4QDG | pdb_00004qdg

Crystal structure of a putative adhesin (BT2657) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution (PSI Community Target, Nakayama)

• PDB DOI: https://doi.org/10.2210/pdb4QDG/pdb

• Classification: CELL ADHESION
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-13 Released: 2014-06-11 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.215 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

A Distinct Type of Pilus from the Human Microbiome.

Xu, Q., Shoji, M., Shibata, S., Naito, M., Sato, K., Elsliger, M.A., Grant, J.C., Axelrod, H.L., Chiu, H.J., Farr, C.L., Jaroszewski, L., Knuth, M.W., Deacon, A.M., Godzik, A., Lesley, S.A., Curtis, M.A., Nakayama, K., Wilson, I.A.

(2016) Cell 165: 690-703

• PubMed: 27062925 
• DOI: https://doi.org/10.1016/j.cell.2016.03.016
• Primary Citation Related Structures: 
  3LIU, 3PAY, 3R4R, 3SY6, 3T2L, 3UFI, 3UP6, 4DGU, 4EPS, 4GPV, 4H40, 4JG5, 4JRF, 4K4K, 4Q98, 4QB7, 4QDG, 4RDB, 5CAG


• PubMed Abstract: 
  

  Pili are proteinaceous polymers of linked pilins that protrude from the cell surface of many bacteria and often mediate adherence and virulence. We investigated a set of 20 Bacteroidia pilins from the human microbiome whose structures and mechanism of assembly were unknown. Crystal structures and biochemical data revealed a diverse protein superfamily with a common Greek-key β sandwich fold with two transthyretin-like repeats that polymerize into a pilus through a strand-exchange mechanism. The assembly mechanism of the central, structural pilins involves proteinase-assisted removal of their N-terminal β strand, creating an extended hydrophobic groove that binds the C-terminal donor strands of the incoming pilin. Accessory pilins at the tip and base have unique structural features specific to their location, allowing initiation or termination of the assembly. The Bacteroidia pilus, therefore, has a biogenesis mechanism that is distinct from other known pili and likely represents a different type of bacterial pilus.

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Organizational Affiliation: 
• Joint Center for Structural Genomics, http://www.jcsg.org; SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA.
Division of Microbiology and Oral Infection, Department of Molecular Microbiology and Immunology, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan.
Joint Center for Structural Genomics, http://www.jcsg.org; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Joint Center for Structural Genomics, http://www.jcsg.org; Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA.
Joint Center for Structural Genomics, http://www.jcsg.org; Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093, USA; Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
Joint Center for Structural Genomics, http://www.jcsg.org; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA.
Centre for Immunology and Infectious Disease (CIID), Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK.
Division of Microbiology and Oral Infection, Department of Molecular Microbiology and Immunology, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan. Electronic address: [e-mail].
Joint Center for Structural Genomics, http://www.jcsg.org; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.97 kDa 
• Atom Count: 5,316 
• Modeled Residue Count: 602 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative adhesin	A, B	310	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_2657
UniProt
Find proteins for Q8A4E2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A4E2  Go to UniProtKB:  Q8A4E2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], D [auth A], E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.215 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34QDG

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.803	α = 90
b = 102.324	β = 98.35
c = 74.466	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-11 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2014-06-11
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Data collection, Refinement description
• Version 1.2: 2020-04-22
  Changes: Database references, Derived calculations
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary