3ZGI | pdb_00003zgi

Crystal structure of the KRT10-binding region domain of the pneumococcal serine rich repeat protein PsrP

PDB DOI: https://doi.org/10.2210/pdb3ZGI/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-12-17 Released: 2013-12-25
Deposition Author(s): Schulte, T., Loefling, J., Mikaelsson, C., Kikhney, A., Hentrich, K., Diamante, A., Ebel, C., Normark, S., Svergun, D., Henriques-Normark, B., Achour, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.214 (Depositor), 0.221 (DCC)
R-Value Work:
0.186 (Depositor), 0.191 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The Basic Keratin 10-Binding Domain of the Virulence-Associated Pneumococcal Serine-Rich Protein Psrp Adopts a Novel Mscramm Fold.

Schulte, T., Lofling, J., Mikaelsson, C., Kikhney, A., Hentrich, K., Diamante, A., Ebel, C., Normark, S., Svergun, D., Henriques-Normark, B., Achour, A.

(2014) Open Biol 4: 0090

PubMed: 24430336 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1098/rsob.130090
Primary Citation Related Structures:
3ZGH, 3ZGI

PubMed Abstract:
Streptococcus pneumoniae is a major human pathogen, and a leading cause of disease and death worldwide. Pneumococcal invasive disease is triggered by initial asymptomatic colonization of the human upper respiratory tract. The pneumococcal serine-rich repeat protein (PsrP) is a lung-specific virulence factor whose functional binding region (BR) binds to keratin-10 (KRT10) and promotes pneumococcal biofilm formation through self-oligomerization. We present the crystal structure of the KRT10-binding domain of PsrP (BR187-385) determined to 2.0 Å resolution. BR187-385 adopts a novel variant of the DEv-IgG fold, typical for microbial surface components recognizing adhesive matrix molecules adhesins, despite very low sequence identity. An extended β-sheet on one side of the compressed, two-sided barrel presents a basic groove that possibly binds to the acidic helical rod domain of KRT10. Our study also demonstrates the importance of the other side of the barrel, formed by extensive well-ordered loops and stabilized by short β-strands, for interaction with KRT10.

Organizational Affiliation

Science for Life Laboratory, Center for Infectious Medicine (CIM), Department of Medicine, Karolinska University Hospital Huddinge, Karolinska Institutet Science Park, Tomtebodavägen 23A Solna, Stockholm 17165, Sweden.

Macromolecule Content

Total Structure Weight: 67.62 kDa
Atom Count: 4,171
Modeled Residue Count: 522
Deposited Residue Count: 615
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL WALL SURFACE ANCHOR FAMILY PROTEIN	A, B, C	205	Streptococcus pneumoniae TIGR4	Mutation(s): 0
UniProt
Find proteins for A0A0H2URK1 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2URK1 Go to UniProtKB: A0A0H2URK1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2URK1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth B] G [auth B] I [auth C] D [auth A], E [auth A], F [auth B], G [auth B], I [auth C], J [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.214 (Depositor), 0.221 (DCC)
R-Value Work: 0.186 (Depositor), 0.191 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.58	α = 90
b = 105.58	β = 90
c = 120.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
Auto-Rickshaw	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-12-25

Deposition Author(s):

Henriques-Normark, B.

Achour, A.

Revision History (Full details and data files)

Version 1.0: 2013-12-25
Type: Initial release
Version 1.1: 2014-01-29
Changes: Database references
Version 1.2: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Other, Structure summary