3CI0 | pdb_00003ci0

The Crystal Structure of the GspK-GspI-GspJ complex from enterotoxigenic Escherichia coli Type 2 Secretion System

PDB DOI: https://doi.org/10.2210/pdb3CI0/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-03-10 Released: 2008-04-29
Deposition Author(s): Korotkov, K.V., Hol, W.G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.259 (Depositor)
R-Value Work:
0.192 (Depositor), 0.204 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of the GspK-GspI-GspJ complex from the enterotoxigenic Escherichia coli type 2 secretion system.

Korotkov, K.V., Hol, W.G.

(2008) Nat Struct Mol Biol 15: 462-468

PubMed: 18438417 Search on PubMed
DOI: https://doi.org/10.1038/nsmb.1426
Primary Citation of Related Structures:
3CI0

PubMed Abstract:
Gram-negative bacteria translocate various proteins including virulence factors across their outer membrane via type 2 secretion systems (T2SSs). T2SSs are thought to contain a pseudopilus, a subcomplex formed by one major and several minor pseudopilins. We report the crystal structure of the complex formed by three minor pseudopilins from enterotoxigenic Escherichia coli. The GspK-GspI-GspJ complex has quasihelical characteristics and an architecture consistent with a localization at the pseudopilus tip. The alpha-domain of GspK has a previously unobserved fold with an unexpected dinuclear metal binding site. The area surrounding its disulfide bridge is conserved and might interact with other T2SS components or with secreted proteins.

Organizational Affiliation

Department of Biochemistry, Biomolecular Structure Center, University of Washington, Box 357742, Seattle, Washington 98195, USA.

Macromolecule Content

Total Structure Weight: 62.64 kDa
Atom Count: 4,302
Modeled Residue Count: 517
Deposited Residue Count: 550
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudopilin GspI	A [auth I]	89	Escherichia coli	Mutation(s): 0 Gene Names: gspI
UniProt
Find proteins for Q8VPC3 (Escherichia coli) Explore Q8VPC3 Go to UniProtKB: Q8VPC3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VPC3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudopilin GspJ	B [auth J]	163	Escherichia coli	Mutation(s): 0 Gene Names: gspJ
UniProt
Find proteins for A0A4C3GMC1 (Escherichia coli) Explore A0A4C3GMC1 Go to UniProtKB: A0A4C3GMC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4C3GMC1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudopilin GspK	C [auth K]	298	Escherichia coli	Mutation(s): 0 Gene Names: gspK
UniProt
Find proteins for Q8VLK7 (Escherichia coli) Explore Q8VLK7 Go to UniProtKB: Q8VLK7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VLK7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth K] SDF format, chain F [auth K] SDF format, chain E [auth I] MOL2 format, chain G [auth K] MOL2 format, chain F [auth K] MOL2 format, chain E [auth I] mmCIF format, chain G [auth K] mmCIF format, chain F [auth K] mmCIF format, chain E [auth I]	E [auth I], F [auth K], G [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth I] Focus chain F [auth K] Focus chain G [auth K] Interactions & Density Focus chain E [auth I] Focus chain F [auth K] Focus chain G [auth K]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth I] MOL2 format, chain D [auth I] mmCIF format, chain D [auth I]	D [auth I]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth I] Interactions & Density Focus chain D [auth I]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A [auth I]	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: 0.259 (Depositor)
R-Value Work: 0.192 (Depositor), 0.204 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.118	α = 90
b = 96.118	β = 90
c = 108.436	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-04-29

Deposition Author(s):

Korotkov, K.V.

Hol, W.G.J.

Revision History (Full details and data files)

Version 1.0: 2008-04-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary