6K7Y | pdb_00006k7y

Intact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits

• PDB DOI: https://doi.org/10.2210/pdb6K7Y/pdb
• EM Map EMD-9945: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2019-06-10 Released: 2020-09-09 
• Deposition Author(s): Zhuo, W., Zhou, H., Yang, M.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Structure of intact human MCU supercomplex with the auxiliary MICU subunits.

Zhuo, W., Zhou, H., Guo, R., Yi, J., Zhang, L., Yu, L., Sui, Y., Zeng, W., Wang, P., Yang, M.

(2021) Protein Cell 12: 220-229

• PubMed: 32862359 
• DOI: https://doi.org/10.1007/s13238-020-00776-w
• Primary Citation of Related Structures:  
  6K7X, 6K7Y

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Organizational Affiliation: 
• Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. [e-mail].
Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Institute for Immunology and School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua University, Beijing, 100084, China.
Cryo-EM Facility Center, Southern University of Science & Technology, Shenzhen, 518055, China. [e-mail].
Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 20-mer - A8B8C2D2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 20-mer - A8B4C2D2E2F2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 518.98 kDa 
• Atom Count: 32,956 
• Modeled Residue Count: 3,872 
• Deposited Residue Count: 4,264 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium uniporter protein, mitochondrial	A, B, C, D, K [auth N], L [auth O], M [auth P], N [auth Q]	276	Homo sapiens	Mutation(s): 0  Gene Names: MCU, C10orf42, CCDC109A Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NE86 (Homo sapiens) Explore Q8NE86  Go to UniProtKB:  Q8NE86
PHAROS:  Q8NE86 GTEx:  ENSG00000156026

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Essential MCU regulator, mitochondrial	E, F, G, H, O [auth R], P [auth S], Q [auth T], R [auth U]	54	Homo sapiens	Mutation(s): 0  Gene Names: SMDT1, C22orf32, EMRE Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H4I9 (Homo sapiens) Explore Q9H4I9  Go to UniProtKB:  Q9H4I9
PHAROS:  Q9H4I9 GTEx:  ENSG00000183172

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium uptake protein 1, mitochondrial	I, S [auth V]	476	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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium uptake protein 2, mitochondrial	J, T [auth W]	336	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL	BA [auth C], GA [auth H], IA [auth N], LA [auth O], OA [auth P], SA [auth Q], V [auth A], Y [auth B]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PLX	AA [auth B], CA [auth C], DA [auth C], EA [auth C], FA [auth D], JA [auth N], KA [auth N], MA [auth O], NA [auth O], PA [auth P], QA [auth P], RA [auth P], TA [auth Q], W [auth A], X [auth A], Z [auth B]	(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL C42 H89 N O8 P YVNJQRQLQPWVSQ-IWSHAHEXSA-O
CA	HA [auth N], U [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX	1.15

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Zhuo, W., Zhou, H., Yang, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	21532004
National Science Foundation (NSF, China)	China	31570733
National Science Foundation (NSF, China)	China	31900857

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2021-03-03
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Refinement description