2QUX

PP7 coat protein dimer in complex with RNA hairpin

PDB DOI: https://doi.org/10.2210/pdb2QUX/pdb
NAKB: 2QUX

Classification: Structural PROTEIN/RNA
Organism(s): Pseudomonas phage PP7
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-08-06 Released: 2007-12-18
Deposition Author(s): Chao, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.236
R-Value Work: 0.175
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural basis for the coevolution of a viral RNA-protein complex.

Chao, J.A., Patskovsky, Y., Almo, S.C., Singer, R.H.

(2008) Nat Struct Mol Biol 15: 103-105

PubMed: 18066080 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nsmb1327
Primary Citation of Related Structures:
2QUD, 2QUX

PubMed Abstract:
The cocrystal structure of the PP7 bacteriophage coat protein in complex with its translational operator identifies a distinct mode of sequence-specific RNA recognition when compared to the well-characterized MS2 coat protein-RNA complex. The structure reveals the molecular basis of the PP7 coat protein's ability to selectively bind its cognate RNA, and it demonstrates that the conserved beta-sheet surface is a flexible architecture that can evolve to recognize diverse RNA hairpins.

Organizational Affiliation

Department of Anatomy, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York 10461, USA.

Macromolecule Content

Total Structure Weight: 213.1 kDa
Atom Count: 15,026
Modelled Residue Count: 1,602
Deposited Residue Count: 1,650
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein	G [auth A] H [auth B] I [auth D] J [auth E] K [auth G] G [auth A], H [auth B], I [auth D], J [auth E], K [auth G], L [auth H], M [auth J], N [auth K], O [auth M], P [auth N], Q [auth P], R [auth Q]	125	Pseudomonas phage PP7	Mutation(s): 0 Gene Names: PP7 coat protein
UniProt
Find proteins for P03630 (Pseudomonas phage PP7) Explore P03630 Go to UniProtKB: P03630
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03630
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (25-MER)	A [auth C] B [auth F] C [auth I] D [auth L] E [auth O] A [auth C], B [auth F], C [auth I], D [auth L], E [auth O], F [auth R]	25	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth E] SDF format, chain CA [auth G] SDF format, chain DA [auth H] SDF format, chain EA [auth J] SDF format, chain FA [auth J] SDF format, chain GA [auth K] SDF format, chain S [auth I] SDF format, chain T [auth L] SDF format, chain U [auth R] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth J] MOL2 format, chain FA [auth J] MOL2 format, chain GA [auth K] MOL2 format, chain S [auth I] MOL2 format, chain T [auth L] MOL2 format, chain U [auth R] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth E] CA [auth G] DA [auth H] EA [auth J] AA [auth D], BA [auth E], CA [auth G], DA [auth H], EA [auth J], FA [auth J], GA [auth K], S [auth I], T [auth L], U [auth R], V [auth A], W [auth A], X [auth B], Y [auth B], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth E] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth J] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain S [auth I] Focus chain T [auth L] Focus chain U [auth R] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth E] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth J] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain S [auth I] Focus chain T [auth L] Focus chain U [auth R] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.236
R-Value Work: 0.175
R-Value Observed: 0.177
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.97	α = 90
b = 145.388	β = 122.94
c = 109.655	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-12-18

Deposition Author(s):

Chao, J.A.

Revision History (Full details and data files)

Version 1.0: 2007-12-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-08-02
Changes: Refinement description, Source and taxonomy
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

2QUX

PP7 coat protein dimer in complex with RNA hairpin

Structural basis for the coevolution of a viral RNA-protein complex.

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Expand