3ZCJ | pdb_00003zcj

Crystal structure of Helicobacter pylori T4SS protein CagL in a tetragonal crystal form with a helical RGD-motif (6 Mol per ASU)

PDB DOI: https://doi.org/10.2210/pdb3ZCJ/pdb

Classification: PROTEIN BINDING
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-11-20 Released: 2013-10-09
Deposition Author(s): Barden, S., Niemann, H.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free:
0.251 (Depositor), 0.248 (DCC)
R-Value Work:
0.205 (Depositor), 0.199 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

A Helical Rgd Motif Promoting Cell Adhesion: Crystal Structures of the Helicobacter Pylori Type Iv Secretion System Pilus Protein Cagl

Barden, S., Lange, S., Tegtmeyer, N., Conradi, J., Sewald, N., Backert, S., Niemann, H.H.

(2013) Structure 21: 1931

PubMed: 24076404 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2013.08.018
Primary Citation Related Structures:
3ZCI, 3ZCJ

PubMed Abstract:
RGD tripeptide motifs frequently mediate ligand binding to integrins. The type IV secretion system (T4SS) protein CagL of the gastric pathogen Helicobacter pylori also contains an RGD motif. CagL decorates the T4SS pilus and may function as an adhesin for host cells. Whether CagL binds integrins via its RGD motif is under debate. Here, we present crystal structures of CagL revealing an elongated four-helix bundle that appears evolutionarily unrelated to the proposed VirB5 orthologs. The RGD motif is surface-exposed but located within a long α helix. This is unprecedented as previously characterized integrin-binding RGD motifs are located within extended or flexible loops. Yet, adhesion of gastric epithelial cells to CagL was strictly RGD-dependent. Comparison of seven crystallographically independent molecules reveals substantial structural flexibility. Intramolecular disulfide bonds engineered to reduce CagL flexibility resulted in more stable protein, but unable to support cell adhesion. CagL may thus partly unfold during receptor binding.

Organizational Affiliation

Structural Biochemistry, Department of Chemistry, Bielefeld University, 33501 Bielefeld, Germany.

Macromolecule Content

Total Structure Weight: 153.93 kDa
Atom Count: 9,442
Modeled Residue Count: 1,142
Deposited Residue Count: 1,320
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAGL	A, B, C, D, E A, B, C, D, E, F	220	Helicobacter pylori 26695	Mutation(s): 0
UniProt
Find proteins for O25272 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25272 Go to UniProtKB: O25272
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O25272
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain R [auth F] MOL2 format, chain L [auth B] MOL2 format, chain R [auth F] mmCIF format, chain L [auth B] mmCIF format, chain R [auth F]	L [auth B], R [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain L [auth B] Focus chain R [auth F] Interactions & Density Focus chain L [auth B] Focus chain R [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain N [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain N [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain N [auth D]	H [auth A] I [auth A] J [auth B] K [auth B] M [auth C] H [auth A], I [auth A], J [auth B], K [auth B], M [auth C], N [auth D], P [auth E], Q [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D] mmCIF format, chain O [auth D]	O [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain O [auth D] Interactions & Density Focus chain O [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.251 (Depositor), 0.248 (DCC)
R-Value Work: 0.205 (Depositor), 0.199 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 197.122	α = 90
b = 197.122	β = 90
c = 106.808	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-10-09

Deposition Author(s):

Barden, S.

Niemann, H.H.

Revision History (Full details and data files)

Version 1.0: 2013-10-09
Type: Initial release
Version 1.1: 2013-11-27
Changes: Database references
Version 1.2: 2019-03-06
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.3: 2019-09-25
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description