[English] 日本語
Yorodumi
- EMDB-73983: Human GGPPS in the Closed Hexamer Conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73983
TitleHuman GGPPS in the Closed Hexamer Conformation
Map dataPost-processed map (cropped, sharpened and density modified with Resolve-CryoEM in Phenix)
Sample
  • Complex: GGPPS hexamer in the closed conformation
    • Protein or peptide: Geranylgeranyl pyrophosphate synthase
KeywordsInhibitor / complex / isoprenoid / synthesis / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


isoprenoid metabolic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / (2E,6E)-farnesyl diphosphate synthase / Lanosterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase activity / isoprenoid biosynthetic process ...isoprenoid metabolic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / (2E,6E)-farnesyl diphosphate synthase / Lanosterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase activity / isoprenoid biosynthetic process / trans, trans-farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / Activation of gene expression by SREBF (SREBP) / Z disc / perinuclear region of cytoplasm / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.36 Å
AuthorsFerens FG / Tsantrizos YS / Lemieux MJ
Funding support Canada, 2 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2023-04396 Canada
Canadian Institutes of Health Research (CIHR)PJT-159743 Canada
CitationJournal: To Be Published
Title: Human GGPPS in the Closed Hexamer Conformation
Authors: Ferens FG / Tsantrizos YS / Lemieux MJ
History
DepositionNov 20, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_73983.png

Downloads & links

-
Map

FileDownload / File: emd_73983.map.gz / Format: CCP4 / Size: 13 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed map (cropped, sharpened and density modified with Resolve-CryoEM in Phenix)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.69 Å/pix.
x 175 pix.
= 120.575 Å		0.69 Å/pix.
x 161 pix.
= 110.929 Å		0.69 Å/pix.
x 121 pix.
= 83.369 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.689 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.532
Minimum - Maximum-4.869704 - 6.4786925
Average (Standard dev.)0.00032816522 (±0.48027378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin125156129
Dimensions161121175
Spacing175161121
CellA: 120.575005 Å / B: 110.929 Å / C: 83.369 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_73983_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_73983_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Raw Half-map B

Fileemd_73983_half_map_1.map
AnnotationRaw Half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Raw Half-map A

Fileemd_73983_half_map_2.map
AnnotationRaw Half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GGPPS hexamer in the closed conformation

EntireName: GGPPS hexamer in the closed conformation
Components
  • Complex: GGPPS hexamer in the closed conformation
    • Protein or peptide: Geranylgeranyl pyrophosphate synthase

-
Supramolecule #1: GGPPS hexamer in the closed conformation

SupramoleculeName: GGPPS hexamer in the closed conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Geranylgeranyl pyrophosphate synthase

MacromoleculeName: Geranylgeranyl pyrophosphate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: Transferases; Transferring alkyl or aryl groups, other than methyl groups
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.972883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GMEKTQETVQ RILLEPYKYL LQLPGKQVRT KLSQAFNHWL KVPEDKLQII IEVTEMLHNA SLLIDDIEDN SKLRRGFPVA HSIYGIPSV INSANYVYFL GLEKVLTLDH PDAVKLFTRQ LLELHQGQGL DIYWRDNYTC PTEEEYKAMV LQKTGGLFGL A VGLMQLFS ...String:
GMEKTQETVQ RILLEPYKYL LQLPGKQVRT KLSQAFNHWL KVPEDKLQII IEVTEMLHNA SLLIDDIEDN SKLRRGFPVA HSIYGIPSV INSANYVYFL GLEKVLTLDH PDAVKLFTRQ LLELHQGQGL DIYWRDNYTC PTEEEYKAMV LQKTGGLFGL A VGLMQLFS DYKEDLKPLL NTLGLFFQIR DDYANLHSKE YSENKSFCED LTEGKFSFPT IHAIWSRPES TQVQNILRQR TE NIDIKKY CVHYLEDVGS FEYTRNTLKE LEAKAYKQID ARGGNPELVA LVKHLSKMFK EENE

UniProtKB: Geranylgeranyl pyrophosphate synthase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
10.0 mMHEPES
100.0 mMSodium ChlorideNaCl
5.0 mMMagnesium ChlorideMgCl2
GridModel: Quantifoil Active R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 10 eV
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4436 / 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 / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 5009293
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab-initio in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 139130
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Ab-initio in cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 10 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9zbd:
Human GGPPS in the Closed Hexamer Conformation

+
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