6XQN | pdb_00006xqn

Structure of a mitochondrial calcium uniporter holocomplex (MICU1, MICU2, MCU, EMRE) in low Ca2+

PDB DOI: https://doi.org/10.2210/pdb6XQN/pdb
EM Map EMD-22290: EMDB EMDataResource

Classification: TRANSPORT PROTEIN/CALCIUM BINDING PROTEIN
Organism(s): Tribolium castaneum, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM PDBTM

Deposited: 2020-07-09 Released: 2020-07-29
Deposition Author(s): Long, S.B., Wang, C., Baradaran, R., Jacewicz, A., Delgado, B.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structures reveal gatekeeping of the mitochondrial Ca 2+ uniporter by MICU1-MICU2.

Wang, C., Jacewicz, A., Delgado, B.D., Baradaran, R., Long, S.B.

(2020) Elife 9

PubMed: 32667285 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.59991
Primary Citation Related Structures:
6XQN, 6XQO

PubMed Abstract:
The mitochondrial calcium uniporter is a Ca ²⁺-gated ion channel complex that controls mitochondrial Ca ²⁺ entry and regulates cell metabolism. MCU and EMRE form the channel while Ca ²⁺-dependent regulation is conferred by MICU1 and MICU2 through an enigmatic process. We present a cryo-EM structure of an MCU-EMRE-MICU1-MICU2 holocomplex comprising MCU and EMRE subunits from the beetle Tribolium castaneum in complex with a human MICU1-MICU2 heterodimer at 3.3 Å resolution. With analogy to how neuronal channels are blocked by protein toxins, a uniporter interaction domain on MICU1 binds to a channel receptor site comprising MCU and EMRE subunits to inhibit ion flow under resting Ca ²⁺ conditions. A Ca ²⁺-bound structure of MICU1-MICU2 at 3.1 Å resolution indicates how Ca ²⁺-dependent changes enable dynamic response to cytosolic Ca ²⁺ signals.

Organizational Affiliation

Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.

Macromolecule Content

Total Structure Weight: 207.1 kDa
Atom Count: 9,433
Modeled Residue Count: 1,290
Deposited Residue Count: 1,799
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein EMRE homolog, mitochondrial-like Protein	A [auth E], D [auth G], F [auth H]	70	Tribolium castaneum	Mutation(s): 0 Gene Names: TcasGA2_TC012057 Membrane Entity: Yes
UniProt
Find proteins for D6X268 (Tribolium castaneum) Explore D6X268 Go to UniProtKB: D6X268
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D6X268
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium uniporter protein	B [auth A], C [auth B], E [auth C], G [auth D]	203	Tribolium castaneum	Mutation(s): 0 Gene Names: TcasGA2_TC013837 Membrane Entity: Yes
UniProt
Find proteins for D6WIX5 (Tribolium castaneum) Explore D6WIX5 Go to UniProtKB: D6WIX5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D6WIX5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium uptake protein 1, mitochondrial	H [auth I]	394	Homo sapiens	Mutation(s): 0 Gene Names: MICU1, CALC, CBARA1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BPX6 (Homo sapiens) Explore Q9BPX6 Go to UniProtKB: Q9BPX6
PHAROS: Q9BPX6 GTEx: ENSG00000107745
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BPX6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium uptake protein 2, mitochondrial	I [auth J]	383	Homo sapiens	Mutation(s): 0 Gene Names: MICU2, EFHA1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYU8 (Homo sapiens) Explore Q8IYU8 Go to UniProtKB: Q8IYU8
PHAROS: Q8IYU8 GTEx: ENSG00000165487
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IYU8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX	1.17.1-3660

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM131921
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30CA008748