2XEW | pdb_00002xew

Crystal structure of K11-linked diubiquitin

PDB DOI: https://doi.org/10.2210/pdb2XEW/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-05-18 Released: 2010-07-14
Deposition Author(s): Bremm, A., Freund, S.M.V., Komander, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.252 (Depositor), 0.249 (DCC)
R-Value Work:
0.205 (Depositor), 0.204 (DCC)
R-Value Observed:
0.207 (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

Lys11-Linked Ubiquitin Chains Adopt Compact Conformations and are Preferentially Hydrolyzed by the Deubiquitinase Cezanne

Bremm, A., Freund, S.M.V., Komander, D.

(2010) Nat Struct Mol Biol 17: 939

PubMed: 20622874 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.1873
Primary Citation Related Structures:
2XEW

PubMed Abstract:
Ubiquitin is a versatile cellular signaling molecule that can form polymers of eight different linkages, and individual linkage types have been associated with distinct cellular functions. Though little is currently known about Lys11-linked ubiquitin chains, recent data indicate that they may be as abundant as Lys48 linkages and may be involved in vital cellular processes. Here we report the generation of Lys11-linked polyubiquitin in vitro, for which the Lys11-specific E2 enzyme UBE2S was fused to a ubiquitin binding domain. Crystallographic and NMR analyses of Lys11-linked diubiquitin reveal that Lys11-linked chains adopt compact conformations in which Ile44 is solvent exposed. Furthermore, we identify the OTU family deubiquitinase Cezanne as the first deubiquitinase with Lys11-linkage preference. Our data highlight the intrinsic specificity of the ubiquitin system that extends to Lys11-linked chains and emphasize that differentially linked polyubiquitin chains must be regarded as independent post-translational modifications.

Organizational Affiliation

Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

Macromolecule Content

Total Structure Weight: 104.6 kDa
Atom Count: 7,921
Modeled Residue Count: 908
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	76	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
PHAROS: P0CG48 GTEx: ENSG00000150991
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG48
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth F]	Y [auth F], Z [auth F]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain Y [auth F] Focus chain Z [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth H] SDF format, chain CA [auth I] SDF format, chain EA [auth J] SDF format, chain FA [auth K] SDF format, chain GA [auth L] SDF format, chain HA [auth L] SDF format, chain IA [auth L] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain Q [auth B] SDF format, chain M [auth A] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain EA [auth J] MOL2 format, chain FA [auth K] MOL2 format, chain GA [auth L] MOL2 format, chain HA [auth L] MOL2 format, chain IA [auth L] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth A] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain EA [auth J] mmCIF format, chain FA [auth K] mmCIF format, chain GA [auth L] mmCIF format, chain HA [auth L] mmCIF format, chain IA [auth L] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth A]	AA [auth F] BA [auth H] CA [auth I] EA [auth J] FA [auth K] AA [auth F], BA [auth H], CA [auth I], EA [auth J], FA [auth K], GA [auth L], HA [auth L], IA [auth L], M [auth A], N [auth A], O [auth A], Q [auth B], R [auth B], S [auth B], T [auth C], V [auth D], X [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain FA [auth K] Focus chain GA [auth L] Focus chain HA [auth L] Focus chain IA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain FA [auth K] Focus chain GA [auth L] Focus chain HA [auth L] Focus chain IA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain X [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth I] SDF format, chain JA [auth L] SDF format, chain KA [auth L] SDF format, chain LA [auth L] SDF format, chain P [auth A] SDF format, chain U [auth C] SDF format, chain W [auth D] MOL2 format, chain DA [auth I] MOL2 format, chain JA [auth L] MOL2 format, chain KA [auth L] MOL2 format, chain LA [auth L] MOL2 format, chain P [auth A] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] mmCIF format, chain DA [auth I] mmCIF format, chain JA [auth L] mmCIF format, chain KA [auth L] mmCIF format, chain LA [auth L] mmCIF format, chain P [auth A] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D]	DA [auth I] JA [auth L] KA [auth L] LA [auth L] P [auth A] DA [auth I], JA [auth L], KA [auth L], LA [auth L], P [auth A], U [auth C], W [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth I] Focus chain JA [auth L] Focus chain KA [auth L] Focus chain LA [auth L] Focus chain P [auth A] Focus chain U [auth C] Focus chain W [auth D] Interactions & Density Focus chain DA [auth I] Focus chain JA [auth L] Focus chain KA [auth L] Focus chain LA [auth L] Focus chain P [auth A] Focus chain U [auth C] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.252 (Depositor), 0.249 (DCC)
R-Value Work: 0.205 (Depositor), 0.204 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.23	α = 90
b = 79.96	β = 90
c = 221.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

Bremm, A.

Freund, S.M.V.

Komander, D.

Revision History (Full details and data files)

Version 1.0: 2010-07-14
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-07-31
Changes: Advisory, Data collection, Derived calculations
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description