[English] 日本語
Yorodumi
- PDB-6lb7: Crystal structure of the Ca2+-free and Ca2+-bound MICU1-MICU2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lb7
TitleCrystal structure of the Ca2+-free and Ca2+-bound MICU1-MICU2 complex
Components
  • Calcium uptake protein 1, mitochondrial
  • Calcium uptake protein 2, mitochondrial
KeywordsMETAL BINDING PROTEIN / Calcium binding protein / Mitochondrial / Uniporter / EF-hand
Function / homology
Function and homology information


mitochondrial crista junction / negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / positive regulation of cristae formation / mitochondrial calcium ion transmembrane transport / Processing of SMDT1 / uniplex complex / positive regulation of mitochondrial calcium ion concentration / Mitochondrial calcium ion transport / mitochondrial calcium ion homeostasis ...mitochondrial crista junction / negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / positive regulation of cristae formation / mitochondrial calcium ion transmembrane transport / Processing of SMDT1 / uniplex complex / positive regulation of mitochondrial calcium ion concentration / Mitochondrial calcium ion transport / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / calcium ion sensor activity / cellular response to calcium ion starvation / calcium ion import / calcium channel inhibitor activity / calcium channel complex / Mitochondrial protein degradation / calcium channel regulator activity / cellular response to calcium ion / defense response / mitochondrial membrane / protein homooligomerization / mitochondrial intermembrane space / mitochondrial inner membrane / protein heterodimerization activity / calcium ion binding / mitochondrion / identical protein binding
Similarity search - Function
Calcium uptake protein 1/2/3 / EF hand / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calcium uptake protein 2, mitochondrial / Calcium uptake protein 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsWu, W. / Shen, Q. / Zheng, J. / Jia, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21773014 China
Citation
Journal: Embo J. / Year: 2020
Title: The structure of the MICU1-MICU2 complex unveils the regulation of the mitochondrial calcium uniporter.
Authors: Wu, W. / Shen, Q. / Zhang, R. / Qiu, Z. / Wang, Y. / Zheng, J. / Jia, Z.
#1: Journal: Embo Rep. / Year: 2019
Title: The crystal structure of MICU2 provides insight into Ca 2+ binding and MICU1-MICU2 heterodimer formation.
Authors: Wu, W. / Shen, Q. / Lei, Z. / Qiu, Z. / Li, D. / Pei, H. / Zheng, J. / Jia, Z.
History
DepositionNov 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Mar 17, 2021Group: Database references / Category: citation / citation_author
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calcium uptake protein 1, mitochondrial
B: Calcium uptake protein 2, mitochondrial
C: Calcium uptake protein 1, mitochondrial
D: Calcium uptake protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,6876
Polymers163,6064
Non-polymers802
Water19,7801098
1
A: Calcium uptake protein 1, mitochondrial
B: Calcium uptake protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8834
Polymers81,8032
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-20 kcal/mol
Surface area29160 Å2
MethodPISA
2
C: Calcium uptake protein 1, mitochondrial
D: Calcium uptake protein 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)81,8032
Polymers81,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-19 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.481, 107.721, 170.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Calcium uptake protein 1, mitochondrial / Atopy-related autoantigen CALC / ara CALC / Calcium-binding atopy-related autoantigen 1


Mass: 43083.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICU1, CALC, CBARA1 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BPX6
#2: Protein Calcium uptake protein 2, mitochondrial / EF-hand domain-containing family member A1


Mass: 38719.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICU2, EFHA1 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8IYU8
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1098 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M ammonium chloride, 5% (w/v) polyethylene glycol (PEG) 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.101→47.3 Å / Num. obs: 92168 / % possible obs: 98 % / Redundancy: 13 % / CC1/2: 0.984 / Rmerge(I) obs: 0.1246 / Rrim(I) all: 0.1297 / Net I/σ(I): 10.87
Reflection shellResolution: 2.101→2.176 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.192 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 8058 / CC1/2: 0.775 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000v716.1data scaling
PDB_EXTRACT3.25data extraction
HKL-2000v716.1data reduction
PHENIX1.10.1-2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NSC, 6IIH

4nsc

6iih


Resolution: 2.101→47.3 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.45
RfactorNum. reflection% reflection
Rfree0.2267 2000 2.2 %
Rwork0.194 --
obs0.1947 90895 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.94 Å2 / Biso mean: 35.5483 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: final / Resolution: 2.101→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9893 0 2 1098 10993
Biso mean--28.51 37.79 -
Num. residues----1205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02110088
X-RAY DIFFRACTIONf_angle_d1.29213508
X-RAY DIFFRACTIONf_chiral_restr0.0631448
X-RAY DIFFRACTIONf_plane_restr0.0131736
X-RAY DIFFRACTIONf_dihedral_angle_d17.1376061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.101-2.1530.23581230.2432548486
2.153-2.21130.30041380.2388608996
2.2113-2.27630.28961400.2362625698
2.2763-2.34980.25591430.2216635299
2.3498-2.43380.2411440.22016403100
2.4338-2.53120.23321420.22086351100
2.5312-2.64640.29061450.21896438100
2.6464-2.78590.24521440.21426395100
2.7859-2.96040.23911450.20746441100
2.9604-3.1890.23651450.19746435100
3.189-3.50980.19931460.18366471100
3.5098-4.01740.17661450.16426475100
4.0174-5.06060.19351480.15286570100
5.0606-47.30.23251520.189673599

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more