2R2V

Sequence Determinants of the Topology of the Lac Repressor Tetrameric Coiled Coil

PDB DOI: https://doi.org/10.2210/pdb2R2V/pdb

Classification: DE NOVO PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-08-27 Released: 2008-06-17
Deposition Author(s): Liu, J., Lu, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

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

Literature

Conformational specificity of the lac repressor coiled-coil tetramerization domain.

Liu, J., Zheng, Q., Deng, Y., Li, Q., Kallenbach, N.R., Lu, M.

(2007) Biochemistry 46: 14951-14959

PubMed: 18052214 Search on PubMed
DOI: https://doi.org/10.1021/bi701930d
Primary Citation of Related Structures:
2R2V

PubMed Abstract:
Predictive understanding of how the folded, functional shape of a native protein is encoded in the linear sequence of its amino acid residues remains an unsolved challenge in modern structural biology. Antiparallel four-stranded coiled coils are relatively simple protein structures that embody a heptad sequence repeat and rich diversity for tertiary packing of alpha-helices. To explore specific sequence determinants of the lac repressor coiled-coil tetramerization domain, we have engineered a set of buried nonpolar side chains at the a-, d-, and e-positions into the hydrophobic interior of the dimeric GCN4 leucine zipper. Circular dichroism and equilibrium ultracentrifugation studies show that this core variant (GCN4-pAeLV) forms a stable tetrameric structure with a reversible and highly cooperative thermal unfolding transition. The X-ray crystal structure at 1.9 A reveals that GCN4-pAeLV is an antiparallel four-stranded coiled coil of the lac repressor type in which the a, d, and e side chains associate by means of combined knobs-against-knobs and knobs-into-holes packing with a characteristic interhelical offset of 0.25 heptad. Comparison of the side chain shape and packing in the antiparallel tetramers shows that the burial of alanine residues at the e positions between the neighboring helices of GCN4-pAeLV dictates both the antiparallel orientation and helix offset. This study fills in a gap in our knowledge of the determinants of structural specificity in antiparallel coiled coils and improves our understanding of how specific side chain packing forms the teritiary structure of a functional protein.

Organizational Affiliation

Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA.

Macromolecule Content

Total Structure Weight: 32.07 kDa
Atom Count: 2,210
Modelled Residue Count: 259
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN4 leucine zipper	A, B, C, D, E A, B, C, D, E, F, G, H	34	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: GCN4, AAS3, ARG9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain O [auth D] SDF format, chain P [auth G] SDF format, chain Q [auth G] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G]	K [auth C], O [auth D], P [auth G], Q [auth G]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain O [auth D] Focus chain P [auth G] Focus chain Q [auth G] Interactions & Density Focus chain K [auth C] Focus chain O [auth D] Focus chain P [auth G] Focus chain Q [auth G]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain L [auth D] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D]	I [auth C], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain I [auth C] Focus chain L [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D]	J [auth C], M [auth D], N [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.696	α = 90
b = 51.696	β = 90
c = 99.793	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-06-17

Deposition Author(s):

Liu, J.

Lu, M.

Revision History (Full details and data files)

Version 1.0: 2008-06-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description