3K7R | pdb_00003k7r

Crystal structure of [TM][CuAtx1]3

PDB DOI: https://doi.org/10.2210/pdb3K7R/pdb

Classification: CHAPERONE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-10-13 Released: 2009-11-24
Deposition Author(s): Xue, Y., Alvarez, H.M., Robinson, C.D., Mondragon, A., O'Halloran, T.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.256 (Depositor), 0.257 (DCC)
R-Value Work:
0.202 (Depositor), 0.201 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Tetrathiomolybdate inhibits copper trafficking proteins through metal cluster formation.

Alvarez, H.M., Xue, Y., Robinson, C.D., Canalizo-Hernandez, M.A., Marvin, R.G., Kelly, R.A., Mondragon, A., Penner-Hahn, J.E., O'Halloran, T.V.

(2010) Science 327: 331-334

PubMed: 19965379 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1179907
Primary Citation Related Structures:
3K7R

PubMed Abstract:
Tetrathiomolybdate (TM) is an orally active agent for treatment of disorders of copper metabolism. Here we describe how TM inhibits proteins that regulate copper physiology. Crystallographic results reveal that the surprising stability of the drug complex with the metallochaperone Atx1 arises from formation of a sulfur-bridged copper-molybdenum cluster reminiscent of those found in molybdenum and iron sulfur proteins. Spectroscopic studies indicate that this cluster is stable in solution and corresponds to physiological clusters isolated from TM-treated Wilson's disease animal models. Finally, mechanistic studies show that the drug-metallochaperone inhibits metal transfer functions between copper-trafficking proteins. The results are consistent with a model wherein TM can directly and reversibly down-regulate copper delivery to secreted metalloenzymes and suggest that proteins involved in metal regulation might be fruitful drug targets.

Organizational Affiliation

The Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA.

Macromolecule Content

Total Structure Weight: 100.97 kDa
Atom Count: 7,163
Modeled Residue Count: 855
Deposited Residue Count: 876
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal homeostasis factor ATX1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	73	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ATX1, N0840, YNL259C
UniProt
Find proteins for P38636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38636 Go to UniProtKB: P38636
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38636
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4SM Query on 4SM Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain EA [auth J] SDF format, chain BA [auth I] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain EA [auth J] MOL2 format, chain BA [auth I] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain EA [auth J] mmCIF format, chain BA [auth I]	BA [auth I], EA [auth J], Q [auth C], T [auth D]	TETRATHIOMOLYBDATE Mo S₄ CXVCSRUYMINUSF-UHFFFAOYSA-N		Interactions Focus chain BA [auth I] Focus chain EA [auth J] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain BA [auth I] Focus chain EA [auth J] Focus chain Q [auth C] Focus chain T [auth D]
MLT Query on MLT Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain HA [auth L] MOL2 format, chain U [auth D] MOL2 format, chain HA [auth L] mmCIF format, chain U [auth D] mmCIF format, chain HA [auth L]	HA [auth L], U [auth D]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain HA [auth L] Focus chain U [auth D] Interactions & Density Focus chain HA [auth L] Focus chain U [auth D]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain Y [auth G] SDF format, chain X [auth G] SDF format, chain W [auth F] SDF format, chain V [auth E] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain P [auth C] SDF format, chain O [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain GA [auth L] SDF format, chain FA [auth K] SDF format, chain DA [auth J] SDF format, chain CA [auth J] SDF format, chain AA [auth I] MOL2 format, chain Z [auth H] MOL2 format, chain Y [auth G] MOL2 format, chain X [auth G] MOL2 format, chain W [auth F] MOL2 format, chain V [auth E] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth L] MOL2 format, chain FA [auth K] MOL2 format, chain DA [auth J] MOL2 format, chain CA [auth J] MOL2 format, chain AA [auth I] mmCIF format, chain Z [auth H] mmCIF format, chain Y [auth G] mmCIF format, chain X [auth G] mmCIF format, chain W [auth F] mmCIF format, chain V [auth E] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth L] mmCIF format, chain FA [auth K] mmCIF format, chain DA [auth J] mmCIF format, chain CA [auth J] mmCIF format, chain AA [auth I]	AA [auth I] CA [auth J] DA [auth J] FA [auth K] GA [auth L] AA [auth I], CA [auth J], DA [auth J], FA [auth K], GA [auth L], M [auth A], N [auth A], O [auth B], P [auth C], R [auth D], S [auth D], V [auth E], W [auth F], X [auth G], Y [auth G], Z [auth H]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain DA [auth J] Focus chain FA [auth K] Focus chain GA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain DA [auth J] Focus chain FA [auth K] Focus chain GA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.256 (Depositor), 0.257 (DCC)
R-Value Work: 0.202 (Depositor), 0.201 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.887	α = 90
b = 182.242	β = 90
c = 52.722	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
SHARP	phasing
autoSHARP	phasing
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-11-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description