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- EMDB-26351: Cryo-EM Structure of Mitochondrial Creatine Kinase -

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Basic information

Entry
Database: EMDB / ID: EMD-26351
TitleCryo-EM Structure of Mitochondrial Creatine Kinase
Map data
Sample
  • Complex: Octamer of Creatine Kinase
    • Protein or peptide: Creatine kinase U-type, mitochondrial
  • Ligand: water
KeywordsCK / creatine kinase / mitochondrial / TRANSFERASE
Function / homology
Function and homology information


Creatine metabolism / creatine kinase / phosphocreatine biosynthetic process / creatine kinase activity / mitochondrial inner membrane / negative regulation of apoptotic process / mitochondrion / ATP binding
Similarity search - Function
ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Creatine kinase U-type, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsMorgan CE / Yu EW / Zhang Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2022
Title: Toward structural-omics of the bovine retinal pigment epithelium.
Authors: Christopher E Morgan / Zhemin Zhang / Masaru Miyagi / Marcin Golczak / Edward W Yu /
Abstract: The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on ...The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on determining the structure of a particular biomacromolecule of interest. Here, we report the use of cryoelectron microscopy (cryo-EM) to define the composition of a raw bovine retinal pigment epithelium (RPE) lysate. From this sample, we simultaneously identify and solve cryo-EM structures of seven different RPE enzymes whose functions affect neurotransmitter recycling, iron metabolism, gluconeogenesis, glycolysis, axonal development, and energy homeostasis. Interestingly, dysfunction of these important proteins has been directly linked to several neurodegenerative disorders, including Huntington's disease, amyotrophic lateral sclerosis (ALS), Parkinson's disease, Alzheimer's disease, and schizophrenia. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.
History
DepositionMar 2, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26351.png

Downloads & links

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Map

FileDownload / File: emd_26351.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-2.0705993 - 3.5268097
Average (Standard dev.)0.000057767502 (±0.09168993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_26351_additional_1.map
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Half map: #2

Fileemd_26351_half_map_1.map
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Half map: #1

Fileemd_26351_half_map_2.map
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Sample components

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Entire : Octamer of Creatine Kinase

EntireName: Octamer of Creatine Kinase
Components
  • Complex: Octamer of Creatine Kinase
    • Protein or peptide: Creatine kinase U-type, mitochondrial
  • Ligand: water

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Supramolecule #1: Octamer of Creatine Kinase

SupramoleculeName: Octamer of Creatine Kinase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Creatine kinase U-type, mitochondrial

MacromoleculeName: Creatine kinase U-type, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: creatine kinase
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 46.965605 KDa
SequenceString: MAGPFSRLLS ARPGLRLLAL AGAGSLAAGF LLRSEPVRAA SERRRLYPPS AEYPDLRKHN NCMASHLTPA VYARLCDKTT PTGWTLDQC IQTGVDNPGH PFIKTVGMVA GDEETYEVFA ELFDPVIQER HNGYDPRTMK HTTDLDASKI RSGYFDERYV L SSRVRTGR ...String:
MAGPFSRLLS ARPGLRLLAL AGAGSLAAGF LLRSEPVRAA SERRRLYPPS AEYPDLRKHN NCMASHLTPA VYARLCDKTT PTGWTLDQC IQTGVDNPGH PFIKTVGMVA GDEETYEVFA ELFDPVIQER HNGYDPRTMK HTTDLDASKI RSGYFDERYV L SSRVRTGR SIRGLSLPPA CTRAERREVE RVVVDALSGL KGDLAGRYYR LSEMTEAEQQ QLIDDHFLFD KPVSPLLTAA GM ARDWPDA RGIWHNNEKS FLIWVNEEDH TRVISMEKGG NMKKVFERFC RGLKEVERLI QERGWEFMWN ERLGYILTCP SNL GTGLRA GVHIKLPLLS KDSRFPKILE NLRLQKRGTG GVDTAATGSV FDISNLDRLG KSEVELVQLV IDGVNFLIDC ERRL ERGQD IRIPPPLPNK H

UniProtKB: Creatine kinase U-type, mitochondrial

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 123 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3) / Number images used: 4018
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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