2GSK | pdb_00002gsk

Structure of the BtuB:TonB Complex

PDB DOI: https://doi.org/10.2210/pdb2GSK/pdb

Classification: SIGNALING PROTEIN/MEMBRANE PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli, Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2006-04-26 Released: 2006-06-13
Deposition Author(s): Shultis, D.D., Purdy, M.P., Banchs, C.N., Wiener, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.251 (Depositor), 0.252 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Outer membrane active transport: structure of the BtuB:TonB complex

Shultis, D.D., Purdy, M.D., Banchs, C.N., Wiener, M.C.

(2006) Science 312: 1396-1399

PubMed: 16741124 Search on PubMed
DOI: https://doi.org/10.1126/science.1127694
Primary Citation Related Structures:
2GSK

PubMed Abstract:
In Gram-negative bacteria, the import of essential micronutrients across the outer membrane requires a transporter, an electrochemical gradient of protons across the inner membrane, and an inner membrane protein complex (ExbB, ExbD, TonB) that couples the proton-motive force to the outer membrane transporter. The inner membrane protein TonB binds directly to a conserved region, called the Ton-box, of the transporter. We solved the structure of the cobalamin transporter BtuB in complex with the C-terminal domain of TonB. In contrast to its conformations in the absence of TonB, the Ton-box forms a beta strand that is recruited to the existing beta sheet of TonB, which is consistent with a mechanical pulling model of transport.

Organizational Affiliation

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.

Macromolecule Content

Total Structure Weight: 78.07 kDa
Atom Count: 5,658
Modeled Residue Count: 671
Deposited Residue Count: 671
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin B12 transporter btuB	A	590	Escherichia coli	Mutation(s): 0 Gene Names: btuB, bfe, cer, dcrC Membrane Entity: Yes
UniProt
Find proteins for P06129 (Escherichia coli (strain K12)) Explore P06129 Go to UniProtKB: P06129
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06129
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
protein TONB	B	81	Escherichia coli	Mutation(s): 0 Gene Names: tonB, exbA Membrane Entity: Yes
UniProt
Find proteins for P02929 (Escherichia coli (strain K12)) Explore P02929 Go to UniProtKB: P02929
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02929
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CNC Query on CNC Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CYANOCOBALAMIN C₆₃ H₈₉ Co N₁₄ O₁₄ P SYZBZQWSWIJYAR-UVKKECPRSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
LDA Query on LDA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	J [auth A], K [auth A], L [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
HEX Query on HEX Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A], N [auth A]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.251 (Depositor), 0.252 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.34	α = 90
b = 82.439	β = 90
c = 122.632	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SERGUI	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-06-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-06-13
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2017-11-01
Changes: Refinement description
Version 2.0: 2021-08-18
Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Refinement description