[English] 日本語
Yorodumi
- EMDB-29870: Human IMPDH2 mutant - L245P, treated with GTP, ATP, IMP, and NAD+... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29870
TitleHuman IMPDH2 mutant - L245P, treated with GTP, ATP, IMP, and NAD+; bent filament segment reconstruction
Map dataMap from PHENIX density modification. Used to build model.
Sample
  • Complex: Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P mutant, bound to GTP, ATP, IMP, and NAD+
    • Protein or peptide: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2
KeywordsFilament / Dehydrogenase / CBS domain / Bateman domain / purine biosynthesis / OXIDOREDUCTASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsO'Neill AG / Kollman JM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118396 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008268 United States
CitationJournal: J Comput Chem / Year: 2004
Title: UCSF Chimera--a visualization system for exploratory research and analysis.
Authors: Eric F Pettersen / Thomas D Goddard / Conrad C Huang / Gregory S Couch / Daniel M Greenblatt / Elaine C Meng / Thomas E Ferrin /
Abstract: The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and ...The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.
History
DepositionFeb 21, 2023-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29870.png

Downloads & links

-
Map

FileDownload / File: emd_29870.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap from PHENIX density modification. Used to build model.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 400 pix.
= 337.2 Å		0.84 Å/pix.
x 400 pix.
= 337.2 Å		0.84 Å/pix.
x 400 pix.
= 337.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.843 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.48
Minimum - Maximum-7.8762755 - 15.922696999999999
Average (Standard dev.)0.000000000000687 (±0.2743121)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 337.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_29870_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Map from Relion Postprocessing.

Fileemd_29870_additional_1.map
AnnotationMap from Relion Postprocessing.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_29870_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_29870_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P muta...

EntireName: Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P mutant, bound to GTP, ATP, IMP, and NAD+
Components
  • Complex: Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P mutant, bound to GTP, ATP, IMP, and NAD+
    • Protein or peptide: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2

-
Supramolecule #1: Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P muta...

SupramoleculeName: Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P mutant, bound to GTP, ATP, IMP, and NAD+
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: 5 uM enzyme was mixed with 20 mM GTP, 1 mM ATP, 1 mM MgCl2, 3 mM IMP, and 5 mM NAD+.
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2

MacromoleculeName: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: IMP dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SEFELMADYL ISGGTSYVPD DGLTAQQLFN CGDGLTYNDF LILPGYIDFT ADQVDLTSAL TKKITLKTPL VSSPMDTVTE AGMAIAMAL TGGIGFIHHN CTPEFQANEV RKVKKYEQGF ITDPVVLSPK DRVRDVFEAK ARHGFCGIPI TDTGRMGSRL V GIISSRDI ...String:
SEFELMADYL ISGGTSYVPD DGLTAQQLFN CGDGLTYNDF LILPGYIDFT ADQVDLTSAL TKKITLKTPL VSSPMDTVTE AGMAIAMAL TGGIGFIHHN CTPEFQANEV RKVKKYEQGF ITDPVVLSPK DRVRDVFEAK ARHGFCGIPI TDTGRMGSRL V GIISSRDI DFLKEEEHDC FLEEIMTKRE DLVVAPAGIT LKEANEILQR SKKGKLPIVN EDDELVAIIA RTDLKKNRDY PL ASKDAKK QLPCGAAIGT HEDDKYRLDL LAQAGVDVVV LDSSQGNSIF QINMIKYIKD KYPNLQVIGG NVVTAAQAKN LID AGVDAL RVGMGSGSIC ITQEVLACGR PQATAVYKVS EYARRFGVPV IADGGIQNVG HIAKALALGA STVMMGSLLA ATTE APGEY FFSDGIRLKK YRGMGSLDAM DKHLSSQNRY FSEADKIKVA QGVSGAVQDK GSIHKFVPYL IAGIQHSCQD IGAKS LTQV RAMMYSGELK FEKRTSSAQV EGGVHSLHSY EKRLF

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 2967 / Average exposure time: 3.0 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 0.28 µm / Nominal defocus min: 1.74 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1421990
Startup modelType of model: EMDB MAP
EMDB ID:

20701


Details: Map was low-pass filtered
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: OTHER / Software: (Name: RELION (ver. 3.1), PHENIX (ver. 1.18.2))
Details: FSCref 0.5 cut-off from PHENIX density modification
Number images used: 91716
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

+
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