4XRP

Structure of the Pnkp1/Rnl/Hen1 RNA repair complex

PDB DOI: https://doi.org/10.2210/pdb4XRP/pdb

Classification: PROTEIN BINDING
Organism(s): Capnocytophaga gingivalis ATCC 33624
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-01-21 Released: 2015-04-22
Deposition Author(s): Huang, R.H., Wang, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.238
R-Value Work: 0.175
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

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

Literature

Reconstitution and structure of a bacterial Pnkp1-Rnl-Hen1 RNA repair complex.

Wang, P., Selvadurai, K., Huang, R.H.

(2015) Nat Commun 6: 6876-6876

PubMed: 25882814 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/ncomms7876
Primary Citation of Related Structures:
4XRP, 4XRU

PubMed Abstract:
Ribotoxins cleave essential RNAs for cell killing, and RNA repair neutralizes the damage inflicted by ribotoxins for cell survival. Here we report a new bacterial RNA repair complex that performs RNA repair linked to immunity. This new RNA repair complex is a 270-kDa heterohexamer composed of three proteins-Pnkp1, Rnl and Hen1-that are required to repair ribotoxin-cleaved RNA in vitro. The crystal structure of the complex reveals the molecular architecture of the heterohexamer as two rhomboid-shaped ring structures of Pnkp1-Rnl-Hen1 heterotrimer fused at the Pnkp1 dimer interface. The four active sites required for RNA repair are located on the inner rim of each ring. The architecture and the locations of the active sites of the Pnkp1-Rnl-Hen1 heterohexamer suggest an ordered series of repair reactions at the broken RNA ends that confer immunity to recurrent damage.

Organizational Affiliation

Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.

Macromolecule Content

Total Structure Weight: 270.4 kDa
Atom Count: 18,888
Modelled Residue Count: 2,255
Deposited Residue Count: 2,284
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pnkp1	A, D	312	Capnocytophaga gingivalis ATCC 33624	Mutation(s): 0 Gene Names: CAPGI0001_2485
UniProt
Find proteins for C2M8N3 (Capnocytophaga gingivalis) Explore C2M8N3 Go to UniProtKB: C2M8N3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C2M8N3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rnl	B, E	394	Capnocytophaga gingivalis ATCC 33624	Mutation(s): 0 Gene Names: CAPGI0001_2487
UniProt
Find proteins for C2M8N4 (Capnocytophaga gingivalis) Explore C2M8N4 Go to UniProtKB: C2M8N4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C2M8N4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hen1	C, F	436	Capnocytophaga gingivalis ATCC 33624	Mutation(s): 0 Gene Names: CAPGI0001_1566
UniProt
Find proteins for C2M7I7 (Capnocytophaga gingivalis) Explore C2M7I7 Go to UniProtKB: C2M7I7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C2M7I7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F]	I [auth A] J [auth A] M [auth B] O [auth C] U [auth E] I [auth A], J [auth A], M [auth B], O [auth C], U [auth E], V [auth E], W [auth F], X [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain S [auth D]	G [auth A], S [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain S [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain Y [auth F] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Y [auth F]	N [auth B], P [auth C], Q [auth C], R [auth C], Y [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain Y [auth F] Interactions & Density Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain Y [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain T [auth D]	H [auth A], K [auth B], L [auth B], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.238
R-Value Work: 0.175
R-Value Observed: 0.177
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.16	α = 90
b = 179.201	β = 103.7
c = 114.333	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-04-22

Deposition Author(s):

Huang, R.H.

Wang, P.

Revision History (Full details and data files)

Version 1.0: 2015-04-22
Type: Initial release
Version 1.1: 2015-04-29
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy

Prepare Data

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Deposit Data

Help and Resources

4XRP

Structure of the Pnkp1/Rnl/Hen1 RNA repair complex

Reconstitution and structure of a bacterial Pnkp1-Rnl-Hen1 RNA repair complex.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)