[English] 日本語
Yorodumi
- EMDB-35901: GK tetramer with adjacent hooks at reaction state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35901
TitleGK tetramer with adjacent hooks at reaction state
Map data
Sample
  • Complex: Arabidopsis thaliana P5CSB incubated with all substrates.
    • Protein or peptide: Delta-1-pyrroline-5-carboxylate synthase B
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: GAMMA-GLUTAMYL PHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsL-proline biosynthesis / filamentous enzyme / PLANT PROTEIN
Function / homology
Function and homology information


glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / pollen development / proline biosynthetic process / L-proline biosynthetic process / embryo development ending in seed dormancy / plasmodesma / chloroplast ...glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / pollen development / proline biosynthetic process / L-proline biosynthetic process / embryo development ending in seed dormancy / plasmodesma / chloroplast / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Delta l-pyrroline-5-carboxylate synthetase / Bifunctional delta 1-pyrroline-5-carboxylate synthetase, glutamate-5-kinase domain / GPR domain / Gamma-glutamyl phosphate reductase GPR, conserved site / Gamma-glutamyl phosphate reductase signature. / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / Glutamate/acetylglutamate kinase / Aspartate/glutamate/uridylate kinase ...Delta l-pyrroline-5-carboxylate synthetase / Bifunctional delta 1-pyrroline-5-carboxylate synthetase, glutamate-5-kinase domain / GPR domain / Gamma-glutamyl phosphate reductase GPR, conserved site / Gamma-glutamyl phosphate reductase signature. / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / Glutamate/acetylglutamate kinase / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Delta-1-pyrroline-5-carboxylate synthase B
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang T / Guo CJ / Liu JL
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: GK tetramer with adjacent hooks at reaction state
Authors: Zhang T / Guo CJ / Liu JL
History
DepositionApr 10, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35901.png

Downloads & links

-
Map

FileDownload / File: emd_35901.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 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: 0.005
Minimum - Maximum-0.009686425 - 0.022491764
Average (Standard dev.)0.00007136869 (±0.0009389028)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_35901_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_35901_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Arabidopsis thaliana P5CSB incubated with all substrates.

EntireName: Arabidopsis thaliana P5CSB incubated with all substrates.
Components
  • Complex: Arabidopsis thaliana P5CSB incubated with all substrates.
    • Protein or peptide: Delta-1-pyrroline-5-carboxylate synthase B
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: GAMMA-GLUTAMYL PHOSPHATE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Arabidopsis thaliana P5CSB incubated with all substrates.

SupramoleculeName: Arabidopsis thaliana P5CSB incubated with all substrates.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 78.9 kDa/nm

-
Macromolecule #1: Delta-1-pyrroline-5-carboxylate synthase B

MacromoleculeName: Delta-1-pyrroline-5-carboxylate synthase B / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: glutamate 5-kinase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 78.97732 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTEIDRSRAF AKDVKRIVVK VGTAVVTGKG GRLALGRLGA ICEQLAELNS DGFEVILVSS GAVGLGRQRL RYRQLVNSSF ADLQKPQME LDGKACAGVG QSSLMAYYET MFDQLDVTVA QMLVTDSSFR DKDFRKQLSE TVKAMLRMRV IPVFNENDAI S TRRAPYKD ...String:
MTEIDRSRAF AKDVKRIVVK VGTAVVTGKG GRLALGRLGA ICEQLAELNS DGFEVILVSS GAVGLGRQRL RYRQLVNSSF ADLQKPQME LDGKACAGVG QSSLMAYYET MFDQLDVTVA QMLVTDSSFR DKDFRKQLSE TVKAMLRMRV IPVFNENDAI S TRRAPYKD STGIFWDNDS LAALLSLELK ADLLILLSDV EGLYTGPPSD STSKLIHTFI KEKHQDEITF GEKSKLGRGG MT AKVKAAV NAAYGGVPVI ITSGYAAENI SKVLRGLRVG TLFHQDAHLW APVVDTTSRD MAVAARESSR KLQALSSEDR KQI LHDIAN ALEVNEKTIK AENDLDVAAA QEAGYEESLV ARLVMKPGKI SSLAASVRQL AEMEDPIGRV LKKTQVADDL ILEK TSSPI GVLLIVFESR PDALVQIASL AIRSGNGLLL KGGKEARRSN AILHKVITDA IPETVGGKLI GLVTSREEIP DLLKL DDVI DLVIPRGSNK LVSQIKNSTK IPVLGHADGI CHVYVDKSGK LDMAKRIVSD AKLDYPAACN AMETLLVHKD LEQNGF LDD LIYVLQTKGV TLYGGPRASA KLNIPETKSF HHEYSSKACT VEIVEDVYGA IDHIHQHGSA HTDCIVTEDS EVAEIFL RQ VDSAAVFHNA STRFSDGFRF GLGAEVGIST SRIHARGPVG VEGLLTTRWI MRGKGQVVDG DNGIVYTHKD LPVLQRTE A VENGI

UniProtKB: Delta-1-pyrroline-5-carboxylate synthase B

-
Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

-
Macromolecule #3: GAMMA-GLUTAMYL PHOSPHATE

MacromoleculeName: GAMMA-GLUTAMYL PHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: RGP
Molecular weightTheoretical: 227.109 Da
Chemical component information

ChemComp-RGP:
GAMMA-GLUTAMYL PHOSPHATE

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7wx3

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 223041
FSC plot (resolution estimation)

+
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