1JOH | pdb_00001joh

THE STRUCTURE OF ANTIAMOEBIN I, A MEMBRANE-ACTIVE PEPTIDE

PDB DOI: https://doi.org/10.2210/pdb1JOH/pdb

Classification: ANTIBIOTIC
Organism(s): Emericellopsis
Mutation(s): No

Deposited: 1997-10-11 Released: 1999-01-20
Deposition Author(s): Snook, C.F., Wallace, B.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

Literature

The Structure and Function of Antiamoebin I, a Proline-Rich Membrane-Active Polypeptide.

Snook, C.F., Woolley, G.A., Oliva, G., Pattabhi, V., Wood, S.F., Blundell, T.L., Wallace, B.A.

(1998) Structure 6: 783

PubMed: 9655831 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(98)00079-3
Primary Citation Related Structures:
1JOH

PubMed Abstract:
Antiamoebin is a member of the peptaibol family of polypeptides and has a unique antibiotic activity: it acts as an antiamoebic agent, but does not effectively haemolyze erythrocytes even though it does exhibit membrane-modifying activity. The structure of antiamoebin I has been determined by X-ray crystallography at 1.4 A resolution. The molecule forms a helical structure, which, as a result of the presence of a number of proline and hydroxyproline residues, has a deep bend in the middle. Circular dichroism spectroscopy, single-channel conductance studies and fluorescence diffusion studies suggest a mode of ion transport that is entirely different from that of the other two members of the peptaibol family (alamethicin and zervamicin) whose structures and functions have been examined in detail. The structure of the polypeptide has been determined and a functional model for its mode of action in membranes is presented. Although under some conditions antiamoebin may form ion channels, unlike the closely related alamethicin and zervamicin polypeptides, its major membrane-modifying activity appears to be as an ion carrier.

Organizational Affiliation

Department of Crystallography Birkbeck College University of London London, WC1E 7HX, UK.

Macromolecule Content

Total Structure Weight: 4.05 kDa
Atom Count: 268
Modeled Residue Count: 34
Deposited Residue Count: 34
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIAMOEBIN I	A, B	17	Emericellopsis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MOH Query on MOH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain K [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain K [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain K [auth A] mmCIF format, chain G [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	METHANOL C H₄ O OKKJLVBELUTLKV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB Query on AIB	A, B	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
DIV Query on DIV	A, B	D-PEPTIDE LINKING	C₅ H₁₁ N O₂		--
HYP Query on HYP	A, B	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO
PHL Query on PHL	A, B	L-PEPTIDE LINKING	C₉ H₁₃ N O		PHE

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000161 Query on PRD_000161	A, B	Antiamoebin 1	Peptaibol / Antibiotic		Interactions Focus chain A Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Observed: 0.156 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.53	α = 88.9
b = 28.82	β = 96.64
c = 9.06	γ = 123.85

Software Package:

Software Name	Purpose
SHELXL-93	model building
SHELXL-93	refinement
SHELXL-93	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1999-01-20

Deposition Author(s):

Snook, C.F.

Wallace, B.A.

Revision History (Full details and data files)

Version 1.0: 1999-01-20
Type: Initial release
Version 1.1: 2011-06-14
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-07-27
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
Version 1.4: 2012-12-12
Changes: Other
Version 1.5: 2020-03-04
Changes: Data collection, Derived calculations, Other, Refinement description, Structure summary
Version 1.6: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.7: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary