[English] 日本語
Yorodumi
- EMDB-63875: Cryo-EM structure of Pyruvate carboxylase from Mycobacterium tube... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63875
TitleCryo-EM structure of Pyruvate carboxylase from Mycobacterium tuberculosis in complex with acetyl-CoA and ADP
Map data
Sample
  • Complex: Pyruvate carboxylase protein with ACO and ADP
    • Protein or peptide: Pyruvate Carboxylase
KeywordsPyruvate Carboxylase / Pyruvate / Acetyl CoA / Mycobacterium tuberculosis / LIGASE
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / biotin carboxylase activity / gluconeogenesis / ATP binding / metal ion binding
Similarity search - Function
: / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain ...: / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Aldolase-type TIM barrel / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Pyruvate carboxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37RV (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSingh A / Sharma D / Raza M / Singh S / Das U
Funding support India, 1 items
OrganizationGrant numberCountry
Not funded India
CitationJournal: To Be Published
Title: Cryo EM structure of Mycobacterium tuberculosis Pyruvate carboxylase
Authors: Das U / Singh A
History
DepositionMar 21, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63875.png

Downloads & links

-
Map

FileDownload / File: emd_63875.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0143
Minimum - Maximum-0.052928943 - 0.15294401
Average (Standard dev.)0.00019305728 (±0.0054630497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 309.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_63875_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened map by DeepEmhancer

Fileemd_63875_additional_1.map
AnnotationSharpened map by DeepEmhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_63875_half_map_1.map
Annotationhalf_map_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_63875_half_map_2.map
Annotationhalf_map_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Pyruvate carboxylase protein with ACO and ADP

EntireName: Pyruvate carboxylase protein with ACO and ADP
Components
  • Complex: Pyruvate carboxylase protein with ACO and ADP
    • Protein or peptide: Pyruvate Carboxylase

-
Supramolecule #1: Pyruvate carboxylase protein with ACO and ADP

SupramoleculeName: Pyruvate carboxylase protein with ACO and ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis H37RV (bacteria)

-
Macromolecule #1: Pyruvate Carboxylase

MacromoleculeName: Pyruvate Carboxylase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: pyruvate carboxylase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFSKVLVANR GEIAIRAFRA AYELGVGTVA VYPYEDRNSQ HRLKADESYQ IGDIGHPVHA YLSVDEIVAT ARRAGADAIY PGYGFLSENP DLAAACAAAG ISFVGPSAEV LELAGNKSRA IAAAREAGLP VLMSSAPSAS VDELLSVAAG MPFPLFVKAV AGGGGRGMRR ...String:
MFSKVLVANR GEIAIRAFRA AYELGVGTVA VYPYEDRNSQ HRLKADESYQ IGDIGHPVHA YLSVDEIVAT ARRAGADAIY PGYGFLSENP DLAAACAAAG ISFVGPSAEV LELAGNKSRA IAAAREAGLP VLMSSAPSAS VDELLSVAAG MPFPLFVKAV AGGGGRGMRR VGDIAALPEA IEAASREAES AFGDPTVYLE QAVINPRHIE VQILADNLGD VIHLYERDCS VQRRHQKVIE LAPAPHLDAE LRYKMCVDAV AFARHIGYSC AGTVEFLLDE RGEYVFIEMN PRVQVEHTVT EEITDVDLVA SQLRIAAGET LEQLGLRQED IAPHGAALQC RITTEDPANG FRPDTGRISA LRTAGGAGVR LDGSTNLGAE ISPYFDSMLV KLTCRGRDLP TAVSRARRAI AEFRIRGVST NIPFLQAVLD DPDFRAGRVT TSFIDERPQL LTARASADRG TKILNFLADV TVNNPYGSRP STIYPDDKLP DLDLRAAPPA GSKQRLVKLG PEGFARWLRE SAAVGVTDTT FRDAHQSLLA TRVRTSGLSR VAPYLARTMP QLLSVECWGG ATYDVALRFL KEDPWERLAT LRAAMPNICL QMLLRGRNTV GYTPYPEIVT SAFVQEATAT GIDIFRIFDA LNNIESMRPA IDAVRETGSA IAEVAMCYTG DLTDPGEQLY TLDYYLKLAE QIVDAGAHVL AIKDMAGLLR PPAAQRLVSA LRSRFDLPVH LHTHDTPGGQ LASYVAAWHA GADAVDGAAA PLAGTTSQPA LSSIVAAAAH TEYDTGLSLS AVCALEPYWE ALRKVYAPFE SGLPGPTGRV YHHEIPGGQL SNLRQQAIAL GLGDRFEEIE EAYAGADRVL GRLVKVTPTS KVVGDLALAL VGAGVSADEF ASDPARFGIP ESVLGFLRGE LGDPPGGWPE PLRTAALAGR GAARPTAQLA ADDEIALSSV GAKRQATLNR LLFPSPTKEF NEHREAYGDT SQLSANQFFY GLRQGEEHRV KLERGVELLI GLEAISEPDE RGMRTVMCIL NGQLRPVLVR DRSIASAVPA AEKADRGNPG HIAAPFAGVV TVGVCVGERV GAGQTIATIE AMKMEAPITA PVAGTVERVA VSDTAQVEGG DLLVVVSGHH HHHHG

UniProtKB: Pyruvate carboxylase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 8.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8400 / Average exposure time: 1.04 sec. / Average electron dose: 50.0 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: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1680907
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 536403
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9ubg:
Cryo-EM structure of Pyruvate carboxylase from Mycobacterium tuberculosis in complex with Acetyl-CoA and ADP

+
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