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- EMDB-40724: Cryo-EM structure of TRPM2 chanzyme in the presence of Calcium -

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Basic information

Entry
Database: EMDB / ID: EMD-40724
TitleCryo-EM structure of TRPM2 chanzyme in the presence of Calcium
Map dataSharpened composite map.
Sample
  • Complex: TRPM2 chanzyme in the presence of Calcium
    • Protein or peptide: TRPM2 chanzyme
  • Ligand: CALCIUM IONCalcium
  • Ligand: CHOLESTEROL
KeywordsTRPM2 Chanzyme / Channel-enzyme / TRANSPORT PROTEIN
Function / homology
Function and homology information


calcium channel activity / plasma membrane
Similarity search - Function
TRPM, SLOG domain / SLOG in TRPM / Nudix hydrolase domain profile. / NUDIX hydrolase domain / Voltage-dependent channel domain superfamily / NUDIX hydrolase-like domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Biological speciesSalpingoeca rosetta (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsHuang Y / Kumar S / Lu W / Du J
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL153219 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS112363 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS111031 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129547 United States
CitationJournal: To Be Published
Title: Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution
Authors: Huang Y / Kumar S / Lu W / Du J
History
DepositionMay 5, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40724.png

Downloads & links

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Map

FileDownload / File: emd_40724.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened composite map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 363.44 Å		0.83 Å/pix.
x 440 pix.
= 363.44 Å		0.83 Å/pix.
x 440 pix.
= 363.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 11.0
Minimum - Maximum-32.029358000000002 - 62.181553000000001
Average (Standard dev.)0.13953374 (±1.4509132)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 363.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened composite map.

Fileemd_40724_additional_1.map
AnnotationUnsharpened composite map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened consensus map.

Fileemd_40724_additional_2.map
AnnotationUnsharpened consensus map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened consensus map.

Fileemd_40724_additional_3.map
AnnotationSharpened consensus map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRPM2 chanzyme in the presence of Calcium

EntireName: TRPM2 chanzyme in the presence of Calcium
Components
  • Complex: TRPM2 chanzyme in the presence of Calcium
    • Protein or peptide: TRPM2 chanzyme
  • Ligand: CALCIUM IONCalcium
  • Ligand: CHOLESTEROL

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Supramolecule #1: TRPM2 chanzyme in the presence of Calcium

SupramoleculeName: TRPM2 chanzyme in the presence of Calcium / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Salpingoeca rosetta (eukaryote)

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Macromolecule #1: TRPM2 chanzyme

MacromoleculeName: TRPM2 chanzyme / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Salpingoeca rosetta (eukaryote)
Molecular weightTheoretical: 168.252484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQRARPGELV EVIMFRPTGK ARVSNLDESM AMEFTDLRTR AMSSAAMIRQ SVAAKTLLIE NEDGKGSTRM EVQDFMKRFH MHASEDDKT GSPSTAWGTL RFPTKEATAP YLRLSVNDDP EDALLFVKAM LAQKYGETYD RPSLILSVTG GARNFTLPPR L ETAIAKGL ...String:
MQRARPGELV EVIMFRPTGK ARVSNLDESM AMEFTDLRTR AMSSAAMIRQ SVAAKTLLIE NEDGKGSTRM EVQDFMKRFH MHASEDDKT GSPSTAWGTL RFPTKEATAP YLRLSVNDDP EDALLFVKAM LAQKYGETYD RPSLILSVTG GARNFTLPPR L ETAIAKGL RLAAQRTNAW VVTGGTNTGV MKLTGQIMEA LSKTQSHFIP PTIGIATYGV IIGGDDMTRG EPPKIGLEYE MH KKDPPKT TPLDDNHNLF LLVDDGSTNK FGKEIKFRAA FENAAGQAFA APVVTIVVQG GPGTLGTALQ AVRQGTPIVV VDG SGLAAD VLAYAYNFMH NPLTRFKSYT IDDLRQKVAQ TFNPKSSQQL TNLLDSALEC VQDPNLVVVY SLQESGIDEF DDCI LKAIF SSQGKLGNKL KQAMYFDQLD VAKRALSEAS KNGQHNEIAA CINDNLMAAM MHNKPHFVEL YLGFDAKIYE LKPSE EVAK TNITALDELP SFALAIEELY KREAKKPHSH VQRLVSLSNT DVLGRHYRVS TQRGDGTTRR IGRDLANTRA YNVLRM DQI FARLVSKDFS VNRDFTIYDS KYDKVPGIQF RRTAQASHML FLWAICLDRF RMARHFWLIG DQSIINALVA SRILERL ST HRALQGPHLA EERAKMQHNA KKFEELAVGV LGECHGSDSH MASEMLHSKN DMFNKKNAIN IAYDAKSLAF LSHPATQS V INADWYGHLK SVTSFWAVLF AFFFPFFVLP FINFSEDHAE QQVEAPRDFF TDAPRSSHSA NSTTSGAHRL RRKFAKFYS APYTRFISDL LSHFVLCVVT SYFVLDKLED TISAIEWILL VWFVALLLEE LRQMIFCDGI AEYISDTWNR LDLIMITLFF VGFFTHASD PSNQDSKVVS KGIHAFLVVV LWLRFMRYYA LSKNLGPKLI MMMEMMKDVS TFVFLLLIFL IGYGVAAQSL L SPDEDFSS RTFIGVLFRP YFQIYGELFL DDLNSEANCL GDTPFTECSR ETVRMVPFFL AVYILGSNVL LVNLLIAMFN DT YMKVQEA AEDLWRKQNY ELCAEYKDRP FLPAPFILLA HVHMLFMRLL RLCGVHTQEH EKIQDDETKR KITTFEELNT DKF LRRWER ERQEMLEARV KMTNDNVVQA MGMMDQLLEH MISFRFSLDQ QATKIKQEIR DDGLPSTEPT GLVSRTPSQP INRL NSAVA VHGHTAEAAE WYVPPEEYPK SGGVKRYLID ASMVPLSIMC PSYDPVEYTH PSVAAQPVWA DPADPRKIKF NVKDE VNGK VVDRTSCHPS GISIDSNTGR PINPWGRTGM TGRGLLGKWG VNQAADTVVT RWKRSPDGSI LERDGKKVLE FVAIQR QDN KMWAIPGGFV DNGEDVALTS GREFMEEALG MGTSADLMSA ESKDSLAALF SSGTIVARIY CEDPRNTDNA WVETTCV NF HDESGRHAAR LKLQGGDDAE HARWMMVHGG LNLFASHRTL LQHVTSALNA YF

UniProtKB: Nudt9 protein

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 12 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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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

Concentration8.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.02 sec. / Average electron dose: 49.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207704

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8sra:
Cryo-EM structure of TRPM2 chanzyme in the presence of Calcium

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