3RTR | pdb_00003rtr

A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases

PDB DOI: https://doi.org/10.2210/pdb3RTR/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-05-03 Released: 2011-07-20
Deposition Author(s): Calabrese, M.F., Scott, D.C., Duda, D.M., Grace, C.R., Kurinov, I., Kriwacki, R.W., Schulman, B.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free:
0.282 (Depositor), 0.286 (DCC)
R-Value Work:
0.238 (Depositor), 0.237 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases.

Calabrese, M.F., Scott, D.C., Duda, D.M., Grace, C.R., Kurinov, I., Kriwacki, R.W., Schulman, B.A.

(2011) Nat Struct Mol Biol 18: 947-949

PubMed: 21765416 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.2086
Primary Citation Related Structures:
3RTR

PubMed Abstract:
How RING E3 ligases mediate E2-to-substrate ubiquitin-like protein (UBL) transfer remains unknown. Here we address how the RING E3 RBX1 positions NEDD8's E2 (UBC12) and substrate (CUL1). We find that existing structures are incompatible with CUL1 NEDD8ylation and report a new conformation of RBX1 that places UBC12 adjacent to CUL1. We propose RING domain rotation as a general mechanism for UBL transfer for the largest family of E3s.

Organizational Affiliation

Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. matthew.calabrese@stjude.org

Macromolecule Content

Total Structure Weight: 219.92 kDa
Atom Count: 14,055
Modeled Residue Count: 1,716
Deposited Residue Count: 1,896
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-1	A, C, E, G	368	Homo sapiens	Mutation(s): 4 Gene Names: CUL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13616 (Homo sapiens) Explore Q13616 Go to UniProtKB: Q13616
PHAROS: Q13616 GTEx: ENSG00000055130
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13616
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 RBX1	B, D, F, H	106	Homo sapiens	Mutation(s): 0 Gene Names: RBX1, RNF75, ROC1 EC: 6.3.2 (PDB Primary Data), 2.3.2.32 (UniProt), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P62877 (Homo sapiens) Explore P62877 Go to UniProtKB: P62877
PHAROS: P62877 GTEx: ENSG00000100387
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62877
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth F] SDF format, chain P [auth F] SDF format, chain Q [auth F] SDF format, chain R [auth H] SDF format, chain S [auth H] SDF format, chain T [auth H] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth F] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth H] MOL2 format, chain S [auth H] MOL2 format, chain T [auth H] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth F] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth H] mmCIF format, chain S [auth H] mmCIF format, chain T [auth H]	I [auth B] J [auth B] K [auth B] L [auth D] M [auth D] I [auth B], J [auth B], K [auth B], L [auth D], M [auth D], N [auth D], O [auth F], P [auth F], Q [auth F], R [auth H], S [auth H], T [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth F] Focus chain R [auth H] Focus chain S [auth H] Focus chain T [auth H] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth F] Focus chain R [auth H] Focus chain S [auth H] Focus chain T [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free: 0.282 (Depositor), 0.286 (DCC)
R-Value Work: 0.238 (Depositor), 0.237 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.475	α = 90
b = 119.796	β = 90
c = 231.861	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release
Version 1.1: 2011-08-24
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description