1RH4 | pdb_00001rh4

RH4 DESIGNED RIGHT-HANDED COILED COIL TETRAMER

• PDB DOI: https://doi.org/10.2210/pdb1RH4/pdb

• Classification: COILED COIL
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 1998-10-07 Released: 1998-12-02 
• Deposition Author(s): Harbury, P.B., Plecs, J.J., Tidor, B., Alber, T., Kim, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.248 (Depositor) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: in silico

Literature

High-resolution protein design with backbone freedom.

Harbury, P.B., Plecs, J.J., Tidor, B., Alber, T., Kim, P.S.

(1998) Science 282: 1462-1467

• PubMed: 9822371 
• DOI: https://doi.org/10.1126/science.282.5393.1462
• Primary Citation of Related Structures:  
  1RH4


• PubMed Abstract: 
  

  Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of alpha-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form alpha-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.

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Organizational Affiliation: 
• Whitehead Institute for Biomedical Research, Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 3.82 kDa 
• Atom Count: 277 
• Modeled Residue Count: 35 
• Deposited Residue Count: 35 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIGHT-HANDED COILED COIL TETRAMER	A	35	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	B [auth A], C [auth A], D [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
IIL	A	L-PEPTIDE LINKING	C6 H13 N O2		ILE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.248 (Depositor) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.556	α = 90
b = 37.556	β = 90
c = 53.384	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data reduction
R-AXIS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-12-02 
Deposition Author(s): Harbury, P.B., Plecs, J.J., Tidor, B., Alber, T., Kim, P.S.

Revision History  

• Version 1.0: 1998-12-02
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary