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- EMDB-10232: Structure of the closed conformation of CtTel1 -

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Basic information

Entry
Database: EMDB / ID: EMD-10232
TitleStructure of the closed conformation of CtTel1
Map dataOne protomer in closed conformation
Sample
  • Complex: CtTel1
    • Protein or peptide: Serine/threonine-protein kinase Tel1
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


chromatin organization / chromosome, telomeric region / non-specific serine/threonine protein kinase / intracellular signal transduction / DNA repair / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / PIK-related kinase, FAT / FATC domain / FATC / FAT domain / FAT domain profile. ...Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / PIK-related kinase, FAT / FATC domain / FATC / FAT domain / FAT domain profile. / FATC domain profile. / FATC domain / PIK-related kinase / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase Tel1
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJansma M / Eustermann SE / Kostrewa D / Lammens K / Hopfner KP
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council Germany
CitationJournal: Structure / Year: 2020
Title: Near-Complete Structure and Model of Tel1ATM from Chaetomium thermophilum Reveals a Robust Autoinhibited ATP State.
Authors: Marijke Jansma / Christian Linke-Winnebeck / Sebastian Eustermann / Katja Lammens / Dirk Kostrewa / Kristina Stakyte / Claudia Litz / Brigitte Kessler / Karl-Peter Hopfner /
Abstract: Tel1 (ATM in humans) is a large kinase that resides in the cell in an autoinhibited dimeric state and upon activation orchestrates the cellular response to DNA damage. We report the structure of an ...Tel1 (ATM in humans) is a large kinase that resides in the cell in an autoinhibited dimeric state and upon activation orchestrates the cellular response to DNA damage. We report the structure of an endogenous Tel1 dimer from Chaetomium thermophilum. Major parts are at 2.8 Å resolution, including the kinase active site with ATPγS bound, and two different N-terminal solenoid conformations are at 3.4 Å and 3.6 Å, providing a side-chain model for 90% of the Tel1 polypeptide. We show that the N-terminal solenoid has DNA binding activity, but that its movements are not coupled to kinase activation. Although ATPγS and catalytic residues are poised for catalysis, the kinase resides in an autoinhibited state. The PIKK regulatory domain acts as a pseudo-substrate, blocking direct access to the site of catalysis. The structure allows mapping of human cancer mutations and defines mechanisms of autoinhibition at near-atomic resolution.
History
DepositionAug 16, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseOct 30, 2019-
UpdateJan 15, 2020-
Current statusJan 15, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0126
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0126
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6skz
  • Surface level: 0.0126
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10232.png

Downloads & links

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Map

FileDownload / File: emd_10232.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOne protomer in closed conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 352 pix.
= 372.768 Å		1.06 Å/pix.
x 352 pix.
= 372.768 Å		1.06 Å/pix.
x 352 pix.
= 372.768 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0126 / Movie #1: 0.0126
Minimum - Maximum-0.04518767 - 0.07342015
Average (Standard dev.)0.00005746563 (±0.0012024009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 372.768 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z372.768372.768372.768
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ307236
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.0450.0730.000

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Supplemental data

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Sample components

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Entire : CtTel1

EntireName: CtTel1
Components
  • Complex: CtTel1
    • Protein or peptide: Serine/threonine-protein kinase Tel1
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: CtTel1

SupramoleculeName: CtTel1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Molecular weightExperimental: 640 KDa

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Macromolecule #1: Serine/threonine-protein kinase Tel1

MacromoleculeName: Serine/threonine-protein kinase Tel1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Molecular weightTheoretical: 329.927031 KDa
SequenceString: MPRVKSYTGG TINFKEIESH LVGSSATARK DAVEALIAYF DGSRTQSQTT FDDKAYHRLF EALFRCTLIE KEAYFNSKKS VKVTAAAAA RLERCPEALR LAVRHGVTTI RRKTARAIID HIVQVLPGPD GAYVMPLLAG YVKVLYEFLD NPASAENIAA L SGEGWEVC ...String:
MPRVKSYTGG TINFKEIESH LVGSSATARK DAVEALIAYF DGSRTQSQTT FDDKAYHRLF EALFRCTLIE KEAYFNSKKS VKVTAAAAA RLERCPEALR LAVRHGVTTI RRKTARAIID HIVQVLPGPD GAYVMPLLAG YVKVLYEFLD NPASAENIAA L SGEGWEVC VDFCIDVLSR FLELGDRESG SLSRASPAPG ATARSGSVAG TQGSGEQIGT HVAVDVLSCL YMLCIAHNAP IQ RKADRLP HVVIQLLQLR QMKIGELQKM AFATFNIVFQ RMQAEDVALC KTLVKQVVPL LSHWWQPRAL SRDAMLNSIR DEM LKTLYG TRLYIQALLR EAADESFPQD VEELLDTLWC DYSRREERAR LQLDDITFTN MLLPPDHPRT GIFSLRPHHT AGEQ NWALL ENLAILEAAY SKHGQQEQSQ QNQQQPEIDQ PRKRRKMSGR QNRVHQKLHS LDPAVRLSAL QLIPFLTRHK KPSLE DVAE TLEDLSKHVT AKQAIVASWA MLACSSLAIH EVSRHPSLSS SWKQLWQLAV RSLSLPPISR ASCVLLNSIL KANLIP RHE LADDINQIVT TADISGPAIL VDASLGLMLN LLRFRNNMFP NASQATSNHI IRWVFVRWSP AELTYASLHG THATPYD LV NLLRACYGIS PLVMAQPLRL FNGPIVLHWK EQAEMEPFIR YLLLLHEEEP DTTVTPAQQE EQLPESNSAT DVAGSNAS R RLALELFYPK VEELQELAES WQKRGGEGAT PVSMERLRSM VLACLTGALL LPDLVNINSS LSRDLESAVF SIVDATLKV ILNSPPSENL FGMILASSAP YIPHLIEPEL IALKRERPHL LKFFGKLSEA LYERSRRESS HRDDQVIDID PDFEPQTSQK NTASKAKTL PRRDILLSYT PEAFYLETSL RIHFLDIIRL NDGEIGRIPE PIINQLAGLS GEQFLCCREF MREIFTSDAI V PLGGATTI LETAGHIVSR YEYACCEVAL CNCIDIMDSF INLWTDNHFD IAEMAGDLYH YLVKQSLPNN SMSAAAQIRL AS LLLHLLE VKSEYASNLG LPSSQSTLLK ILQDGPMKLK HYIGLEIPKL FGLYVLKTHD DIFVDVLEHL PSDPDVVEGL AFR LFVLAE LACRWPTLLR RSIYHTFEIP GKITKISKSQ SCVTHSALYA ASCIKRIAQT LKLSGPQELF KLFAPQLLYT WLDN DSIQD IAYEIFGFSS LLDLLREAQT EAAAIMMMRG QEQEVCQLAQ SLGLTPEKLV QQSFTKIIAY SIAHDISIAG GPDYV TGES RMRKILGKEE YLANIHLNFA DIISTFFDIF DQEDPIEKAF RRDERFAYAA ETLEEIKKLG HLPTALPPNQ QPMFRA KYL PREIVHLCSR TQYEPENIWT PALVVFVARK LLKTIHPALG PLHACSVLRK IRVLICLAGD HAISGYPLEM LLHSLRV FV VDPECADDAL GITQYLIKRG DEYLKRTPSF LAGYALSSLA DLRVFLESSQ SSTTQESQFK ATKSKAQEFH AWFSKYLA A YDSPEFKDEG QKQAFRSITE NAAHIRASGN AEKGTHESNL LLEILKDWGR ENQLLNEPAR DVALSMLCGV FNIPPSSRL DVIETDEDAI KNGAVVWKSC SSQRLGGEYL AWAGRVLGRS FAASGEVPED LLRESQLQEY RRLSQGVGSS EEGLLNLIKS LTISGDCFT AGLAEAALRT IVSDAISDND HDLLSACQES LPEPLLIASN WDPYRTPLSD QFKVDPPANT EVFSARALEN P NWSQHLAI RLALSAPKIV TLRVLPPILS KVKGFAERAF PFVVHLVLAY QLDKQQSAKR ELSESLQEWL NFTSEPAKEN LK LLINTIL YLRTQPLPGE SSIADRAHWL DVNMASAAAA ATRCGMYKVA LLFAELAAES TRGSRRSSAA RETDDSSDIL LEI FENIDD PDAYYGLSQD ASLSTVLARL EYENDGAKSL AFRGAQYDSH LRGRDLQSRQ DCNALIKALS SLGLAGLSNS LLQS QQSID GSSDSLDATF TTARKLEIWN LPAPVNSDSW AVTVYKAYQS MYQAQELDTV RSMVHDGLKN TVRHLSSGSL NTSVL RQQL GALAALTELD DILNVRDQSE LQCTLATFEK RSKWMMSGRY ADVSQILSCR ETTLSMWSQR HNLRAAGLTS ADARLV QIR GMLLSSDIFR FHRARQETLN LSTALSDLIP SCESLGLSVD AAIKMEAANA LWDHGEMISS IRMLQAIDKD SSLKKQS VP LSRSDLLSKI GYQVSVARLE SPDAIQKKYL EPALKELKGK IEGREAGQVF HQFAVFCDEQ LQNPDSLEDL ARLQNLKK G KDEEVAQLKA LIASAKDSQL RNRYQSHLAK AKQWQELDQQ ELRRVEQTRS EFLKLCIENY LLSLAASDEH DNDALRFMA LWLEKSEEEV ANEVVKKWIN KVPTRKFALL MNQLSSRLQD HNTLFQKLLI DLVYRICVDH PYHGMYHIWT GARTRVNKDD EVAVSRQRA TDKIAKALSK NNKVSSIWPA IDQTSRVYHA LAMDRDPTRY KSGQKVPIKN SPVGQNFLST MSNNPIPPPT L QIEVSANL DYSHVPMIHK FAPEMAIASG VSAPKILTAI GTDGRKYKQL VKGGNDDLRQ DAIMEQVFAA VSELLKLHRE TR QRNLGIR TYKVLPLTSS SGLIEFVSNT IPLHEYLMPA HERYYPKDLK GSQCRKEIAN AQTKNTETRI AVYRRVTERF HPV MRYFFM EYFPDPDEWF QKRTNYTRTT AAISMLGHVL GLGDRHGHNI LLDHKTGEVV HIDLGVAFEM GRVLPVPELV PFRL TRDIV DGMGITKTEG VFRRCCEFTL DALREEAASI QTILDSLRHD TLYQWSISPV RMAKLQNARE VGGEDGGVGG GEDGE GGGV PKEKKQRPAN EPSEADRAIE VVKKKLSKTL SVMATVNDLI NQATSVSNLA VLYSGWAAYA

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Macromolecule #2: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 1 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.15 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormula
25.0 mMHEPES-NaOH
150.0 mMNaCl

Details: 1 mM MgCl2 and 0.1 mM ATPgS (final concentrations) added before plunging
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288.15 K / Instrument: LEICA EM GP
Details: TWEEN-20 was added to a final concentration of 0.05% immediately before vitrification. Sample was preincubated 45 seconds before plunging into liquid ethane..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 13786 / Average exposure time: 8.0 sec. / Average electron dose: 55.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 863937
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13) / Software - details: As implemented in RELION
Startup modelType of model: OTHER
Details: Startup model was based on earlier lower resolution CtTel1 reconstruction, which in turn was based on EMDB entry EMD-6399
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.2) / Number images used: 132127
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.2)
FSC plot (resolution estimation)

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