[English] 日本語
Yorodumi
- EMDB-44055: Cryo-EM structure of E227Q variant of uMtCK1 in complex with tran... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44055
TitleCryo-EM structure of E227Q variant of uMtCK1 in complex with transition state analog
Map data
Sample
  • Complex: Octameric u-type mitochondrial creatine kinase
    • Protein or peptide: Creatine kinase U-type, mitochondrial
  • Ligand: N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: NITRATE ION
  • Ligand: MAGNESIUM ION
Keywordsmitochondrial creatine kinase / TRANSFERASE
Function / homology
Function and homology information


creatine kinase / Creatine metabolism / phosphocreatine biosynthetic process / creatine kinase activity / mitochondrial inner membrane / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsDemir M / Koepping L / Zhao J / Sergienko E
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorOD026926 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA030199 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA251910 United States
CitationJournal: Structure / Year: 2025
Title: Structural basis for substrate binding, catalysis, and inhibition of cancer target mitochondrial creatine kinase by a covalent inhibitor.
Authors: Merve Demir / Laura Koepping / Ya Li / Lynn Fujimoto / Andrey Bobkov / Jianhua Zhao / Taro Hitosugi / Eduard Sergienko /
Abstract: Mitochondrial creatine kinases (MtCKs) are key players in maintaining energy homeostasis in cells that work with cytosolic creatine kinases for energy transport from mitochondria to cytoplasm. The ...Mitochondrial creatine kinases (MtCKs) are key players in maintaining energy homeostasis in cells that work with cytosolic creatine kinases for energy transport from mitochondria to cytoplasm. The inhibition of breast cancer growth by cyclocreatine targeting CKs indicates dependence of cancer cells on the "energy shuttle" for cell growth and survival. Hence, understanding key mechanistic features of creatine kinases and their inhibition plays an important role in the development of cancer therapeutics. Herein, we present mutational and structural investigations on understudied ubiquitous MtCK that showed closure of the loop comprising His61 is specific to and relies on creatine binding and mechanism of phosphoryl transfer depends on electrostatics of active site. We demonstrate that previously identified pan-CK covalent inhibitor CKi inhibit breast cancer cell proliferation; however, our biochemical and structural data indicated that inhibition by CKi is highly dependent on covalent link formation and conformational changes upon creatine binding are not observed.
History
DepositionMar 12, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44055.png

Downloads & links

-
Map

FileDownload / File: emd_44055.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 272.384 Å		1.06 Å/pix.
x 256 pix.
= 272.384 Å		1.06 Å/pix.
x 256 pix.
= 272.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.37322628 - 0.7356558
Average (Standard dev.)-0.00010038934 (±0.02339043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.384 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_44055_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_44055_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_44055_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Octameric u-type mitochondrial creatine kinase

EntireName: Octameric u-type mitochondrial creatine kinase
Components
  • Complex: Octameric u-type mitochondrial creatine kinase
    • Protein or peptide: Creatine kinase U-type, mitochondrial
  • Ligand: N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: NITRATE ION
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Octameric u-type mitochondrial creatine kinase

SupramoleculeName: Octameric u-type mitochondrial creatine kinase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
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: Homo sapiens (human)
Molecular weightTheoretical: 47.597734 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MENLYFQGAA SERRRLYPPS AEYPDLRKHN NCMASHLTPA VYARLCDKTT PTGWTLDQCI QTGVDNPGH PFIKTVGMVA GDEETYEVFA DLFDPVIQER HNGYDPRTMK HTTDLDASKI RSGYFDERYV LSSRVRTGRS I RGLSLPPA ...String:
MGSSHHHHHH SSGLVPRGSH MENLYFQGAA SERRRLYPPS AEYPDLRKHN NCMASHLTPA VYARLCDKTT PTGWTLDQCI QTGVDNPGH PFIKTVGMVA GDEETYEVFA DLFDPVIQER HNGYDPRTMK HTTDLDASKI RSGYFDERYV LSSRVRTGRS I RGLSLPPA CTRAERREVE RVVVDALSGL KGDLAGRYYR LSEMTEAEQQ QLIDDHFLFD KPVSPLLTAA GMARDWPDAR GI WHNNEKS FLIWVNEQDH TRVISMEKGG NMKRVFERFC RGLKEVERLI QERGWEFMWN ERLGYILTCP SNLGTGLRAG VHI KLPLLS KDSRFPKILE NLRLQKRGTG GVDTAATGGV FDISNLDRLG KSEVELVQLV IDGVNYLIDC ERRLERGQDI RIPT PVIHT KHGSSDYKDD DDK

UniProtKB: Creatine kinase U-type, mitochondrial

-
Macromolecule #2: N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE

MacromoleculeName: N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE / type: ligand / ID: 2 / Number of copies: 8 / Formula: CRN
Molecular weightTheoretical: 131.133 Da
Chemical component information

ChemComp-CRN:
N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE

-
Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Macromolecule #4: NITRATE ION

MacromoleculeName: NITRATE ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: NO3
Molecular weightTheoretical: 62.005 Da
Chemical component information

ChemComp-NO3:
NITRATE ION

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMtris(hydroxymethyl)aminomethane
200.0 mMsodium chlorideNaCl
50.0 mMmagnesium chlorideMgCl2

Details: 10 mM creatine, 1 mM ADP, and 50 mM sodium nitrate
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3851095
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1qk1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1053188
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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