2K9F | pdb_00002k9f

Structural features of the complex between the DsbD N-terminal and the PilB N-terminal domains from Neisseria meningitidis


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 300 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Formation of the complex between DsbD and PilB N-terminal domains from Neisseria meningitidis necessitates an adaptability of nDsbD.

Quinternet, M.Tsan, P.Selme-Roussel, L.Jacob, C.Boschi-Muller, S.Branlant, G.Cung, M.T.

(2009) Structure 17: 1024-1033

  • DOI: https://doi.org/10.1016/j.str.2009.05.011
  • Primary Citation Related Structures: 
    2K9F

  • PubMed Abstract: 

    DsbD transmembrane protein dispatches electrons to periplasmic Trx/DsbE-like partners via specific interactions with its N-terminal domain, nDsbD. In the present study, PilB N-terminal domain (NterPilB) is shown to efficiently accept electrons coming from nDsbD from Neisseria meningitidis. Using an NMR-driven docking approach, we have modeled the structure of a mixed disulfide complex between NterPilB and nDsbD. We show the needed opening of nDsbD cap-loop whereas NterPilB FLHE loop does not seem essential in the formation and stabilization of the complex. Relaxation analysis performed on backbone amide groups highlights a kind of dynamics transfer from nDsbD cap-loop on NterPilB alpha1 helix, suggesting that a mobility contribution is required not only for the formation of the mixed disulfide complex, but also for its disruption. Taking into account previous X-ray data on covalent complexes involving nDsbD, a cartoon of interactions between Trx-like partners and nDsbD is proposed that illustrates the adaptability of nDsbD.


  • Organizational Affiliation
    • Laboratoire de Chimie Physique Macromoléculaire UMR 7568 CNRS-INPL, Nancy Université, 1 rue Grandville, B.P. 20451, 54001 Nancy Cedex, France.

Macromolecule Content 

  • Total Structure Weight: 30.02 kDa 
  • Atom Count: 2,120 
  • Modeled Residue Count: 272 
  • Deposited Residue Count: 272 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thioredoxin144Neisseria meningitidis serogroup AMutation(s): 0 
Gene Names: msrABpilB
EC: 1.8.4.11 (UniProt), 1.8.4.12 (UniProt)
UniProt
Find proteins for Q9JWM8 (Neisseria meningitidis serogroup A / serotype 4A (strain DSM 15465 / Z2491))
Explore Q9JWM8 
Go to UniProtKB:  Q9JWM8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JWM8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Thiol:disulfide interchange protein dsbD128Neisseria meningitidis serogroup BMutation(s): 1 
Gene Names: dsbD
EC: 1.8.1.8
UniProt
Find proteins for Q9JYM0 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58))
Explore Q9JYM0 
Go to UniProtKB:  Q9JYM0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JYM0
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 300 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary