. / Applegate, V. / Port, A. / Reiners, J. / 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: To Be Published
Title: Structure of SemD in complex
Authors: Kocher, F. / Applegate, V. / Port, A. / Reiners, J. / Spona, D. / Haensch, S. / Smits, S.H. / Hegemann, J. / Moelleken, K.
History
DepositionFeb 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Effector SemD
A: Neural Wiskott-Aldrich syndrome protein


Theoretical massNumber of molelcules
Total (without water)45,6822
Polymers45,6822
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-12 kcal/mol
Surface area17700 Å2
Unit cell
Length a, b, c (Å)120.222, 120.222, 65.241
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Effector SemD


Mass: 35046.117 Da / Num. of mol.: 1
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: Protein Neural Wiskott-Aldrich syndrome protein


Mass: 10635.929 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: WASL / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6P6IA87

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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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium formate, 0.1 M MES (pH 6.2), 25% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 3.3→55.28 Å / Num. obs: 15861 / % possible obs: 99.6 % / Redundancy: 20 % / Biso Wilson estimate: 92.85 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.32
Reflection shellResolution: 3.3→3.418 Å / Mean I/σ(I) obs: 3.4 / Num. unique obs: 852 / CC1/2: 0.922

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→55.28 Å / SU ML: 0.4286 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0797
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2368 1560 9.84 %
Rwork0.19 14301 -
obs0.1946 15861 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.19 Å2
Refinement stepCycle: LAST / Resolution: 3.3→55.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 0 0 2617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01122661
X-RAY DIFFRACTIONf_angle_d1.23483600
X-RAY DIFFRACTIONf_chiral_restr0.0597408
X-RAY DIFFRACTIONf_plane_restr0.0108471
X-RAY DIFFRACTIONf_dihedral_angle_d6.269356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.410.34771400.30831332X-RAY DIFFRACTION99.93
3.41-3.530.31311440.28031291X-RAY DIFFRACTION100
3.53-3.670.35351440.24371276X-RAY DIFFRACTION100
3.67-3.840.26851420.22311319X-RAY DIFFRACTION99.86
3.84-4.040.28171440.2171314X-RAY DIFFRACTION100
4.04-4.290.23141380.1931298X-RAY DIFFRACTION99.93
4.29-4.620.29841460.19181287X-RAY DIFFRACTION100
4.62-5.090.20361400.19161308X-RAY DIFFRACTION100
5.09-5.820.28581410.22161276X-RAY DIFFRACTION99.09
5.83-7.330.18891360.19351314X-RAY DIFFRACTION99.86
7.34-55.280.1671450.11861286X-RAY DIFFRACTION98.89

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