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 OPM PDBTM MemProtMD mpstruc

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)

Experimental Data Snapshot

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

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

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

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1007/s13238-020-00776-w
Primary Citation Related Structures:
6K7X, 6K7Y

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. zhuowei@tsinghua.edu.cn.

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

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium uniporter protein, mitochondrial	A B C D K [auth N] 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NE86
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Essential MCU regulator, mitochondrial	E F G H O [auth R] 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H4I9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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 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	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
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain SA [auth Q] SDF format, chain V [auth A] SDF format, chain Y [auth B] SDF format, chain OA [auth P] SDF format, chain LA [auth O] SDF format, chain IA [auth N] SDF format, chain GA [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain SA [auth Q] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain OA [auth P] MOL2 format, chain LA [auth O] MOL2 format, chain IA [auth N] MOL2 format, chain GA [auth H] mmCIF format, chain BA [auth C] mmCIF format, chain SA [auth Q] mmCIF format, chain V [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain OA [auth P] mmCIF format, chain LA [auth O] mmCIF format, chain IA [auth N] mmCIF format, chain GA [auth H]	BA [auth C] GA [auth H] IA [auth N] LA [auth O] OA [auth P] 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		Interactions Focus chain BA [auth C] Focus chain GA [auth H] Focus chain IA [auth N] Focus chain LA [auth O] Focus chain OA [auth P] Focus chain SA [auth Q] Focus chain V [auth A] Focus chain Y [auth B] Interactions & Density Focus chain BA [auth C] Focus chain GA [auth H] Focus chain IA [auth N] Focus chain LA [auth O] Focus chain OA [auth P] Focus chain SA [auth Q] Focus chain V [auth A] Focus chain Y [auth B]
PLX Query on PLX Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain EA [auth C] SDF format, chain FA [auth D] SDF format, chain KA [auth N] SDF format, chain NA [auth O] SDF format, chain QA [auth P] SDF format, chain RA [auth P] SDF format, chain W [auth A] SDF format, chain Z [auth B] SDF format, chain X [auth A] SDF format, chain TA [auth Q] SDF format, chain PA [auth P] SDF format, chain MA [auth O] SDF format, chain JA [auth N] SDF format, chain DA [auth C] SDF format, chain CA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain KA [auth N] MOL2 format, chain NA [auth O] MOL2 format, chain QA [auth P] MOL2 format, chain RA [auth P] MOL2 format, chain W [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth A] MOL2 format, chain TA [auth Q] MOL2 format, chain PA [auth P] MOL2 format, chain MA [auth O] MOL2 format, chain JA [auth N] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain KA [auth N] mmCIF format, chain NA [auth O] mmCIF format, chain QA [auth P] mmCIF format, chain RA [auth P] mmCIF format, chain W [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth A] mmCIF format, chain TA [auth Q] mmCIF format, chain PA [auth P] mmCIF format, chain MA [auth O] mmCIF format, chain JA [auth N] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C]	AA [auth B] CA [auth C] DA [auth C] EA [auth C] FA [auth D] 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		Interactions Focus chain AA [auth B] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth D] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain MA [auth O] Focus chain NA [auth O] Focus chain PA [auth P] Focus chain QA [auth P] Focus chain RA [auth P] Focus chain TA [auth Q] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth D] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain MA [auth O] Focus chain NA [auth O] Focus chain PA [auth P] Focus chain QA [auth P] Focus chain RA [auth P] Focus chain TA [auth Q] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain HA [auth N] SDF format, chain U [auth A] MOL2 format, chain HA [auth N] MOL2 format, chain U [auth A] mmCIF format, chain HA [auth N] mmCIF format, chain U [auth A]	HA [auth N], U [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain HA [auth N] Focus chain U [auth A] Interactions & Density Focus chain HA [auth N] Focus chain U [auth A]

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-09

Deposition Author(s):

Zhuo, W.

Zhou, H.

Yang, M.

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 (Full details and data files)

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

6K7Y | pdb_00006k7y

Intact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)