8S5T

Structure of SemD in complex

• PDB DOI: https://doi.org/10.2210/pdb8S5T/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Chlamydia, Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-25 Released: 2024-08-07 
• Deposition Author(s): Kocher, F., Applegate, V., Port, A., Reiners, J., Spona, D., Haensch, S., Smits, S.H., Hegemann, J., Moelleken, K.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.237 
• R-Value Work: 0.190 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Structure of SemD in complex

Kocher, F., Applegate, V., Port, A., Reiners, J., Spona, D., Haensch, S., Smits, S.H., Hegemann, J., Moelleken, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 45.68 kDa 
• Atom Count: 2,617 
• Modelled Residue Count: 336 
• Deposited Residue Count: 419 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Effector SemD	A [auth D]	326	Chlamydia	Mutation(s): 0  Gene Names:  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
UniProt
Find proteins for Q9Z7M7 (Chlamydia pneumoniae) Explore Q9Z7M7  Go to UniProtKB:  Q9Z7M7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neural Wiskott-Aldrich syndrome protein	B [auth A]	93	Rattus norvegicus	Mutation(s): 0  Gene Names: WASL
UniProt
Find proteins for A0A6P6IA87 (Puma concolor) Explore A0A6P6IA87  Go to UniProtKB:  A0A6P6IA87

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.237 
• R-Value Work: 0.190 
• R-Value Observed: 0.195 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.222	α = 90
b = 120.222	β = 90
c = 65.241	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Kocher, F., Applegate, V., Port, A., Reiners, J., Spona, D., Haensch, S., Smits, S.H., Hegemann, J., Moelleken, K.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	417919780
German Research Foundation (DFG)	Germany	267205415

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release