5JNB | pdb_00005jnb

structure of GLD-2/RNP-8 complex

PDB DOI: https://doi.org/10.2210/pdb5JNB/pdb

Classification: TRANSFERASE
Organism(s): Caenorhabditis elegans
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2016-04-29 Released: 2016-06-22
Deposition Author(s): Nakel, K., Bonneau, F., Basquin, C., Eckmann, C.R., Conti, E.
Funding Organization(s): German Research Foundation, European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.242 (Depositor), 0.244 (DCC)
R-Value Work:
0.192 (Depositor), 0.198 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structural basis for the antagonistic roles of RNP-8 and GLD-3 in GLD-2 poly(A)-polymerase activity.

Nakel, K., Bonneau, F., Basquin, C., Habermann, B., Eckmann, C.R., Conti, E.

(2016) RNA 22: 1139-1145

PubMed: 27288313 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1261/rna.056598.116
Primary Citation Related Structures:
5JNB

PubMed Abstract:
Cytoplasmic polyadenylation drives the translational activation of specific mRNAs in early metazoan development and is performed by distinct complexes that share the same catalytic poly(A)-polymerase subunit, GLD-2. The activity and specificity of GLD-2 depend on its binding partners. In Caenorhabditis elegans, GLD-2 promotes spermatogenesis when bound to GLD-3 and oogenesis when bound to RNP-8. GLD-3 and RNP-8 antagonize each other and compete for GLD-2 binding. Following up on our previous mechanistic studies of GLD-2-GLD-3, we report here the 2.5 Å resolution structure and biochemical characterization of a GLD-2-RNP-8 core complex. In the structure, RNP-8 embraces the poly(A)-polymerase, docking onto several conserved hydrophobic hotspots present on the GLD-2 surface. RNP-8 stabilizes GLD-2 and indirectly stimulates polyadenylation. RNP-8 has a different amino-acid sequence and structure as compared to GLD-3. Yet, it binds the same surfaces of GLD-2 by forming alternative interactions, rationalizing the remarkable versatility of GLD-2 complexes.

Organizational Affiliation

Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany.

Macromolecule Content

Total Structure Weight: 189.73 kDa
Atom Count: 10,776
Modeled Residue Count: 1,350
Deposited Residue Count: 1,648
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(A) RNA polymerase gld-2	A, B, C, D	338	Caenorhabditis elegans	Mutation(s): 1 Gene Names: gld-2, ZC308.1 EC: 2.7.7.19
UniProt
Find proteins for O17087 (Caenorhabditis elegans) Explore O17087 Go to UniProtKB: O17087
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O17087
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNP (RRM RNA binding domain) containing	E, F, G, H	74	Caenorhabditis elegans	Mutation(s): 0 Gene Names: rnp-8, CELE_R119.7, R119.7
UniProt
Find proteins for O61711 (Caenorhabditis elegans) Explore O61711 Go to UniProtKB: O61711
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O61711
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain I [auth A] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A]	I [auth A], N [auth B], S [auth C], V [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain V [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain W [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain W [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A] L [auth A] M [auth A] O [auth B] P [auth B] K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], T [auth C], U [auth C], W [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain J [auth A]	J [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.242 (Depositor), 0.244 (DCC)
R-Value Work: 0.192 (Depositor), 0.198 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.347	α = 89.88
b = 86.435	β = 93.13
c = 91.907	γ = 90.22

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-06-22

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB646
German Research Foundation	Germany	SFB1035
German Research Foundation	Germany	GRK1721
German Research Foundation	Germany	FOR1680
European Commission	Germany	ERC Advanced Investigator Grant 294371
European Commission	Germany	Marie Curie ITN RNPnet
German Research Foundation	Germany	EC369/3-1
German Research Foundation	Germany	GRK1591
German Research Foundation	Germany	BU2451/1-2

Revision History (Full details and data files)

Version 1.0: 2016-06-22
Type: Initial release
Version 1.1: 2016-07-06
Changes: Data collection
Version 1.2: 2016-07-27
Changes: Database references
Version 1.3: 2017-09-06
Changes: Author supporting evidence
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Refinement description