3PG6

The carboxyl terminal domain of human deltex 3-like

PDB DOI: https://doi.org/10.2210/pdb3PG6/pdb

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

Deposited: 2010-10-30 Released: 2010-12-01
Deposition Author(s): Walker, J.R., Obiero, J., Kania, J., Schuler, H., Bountra, C., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.186 (Depositor), 0.200 (DCC)
R-Value Work:
0.165 (Depositor), 0.180 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Fold of the conserved DTC domain in Deltex proteins.

Obiero, J., Walker, J.R., Dhe-Paganon, S.

(2012) Proteins 80: 1495-1499

PubMed: 22411408 Search on PubMed
DOI: https://doi.org/10.1002/prot.24054
Primary Citation of Related Structures:
3PG6

PubMed Abstract:
Human Deltex 3-like (DTX3L) is a member of the Deltex family of proteins. Initially identified as a B-lymphoma and BAL-associated protein, DTX3L is an E3 ligase that regulates subcellular localization of its partner protein, BAL, by a dynamic nucleocytoplasmic trafficking mechanism. Unlike other members of the Deltex family of proteins, DTX3L lacks the highly basic N-terminal motif and the central proline-rich motif present in other Deltex proteins, and instead contains other unique N-terminal domains. The C-terminal domains are, however, homologous with other members of the Deltex family of proteins; these include a RING domain and a previously unidentified C-terminal domain. In this study, we report the high-resolution crystal structure of this previously uncharacterized C-terminal domain of human DTX3L, which we term the Deltex C-terminal domain.

Organizational Affiliation

Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Macromolecule Content

Total Structure Weight: 72.67 kDa
Atom Count: 5,113
Modelled Residue Count: 538
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase DTX3L	A, B, C, D	159	Homo sapiens	Mutation(s): 0 Gene Names: BBAP, DTX3L EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDB6 (Homo sapiens) Explore Q8TDB6 Go to UniProtKB: Q8TDB6
PHAROS: Q8TDB6 GTEx: ENSG00000163840
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8TDB6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C]	E [auth A], H [auth B], K [auth C]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	F [auth A], G [auth B], I [auth B], J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth B] Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.186 (Depositor), 0.200 (DCC)
R-Value Work: 0.165 (Depositor), 0.180 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.323	α = 90
b = 76.146	β = 90
c = 138.753	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-12-01

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-11-28
Changes: Database references
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations