3R3Q | pdb_00003r3q

Crystal structure of the yeast Vps23 UEV domain

PDB DOI: https://doi.org/10.2210/pdb3R3Q/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-03-16 Released: 2011-05-04
Deposition Author(s): Ren, X., Hurley, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.184 (Depositor), 0.183 (DCC)
R-Value Work:
0.164 (Depositor), 0.162 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for endosomal recruitment of ESCRT-I by ESCRT-0 in yeast.

Ren, X., Hurley, J.H.

(2011) EMBO J 30: 2130-2139

PubMed: 21505419 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/emboj.2011.122
Primary Citation Related Structures:
3R3Q, 3R42

PubMed Abstract:
The ESCRT-0 and ESCRT-I complexes coordinate the clustering of ubiquitinated cargo with intralumenal budding of the endosomal membrane, two essential steps in vacuolar/lysosomal protein sorting from yeast to humans. The 1.85-Å crystal structure of interacting regions of the yeast ESCRT-0 and ESCRT-I complexes reveals that PSDP motifs of the Vps27 ESCRT-0 subunit bind to a novel electropositive N-terminal site on the UEV domain of the ESCRT-I subunit Vps23 centred on Trp16. This novel site is completely different from the C-terminal part of the human UEV domain that binds to P(S/T)AP motifs of human ESCRT-0 and HIV-1 Gag. Disruption of the novel PSDP-binding site eliminates the interaction in vitro and blocks enrichment of Vps23 in endosome-related class E compartments in yeast cells. However, this site is non-essential for sorting of the ESCRT cargo Cps1. Taken together, these results show how a conserved motif/domain pair can evolve to use strikingly different binding modes in different organisms.

Organizational Affiliation

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.

Macromolecule Content

Total Structure Weight: 19.35 kDa
Atom Count: 1,427
Modeled Residue Count: 153
Deposited Residue Count: 162
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease	A	162	Saccharomyces cerevisiae	Mutation(s): 1 Gene Names: STP22, VPS23, YCL008C, YCL8C
UniProt
Find proteins for P25604 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25604 Go to UniProtKB: P25604
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25604
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A]	L [auth A] M [auth A] N [auth A] O [auth A] P [auth A] L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], T [auth A], U [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth A] Focus chain U [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain V [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain V [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain V [auth A]	Q [auth A], R [auth A], S [auth A], V [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.184 (Depositor), 0.183 (DCC)
R-Value Work: 0.164 (Depositor), 0.162 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.059	α = 90
b = 47.139	β = 90
c = 92.946	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-05-04

Deposition Author(s):

Ren, X.

Hurley, J.H.

Revision History (Full details and data files)

Version 1.0: 2011-05-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

3R3Q | pdb_00003r3q

Crystal structure of the yeast Vps23 UEV domain

Literature

Structural basis for endosomal recruitment of ESCRT-I by ESCRT-0 in yeast.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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