[English] 日本語
Yorodumi
- EMDB-10347: Structure of the SMG1-SMG8-SMG9 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10347
TitleStructure of the SMG1-SMG8-SMG9 complex
Map dataCryoEM map of the SMG1-SMG8-SMG9 complex core
Sample
  • Complex: SMG1-SMG8-SMG9 PIKK Kinase complex
    • Protein or peptide: SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1
    • Protein or peptide: Protein SMG8
    • Protein or peptide: Protein SMG9
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsKinase / NMD / IP6 / G-fold protein / PIKK family / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of protein kinase activity / diacylglycerol-dependent serine/threonine kinase activity / chromatoid body / eye development / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / phosphatidylinositol phosphate biosynthetic process / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...regulation of protein kinase activity / diacylglycerol-dependent serine/threonine kinase activity / chromatoid body / eye development / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / phosphatidylinositol phosphate biosynthetic process / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / brain development / heart development / peptidyl-serine phosphorylation / in utero embryonic development / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA damage response / negative regulation of apoptotic process / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Nonsense-mediated mRNA decay factor SMG8/SMG9 / Smg8_Smg9 / Nonsense-mediated mRNA decay factor SMG9 / Serine/threonine-protein kinase SMG1 / Serine/threonine-protein kinase SMG1, N-terminal / SMG1, PIKK catalytic domain / Serine/threonine-protein kinase smg-1 / Serine/threonine-protein kinase SMG1 N-terminal / Rapamycin binding domain / : ...Nonsense-mediated mRNA decay factor SMG8/SMG9 / Smg8_Smg9 / Nonsense-mediated mRNA decay factor SMG9 / Serine/threonine-protein kinase SMG1 / Serine/threonine-protein kinase SMG1, N-terminal / SMG1, PIKK catalytic domain / Serine/threonine-protein kinase smg-1 / Serine/threonine-protein kinase SMG1 N-terminal / Rapamycin binding domain / : / FATC domain / FATC / FAT domain profile. / FATC domain profile. / FATC domain / PIK-related kinase / 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-like helical / Armadillo-type fold / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nonsense-mediated mRNA decay factor SMG8 / Serine/threonine-protein kinase SMG1 / Nonsense-mediated mRNA decay factor SMG9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsGat Y / Schuller JM
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: InsP binding to PIKK kinases revealed by the cryo-EM structure of an SMG1-SMG8-SMG9 complex.
Authors: Yair Gat / Jan Michael Schuller / Mahesh Lingaraju / Elisabeth Weyher / Fabien Bonneau / Mike Strauss / Peter J Murray / Elena Conti /
Abstract: We report the 3.45-Å resolution cryo-EM structure of human SMG1-SMG8-SMG9, a phosphatidylinositol-3-kinase (PI(3)K)-related protein kinase (PIKK) complex central to messenger RNA surveillance. ...We report the 3.45-Å resolution cryo-EM structure of human SMG1-SMG8-SMG9, a phosphatidylinositol-3-kinase (PI(3)K)-related protein kinase (PIKK) complex central to messenger RNA surveillance. Structural and MS analyses reveal the presence of inositol hexaphosphate (InsP) in the SMG1 kinase. We show that the InsP-binding site is conserved in mammalian target of rapamycin (mTOR) and potentially other PIKK members, and that it is required for optimal in vitro phosphorylation of both SMG1 and mTOR substrates.
History
DepositionOct 1, 2019-
Header (metadata) releaseOct 23, 2019-
Map releaseDec 11, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6syt
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10347.png

Downloads & links

-
Map

FileDownload / File: emd_10347.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of the SMG1-SMG8-SMG9 complex core
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.23418635 - 0.3813731
Average (Standard dev.)0.00020808347 (±0.0080173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z318.000318.000318.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2340.3810.000

-
Supplemental data

-
Sample components

-
Entire : SMG1-SMG8-SMG9 PIKK Kinase complex

EntireName: SMG1-SMG8-SMG9 PIKK Kinase complex
Components
  • Complex: SMG1-SMG8-SMG9 PIKK Kinase complex
    • Protein or peptide: SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1
    • Protein or peptide: Protein SMG8
    • Protein or peptide: Protein SMG9
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: SMG1-SMG8-SMG9 PIKK Kinase complex

SupramoleculeName: SMG1-SMG8-SMG9 PIKK Kinase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-p...

MacromoleculeName: SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1
type: protein_or_peptide / ID: 1
Details: Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of ...Details: Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R
Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 401.403938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)FSTNFR DTVDILVGWH IDHTQKPSLT QQVS GWLQS LEPFWVADLA FSTTLLGQFL EDMEAYAEDL SHVASGESVD EDVPPPSVSL PKLAALLRVF STVVRSIGER FSPIR GPPI TEAYVTDVLY RVMRCVTAAN QVFFSEAVLT AANECVGVLL GSLDPSMTIH CDMVITYGLD QLENCQTCGT DYIISV LNL LTLIVEQINT KLPSSFVEKL FIPSSKLLFL RYHKEKEVVA VAHAVYQAVL SLKNIPVLET AYKLILGEMT CALNNLL HS LQLPEACSEI KHEAFKNHVF NVDNAKFVVI FDLSALTTIG NAKNSLIGMW ALSPTVFALL SKNLMIVHSD LAVHFPAI Q YAVLYTLYSH CTRHDHFISS SLSSSSPSLF DGAVISTVTT ATKKHFSIIL NLLGILLKKD NLNQDTRKLL MTWALEAAV LMRKSETYAP LFSLPSFHKF CKGLLANTLV EDVNICLQAC SSLHALSSSL PDDLLQRCVD VCRVQLVHSG TRIRQAFGKL LKSIPLDVV LSNNNHTEIQ EISLALRSHM SKAPSNTFHP QDFSDVISFI LYGNSHRTGK DNWLERLFYS CQRLDKRDQS T IPRNLLKT DAVLWQWAIW EAAQFTVLSK LRTPLGRAQD TFQTIEGIIR SLAAHTLNPD QDVSQWTTAD NDEGHGNNQL RL VLLLQYL ENLEKLMYNA YEGCANALTS PPKVIRTFFY TNRQTCQDWL TRIRLSIMRV GLLAGQPAVT VRHGFDLLTE MKT TSLSQG NELEVTIMMV VEALCELHCP EAIQGIAVWS SSIVGKNLLW INSVAQQAEG RFEKASVEYQ EHLCAMTGVD CCIS SFDKS VLTLANAGRN SASPKHSLNG ESRKTVLSKP TDSSPEVINY LGNKACECYI SIADWAAVQE WQNAIHDLKK STSST SLNL KADFNYIKSL SSFESGKFVE CTEQLELLPG ENINLLAGGS KEKIDMKKLL PNMLSPDPRE LQKSIEVQLL RSSVCL ATA LNPIEQDQKW QSITENVVKY LKQTSRIAIG PLRLSTLTVS QSLPVLSTLQ LYCSSALENT VSNRLSTEDC LIPLFSE AL RSCKQHDVRP WMQALRYTMY QNQLLEKIKE QTVPIRSHLM ELGLTAAKFA RKRGNVSLAT RLLAQCSEVQ LGKTTTAQ D LVQHFKKLST QGQVDEKWGP ELDIEKTKLL YTAGQSTHAM EMLSSCAISF CKSVKAEYAV AKSILTLAKW IQAEWKEIS GQLKQVYRAQ HQQNFTGLST LSKNILTLIE LPSVNTMEEE YPRIESESTV HIGVGEPDFI LGQLYHLSSV QAPEVAKSWA ALASWAYRW GRKVVDNAS(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)EGVIKVWR KVVDRIFSLY KL SCSAYFT FLKLNAGQIP LDEDDPRLHL SHRVEQSTDD MIVMATLRLL RLLVKHAGEL RQYLEHGLET TPTAPWRGII PQL FSRLNH PEVYVRQSIC NLLCRVAQDS PHLILYPAIV GTISLSSESQ ASGNKFSTAI PTLLGNIQGE ELLVSECEGG SPPA SQDSN KDEPKSGLNE DQAMMQDCYS KIVDKLSSAN PTMVLQVQML VAELRRVTVL WDELWLGVLL QQHMYVLRRI QQLED EV(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)PHEK W FQDNYGDA IENALEKLK(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)YILRLEEIS PWLAAMTNTE IALPGEVSAR DTVTIHSVGG TITILPTKTK PKKLLFLGSD GKSYPYLFKG L EDLHLDER IMQFLSIVNT MFATINRQET PRFHARHYSV TPLGTRSGLI QWVDGATPLF GLYKRWQQRE AALQAQK(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)WPLHVMKA VLEELMEATP PNLLAKELWS SCTTPDE WW RVTQSYARST AVMSMVGYII GLGARHLDNV LIDMTTGEVV HIDYNVCFEK GKSLRVPEKV PFRMTQNIET ALGVTGVE G VFRLSCEQVL HIMRRGRETL LTLLEAFVYD PLVDWTAGGE AGFAGAVYGG GGQQAESKQS KREMEREITR SLFSSRVAE IKVNWFKNRD EMLVVLPKLD GSLDEYLSLQ EQLTDVEKLQ GKLLEEIEFL EGAEGVDHPS HTLQHRYSEH TQLQTQQRAV QEAIQVKLN EFEQWITHYQ AAFNNLEATQ LASLLQEIST QMDLGPPSYV PATAFLQNAG QAHLISQCEQ LEGEVGALLQ Q RRSVLRGC LEQLHHYATV ALQYPKAIFQ KHRIEQWKTW MEELICNTTV ERCQELYRKY EMQYAPQPPP TVCQFITATE MT LQRYAAD INSRLIRQVE RLKQEAVTVP VCEDQLKEIE RCIKVFLHEN GEEGSLSLAS VIISALCTLT RRNLMMEGAA SSA GEQLVD LTSRDGAWFL EELCSMSGNV TCLVQLLKQC HLVPQDLDIP NPMEASETVH LANGVYTSLQ ELNSNFRQII FPEA LRCLM KGEYTLESML HELDGLIEQT TDGVPLQTLV ESLQAYLRNA AMGLEEETHA HYIDVARLLH AQYGELIQPR NGSVD ETPK MSAGQMLLVA FDGMFAQVET AFSLLVEKLN KMEIPIAWRK IDIIREARST QVNFFDDDNH RQVLEEIFFL KRLQTI KEF FRLCGTFSKT LSGSSSLEDQ NTVNGPVQIV NVKTLFRNSC FSEDQMAKPI KAFTADFVRQ LLIGLPNQAL GLTLCSF IS ALGVDIIAQV EAKDFGAESK VSVDDLCKKA VEHNIQIGKF SQLVMNRATV LASSYDTAWK KHDLVRRLET SISSCKTS L QRVQLHIAMF QWQHEDLLIN RPQAMSVTPP PRSAILTSMK KKLHTLSQIE TSIATVQEKL AALESSIEQR LKWAGGANP ALAPVLQDFE ATIAERRNLV LKESQRASQV TFLCSNIIHF ESLRTRTAEA LNLDAALFEL IKRCQQMCSF ASQFNSSVSE LELRLLQRV DTGLEHPIGS SEWLLSAHKQ LTQDMSTQRA IQTEKEQQIE TVCETIQNLV DNIKTVLTGH NRQLGDVKHL L KAMAKDEE AALADGEDVP YENSVRQFLG EYKSWQDNIQ TVLFTLVQAM GQVRSQEHVE MLQEITPTLK ELKTQSQSIY NN LVSFASP LVTDATNECS SPTSSATYQP SFAAAVRSNT GQKTQPDVMS QNARKLIQKN LATSADTPPS TVPGTGKSVA CSP KKAVRD PKTGKAVQER NSYAVSVWKR VKAKLEGRDV DPNRRMSVAE QVDYVIKEAT NLDNLAQLYE GWTAWV

UniProtKB: Serine/threonine-protein kinase SMG1, Serine/threonine-protein kinase SMG1, Serine/threonine-protein kinase SMG1, Serine/threonine-protein kinase SMG1, Serine/threonine-protein kinase SMG1

-
Macromolecule #2: Protein SMG8

MacromoleculeName: Protein SMG8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.82575 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGPVSLRDL LMGASAWMGS ESPGGSPTEG GGSAAGGPEP PWREDEICVV GIFGKTALRL NSEKFSLVNT VCDRQVFPLF RHQDPGDPG PGIRTEAGAV GEAGGAEDPG AAAGGSVRGS GAVAEGNRTE AGSQDYSLLQ AYYSQESKVL YLLLTSICDN S QLLRACRA ...String:
MAGPVSLRDL LMGASAWMGS ESPGGSPTEG GGSAAGGPEP PWREDEICVV GIFGKTALRL NSEKFSLVNT VCDRQVFPLF RHQDPGDPG PGIRTEAGAV GEAGGAEDPG AAAGGSVRGS GAVAEGNRTE AGSQDYSLLQ AYYSQESKVL YLLLTSICDN S QLLRACRA LQSGEAGGGL SLPHAEAHEF WKHQEKLQCL SLLYLFSVCH ILLLVHPTCS FDITYDRVFR ALDGLRQKVL PL LKTAIKD CPVGKDWKLN CRPCPPRLLF LFQLNGALKV EPPRNQDPAH PDKPKKHSPK RRLQHALEDQ IYRIFRKSRV LTN QSINCL FTVPANQAFV YIVPGSQEED PVGMLLDQLR SHCTVKDPES LLVPAPLSGP RRYQVMRQHS RQQLSFHIDS SSSS SSGQL VDFTLREFLW QHVELVLSKK GFDDSVGRNP QPSHFELPTY QKWISAASKL YEVAIDGKEE DLGSPTGELT SKILS SIKV LEGFLDIDTK FSENRCQKAL PMAHSAYQSN LPHNYTMTVH KNQLAQALRV YSQHARGPAF HKYAMQLHED CYKFWS NGH QLCEERSLTD QHCVHKFHSL PKSGEKPEAD RNPPVLYHNS RARSTGACNC GRKQAPRDDP FDIKAANYDF YQLLEEK CC GKLDHINFPV FEPSTPDPAP AKNESSPAPP DSDADKLKEK EPQTQGESTS LSLALSLGQS TDSLGTYPAD PQAGGDNP E VHGQVEVKTE KRPNFVDRQA STVEYLPGML HSNCPKGLLP KFSSWSLVKL GPAKSYNFHT GLDQQGFIPG TNYLMPWDI VIRTRAEDEG DLDTNSWPAP NKAIPGKRSA VVMGRGRRRD DIARAFVGFE YEDSRGRRFM CSGPDKVMKV MGSGPKESAL KALNSDMPL YILSSSQGRG LKPHYAQLMR LFVVVPDAPL QIILMPQVQP GPPPCPVFYP EKQEITLPPD GLWVLRFPYA Y VTERGPCF PPKENVQLMS YKVLRGVLKA VTQ

UniProtKB: Nonsense-mediated mRNA decay factor SMG8

-
Macromolecule #3: Protein SMG9

MacromoleculeName: Protein SMG9 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.717473 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSESGHSQPG LYGIERRRRW KEPGSGGPQN LSGPGGRERD YIAPWERERR DASEETSTSV MQKTPIILSK PPAERSKQPP PPTAPAAPP APAPLEKPIV LMKPREEGKG PVAVTGASTP EGTAPPPPAA PAPPKGEKEG QRPTQPVYQI QNRGMGTAAP A AMDPVVGQ ...String:
MSESGHSQPG LYGIERRRRW KEPGSGGPQN LSGPGGRERD YIAPWERERR DASEETSTSV MQKTPIILSK PPAERSKQPP PPTAPAAPP APAPLEKPIV LMKPREEGKG PVAVTGASTP EGTAPPPPAA PAPPKGEKEG QRPTQPVYQI QNRGMGTAAP A AMDPVVGQ AKLLPPERMK HSIKLVDDQM NWCDSAIEYL LDQTDVLVVG VLGLQGTGKS MVMSLLSANT PEEDQRTYVF RA QSAEMKE RGGNQTSGID FFITQERIVF LDTQPILSPS ILDHLINNDR KLPPEYNLPH TYVEMQSLQI AAFLFTVCHV VIV VQDWFT DLSLYRFLQT AEMVKPSTPS PSHESSSSSG SDEGTEYYPH LVFLQNKARR EDFCPRKLRQ MHLMIDQLMA HSHL RYKGT LSMLQCNVFP GLPPDFLDSE VNLFLVPFMD SEAESENPPR AGPGSSPLFS LLPGYRGHPS FQSLVSKLRS QVMSM ARPQ LSHTILTEKN WFHYAARIWD GVRKSSALAE YSRLLA

UniProtKB: Nonsense-mediated mRNA decay factor SMG9

-
Macromolecule #4: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

-
Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: PBS
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 52.8 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

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 214254
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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