4CCG | pdb_00004ccg

Structure of an E2-E3 complex

PDB DOI: https://doi.org/10.2210/pdb4CCG/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-10-22 Released: 2014-01-08
Deposition Author(s): Hodson, C., Purkiss, A., Walden, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.248 (Depositor), 0.260 (DCC)
R-Value Work:
0.212 (Depositor), 0.227 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of the Human Fancl Ring-Ube2T Complex Reveals Determinants of Cognate E3-E2 Selection.

Hodson, C., Purkiss, A., Miles, J.A., Walden, H.

(2014) Structure 22: 337

PubMed: 24389026 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2013.12.004
Primary Citation Related Structures:
4CCG

PubMed Abstract:
The combination of an E2 ubiquitin-conjugating enzyme with an E3 ubiquitin-ligase is essential for ubiquitin modification of a substrate. Moreover, the pairing dictates both the substrate choice and the modification type. The molecular details of generic E3-E2 interactions are well established. Nevertheless, the determinants of selective, specific E3-E2 recognition are not understood. There are ∼40 E2s and ∼600 E3s giving rise to a possible ∼24,000 E3-E2 pairs. Using the Fanconi Anemia pathway exclusive E3-E2 pair, FANCL-Ube2T, we report the atomic structure of the FANCL RING-Ube2T complex, revealing a specific and extensive network of additional electrostatic and hydrophobic interactions. Furthermore, we show that these specific interactions are required for selection of Ube2T over other E2s by FANCL.

Organizational Affiliation

Protein Structure and Function Laboratory, Lincoln's Inn Fields Laboratories of the London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.

Macromolecule Content

Total Structure Weight: 69.55 kDa
Atom Count: 3,704
Modeled Residue Count: 446
Deposited Residue Count: 600
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN-CONJUGATING ENZYME E2 T	A, B	212	Homo sapiens	Mutation(s): 0 EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPD8 (Homo sapiens) Explore Q9NPD8 Go to UniProtKB: Q9NPD8
PHAROS: Q9NPD8 GTEx: ENSG00000077152
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NPD8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 UBIQUITIN-PROTEIN LIGASE FANCL	C [auth X], D [auth Y]	88	Homo sapiens	Mutation(s): 0 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NW38 (Homo sapiens) Explore Q9NW38 Go to UniProtKB: Q9NW38
PHAROS: Q9NW38 GTEx: ENSG00000115392
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NW38
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth Y] SDF format, chain I [auth A] MOL2 format, chain S [auth Y] MOL2 format, chain I [auth A] mmCIF format, chain S [auth Y] mmCIF format, chain I [auth A]	I [auth A], S [auth Y]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain S [auth Y] Interactions & Density Focus chain I [auth A] Focus chain S [auth Y]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth X] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain O [auth X] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain O [auth X] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], K [auth B], O [auth X]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth X] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth X]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain R [auth Y] SDF format, chain Q [auth Y] SDF format, chain N [auth X] SDF format, chain M [auth X] MOL2 format, chain R [auth Y] MOL2 format, chain Q [auth Y] MOL2 format, chain N [auth X] MOL2 format, chain M [auth X] mmCIF format, chain R [auth Y] mmCIF format, chain Q [auth Y] mmCIF format, chain N [auth X] mmCIF format, chain M [auth X]	M [auth X], N [auth X], Q [auth Y], R [auth Y]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth X] Focus chain N [auth X] Focus chain Q [auth Y] Focus chain R [auth Y] Interactions & Density Focus chain M [auth X] Focus chain N [auth X] Focus chain Q [auth Y] Focus chain R [auth Y]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain P [auth X] MOL2 format, chain P [auth X] mmCIF format, chain P [auth X]	P [auth X]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain P [auth X] Interactions & Density Focus chain P [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.248 (Depositor), 0.260 (DCC)
R-Value Work: 0.212 (Depositor), 0.227 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.224	α = 90
b = 109.224	β = 90
c = 117.728	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-01-08

Deposition Author(s):

Hodson, C.

Purkiss, A.

Walden, H.

Revision History (Full details and data files)

Version 1.0: 2014-01-08
Type: Initial release
Version 1.1: 2014-01-15
Changes: Database references
Version 1.2: 2014-02-19
Changes: Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description