[English] 日本語
Yorodumi
- EMDB-61525: Nematostella vectensis TRPM2 protomer in complex with ADPRP/Ca2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61525
TitleNematostella vectensis TRPM2 protomer in complex with ADPRP/Ca2+
Map data
Sample
  • Complex: nvTRPM2 protomer in complex with ADPRP/Ca2+
    • Protein or peptide: Transient receptor potential cation channel subfamily M member-like 2
  • Ligand: CALCIUM ION
  • Ligand: [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE
KeywordsNematostella vectensis / TRPM2 / ADPRP / Ca2+ / MEMBRANE PROTEIN
Function / homology
Function and homology information


ADP-ribose diphosphatase activity / ligand-gated calcium channel activity / ligand-gated sodium channel activity / sodium ion transmembrane transport / calcium ion transmembrane transport / metal ion binding / plasma membrane
Similarity search - Function
TRPM, SLOG domain / : / SLOG in TRPM / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member-like 2
Similarity search - Component
Biological speciesNematostella vectensis (starlet sea anemone)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsJiang Y / Zhang Z / Toth B / Szollosi A / Csanady L
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)YFA1302300 China
National Natural Science Foundation of China (NSFC)32171201 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: A conserved mechanism couples cytosolic domain movements to pore gating in the TRPM2 channel.
Authors: Balázs Tóth / Yuefeng Jiang / Andras Szollosi / Zhe Zhang / László Csanády /
Abstract: Transient Receptor Potential Melastatin 2 (TRPM2) cation channels contribute to immunocyte activation, insulin secretion, and central thermoregulation. TRPM2 opens upon binding cytosolic Ca and ADP ...Transient Receptor Potential Melastatin 2 (TRPM2) cation channels contribute to immunocyte activation, insulin secretion, and central thermoregulation. TRPM2 opens upon binding cytosolic Ca and ADP ribose (ADPR). We present here the 2.5 Å cryo-electronmicroscopy structure of TRPM2 from (nvTRPM2) in a lipid nanodisc, complexed with Ca and ADPR-2'-phosphate. Comparison with nvTRPM2 without nucleotide reveals that nucleotide binding-induced movements in the protein's three "core" layers deconvolve into a set of rigid-body rotations conserved from cnidarians to man. By covalently crosslinking engineered cysteine pairs we systematically trap the cytosolic layers in specific conformations and study effects on gate opening/closure. The data show that nucleotide binding in Layer 3 disrupts inhibitory intersubunit interactions, allowing rotation of Layer 2 which in turn expands the gate located in Layer 1. Channels trapped in that "activated" state are no longer nucleotide dependent, but are opened by binding of Ca alone.
History
DepositionSep 13, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61525.png

Downloads & links

-
Map

FileDownload / File: emd_61525.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 328 pix.
= 350.96 Å		1.07 Å/pix.
x 328 pix.
= 350.96 Å		1.07 Å/pix.
x 328 pix.
= 350.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.8685887 - 1.3016737
Average (Standard dev.)0.0010954255 (±0.022397658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions328328328
Spacing328328328
CellA=B=C: 350.96002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_61525_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61525_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : nvTRPM2 protomer in complex with ADPRP/Ca2+

EntireName: nvTRPM2 protomer in complex with ADPRP/Ca2+
Components
  • Complex: nvTRPM2 protomer in complex with ADPRP/Ca2+
    • Protein or peptide: Transient receptor potential cation channel subfamily M member-like 2
  • Ligand: CALCIUM ION
  • Ligand: [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE

-
Supramolecule #1: nvTRPM2 protomer in complex with ADPRP/Ca2+

SupramoleculeName: nvTRPM2 protomer in complex with ADPRP/Ca2+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nematostella vectensis (starlet sea anemone)
Molecular weightTheoretical: 170 KDa

-
Macromolecule #1: Transient receptor potential cation channel subfamily M member-like 2

MacromoleculeName: Transient receptor potential cation channel subfamily M member-like 2
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nematostella vectensis (starlet sea anemone)
Molecular weightTheoretical: 176.663438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGKDSFTPLY DGGDSSHVHL NKFGSNQLSQ SKKSWIARNF SRRECIRFVP KSHDVSRCKC GRPRERHSQQ ALESGQGSEE WNVASCTTK HPTNAYGEID FEGYGGQKRA PYLRMSHDTD ANLVITLMLK RWNLEIPNLV ISVTGGAKSF VLKPRLREMF R RGLIKAAK ...String:
MGKDSFTPLY DGGDSSHVHL NKFGSNQLSQ SKKSWIARNF SRRECIRFVP KSHDVSRCKC GRPRERHSQQ ALESGQGSEE WNVASCTTK HPTNAYGEID FEGYGGQKRA PYLRMSHDTD ANLVITLMLK RWNLEIPNLV ISVTGGAKSF VLKPRLREMF R RGLIKAAK TTGAWIITGG TNTGVMKHVG EAVKEQQLMF GSDTQVNVIG IATWGIVDKQ SDLISEKNGK YPALYSMEPT PG HQGAMLD PNHSHFFLVD DGTEGKYGVE IGMRSRIEEA IMKVKTDSRS EAGSIGVPVV LLVLEGGPNT VATMYELIKK KVP AVVIDG SGRAASVVGF AYNHTIKRNV DGQTINVIDP QYEDEVRAKV VEVFGAKGAD KTYSMIKDVL EDEKMISVYS LDGE ISQDI DLAILKALLK ANRSSPVAQL NLALAWNRID LAKSDIFTEE QQWTTETLSA AMLTALLDDK AEFAELFLQN GLSMR EFLS LDILCKLYAE VPGNTTIKPL LQKEMGKRQV KTIDMDVVGE VIEELMGDMF ESYYRKDGHY FGELASYAEG LVLKNR KSS KDLLANINRI DPLPTPYLDV FLWAVLCNRR ELARVLWEAG REPMAAALMA SRLLKRMASR AQEDNTITDI SSDLYDH AR LFEERAVGVL DECFNENETL SQTLLVRELD HYSRMTALEL AVSAESQDFI AHTSCQVLLT RLWMGTMAMN TRWWKVLV C LYLPVLIFPI IYFVPDEQHE RQAAEREHQK SLNQKSSKVK SHKEKNDAPV VPVYRSKEEK AVSNDEEARV GTENEEEDF QLEDYIPEIR EDDSMEVIMR NKKLGFCDRI MHFYSAPFSK FVGNVVGYLA FIFLYAYVVL FNFPRFDPAK TLGGIHPTEI VLYFWVFTI LIEEIRQLAA KPPKYIKDKV SVYFSDTWNF VDIFSLTVFI IAIILRFFTN SRIFTASRII LSLDIIFFIV R SLQIFSVN RLLGPKLVMI QKMMQDLAQF IIILAVFTIA YGIALHAVMF PSPGIYARNN TWVTITSVVQ YPYWQMYGEL FL DEIQGEK PKEFGEVDPD GRWLSPLLLA IYMVFTNILL LNLLIAIFNY TFERVQEDSD KVWKFQRYDL VQEYHSRPVF APP LVLLGH ILIFIRWVWR MCRCGHPPRG STMKIGLSPA EMEQMDNWEF QAAEMYIHQQ QQKNSGTLEE RVRALGDRVD CINS QLNRV LDSMSGTRAH ALTDGNGLEG GHDSEGRLAR MEVELSSNSE SLQKILALLQ QQPPVKGQAA VPIQLTLLHY KARSS PYPG STAKRFAVQD NMVDWQVPFP DYKPVNYTAP VVLANPVWAD KDLMAMSPRP ELPYNQMDHT CNVNRVSYNG TYVVKD GLP LNPMGRTGMQ GRGLLGRFGP NHAADPVVTR WKRTSAGVML QGGKKVLEFV AIQRKDNNQW AIPGGMVEPG QLVTQAL KA EFGEEAMAKL NVSQEEKERI AKQIERLFQQ GQEIYKGYVD DPRNTDNAWM ETVAVNFHDD KGDLFGDITL QAGDDAAA V RWQRVSGNIP LYASHVSILE KVAKMRDAAF SNSLEVLFQ

UniProtKB: Transient receptor potential cation channel subfamily M member-like 2

-
Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #4: [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOX...

MacromoleculeName: [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE
type: ligand / ID: 4 / Number of copies: 1 / Formula: A2R
Molecular weightTheoretical: 639.296 Da
Chemical component information

ChemComp-A2R:
[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 474307
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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