5FB7 | pdb_00005fb7

Ligand binding domain 2 of Penicillium marneffei MP1 protein complexed with multiple arachidonic acids

• PDB DOI: https://doi.org/10.2210/pdb5FB7/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Talaromyces marneffei PM1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2015-12-14 Released: 2016-12-14 
• Deposition Author(s): Lam, W.H., Zhang, H., Hao, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Talaromyces marneffei Mp1p Is a Virulence Factor that Binds and Sequesters a Key Proinflammatory Lipid to Dampen Host Innate Immune Response

Sze, K.H., Lam, W.H., Zhang, H., Ke, Y.H., Tse, M.K., Woo, P.C., Lau, S.K., Lau, C.C., Cai, J.P., Tung, E.T., Lo, R.K., Xu, S., Kao, R.Y., Hao, Q., Yuen, K.Y.

(2017) Cell Chem Biol 24: 182-194

• PubMed: 28111099 
• DOI: https://doi.org/10.1016/j.chembiol.2016.12.014
• Primary Citation Related Structures: 
  5CSD, 5FB7


• PubMed Abstract: 
  

  Talaromyces (Penicillium) marneffei is one of the leading causes of systemic mycosis in immunosuppressed or AIDS patients in Southeast Asia. How this intracellular pathogen evades the host immune defense remains unclear. We provide evidence that T. marneffei depletes levels of a key proinflammatory lipid mediator arachidonic acid (AA) to evade the host innate immune defense. Mechanistically, an abundant secretory mannoprotein Mp1p, shown previously to be a virulence factor, does so by binding AA with high affinity via a long hydrophobic central cavity found in the LBD2 domain. This sequesters a critical proinflammatory signaling lipid, and we see evidence that AA, AA's downstream metabolites, and the cytokines interleukin-6 and tumor necrosis factor α are downregulated in T. marneffei-infected J774 macrophages. Given that Mp1p-LBD2 homologs are identified in other fungal pathogens, we expect that this novel class of fatty-acid-binding proteins sequestering key proinflammatory lipid mediators represents a general virulence mechanism of pathogenic fungi.

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Organizational Affiliation: 
• State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China; Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, China.
School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China; Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen 518000, China.
School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China; Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen 518000, China; Department of Biology, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen 518055, China.
State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China.
State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China; Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, China. Electronic address: [e-mail].
School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China; Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen 518000, China. Electronic address: [e-mail].
State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China; Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.84 kDa 
• Atom Count: 5,317 
• Modeled Residue Count: 612 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein	A, B, C, D	155	Talaromyces marneffei PM1	Mutation(s): 0  Gene Names: GQ26_0022220 Membrane Entity: Yes
UniProt
Find proteins for A0A093VKV7 (Talaromyces marneffei PM1) Explore A0A093VKV7  Go to UniProtKB:  A0A093VKV7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACD	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	ARACHIDONIC ACID C20 H32 O2 YZXBAPSDXZZRGB-DOFZRALJSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ACD	BindingDB:  5FB7	ΔG: min: -6.07e+1, max: 26.98 (kJ/mol) from 12 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.239	α = 90
b = 98.495	β = 90.01
c = 100.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Lam, W.H., Zhang, H., Hao, Q.

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2017-02-01
  Changes: Database references
• Version 1.2: 2017-03-08
  Changes: Database references
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description