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- EMDB-30601: Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (state II) -

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Basic information

Entry
Database: EMDB / ID: EMD-30601
TitleCryo-EM structure of GMPPA/GMPPB complex bound to GTP (state II)
Map data
Sample
  • Complex: complex
    • Protein or peptide: Mannose-1-phosphate guanyltransferase alpha
    • Protein or peptide: Mannose-1-phosphate guanyltransferase beta
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
Function / homology
Function and homology information


GDP-mannose pyrophosphorylase complex / mannose-1-phosphate guanylyltransferase / mannose-1-phosphate guanylyltransferase (GTP) activity / GDP-mannose metabolic process / Synthesis of GDP-mannose / GDP-mannose biosynthetic process / enzyme inhibitor activity / biosynthetic process / protein glycosylation / transferase activity ...GDP-mannose pyrophosphorylase complex / mannose-1-phosphate guanylyltransferase / mannose-1-phosphate guanylyltransferase (GTP) activity / GDP-mannose metabolic process / Synthesis of GDP-mannose / GDP-mannose biosynthetic process / enzyme inhibitor activity / biosynthetic process / protein glycosylation / transferase activity / GTP binding / enzyme binding / extracellular exosome / cytoplasm
Similarity search - Function
Mannose-1-phosphate guanyltransferase, N-terminal domain / : / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Mannose-1-phosphate guanylyltransferase regulatory subunit alpha / Mannose-1-phosphate guanylyltransferase catalytic subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.1 Å
AuthorsZheng L / Liu Z / Wang Y / Yang F / Wang J / Qing J / cai X / Mo X / Gao N / Jia D
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Cryo-EM structures of human GMPPA-GMPPB complex reveal how cells maintain GDP-mannose homeostasis.
Authors: Lvqin Zheng / Zhe Liu / Yan Wang / Fan Yang / Jinrui Wang / Wenjie Huang / Jiao Qin / Min Tian / Xiaotang Cai / Xiaohui Liu / Xianming Mo / Ning Gao / Da Jia /
Abstract: GDP-mannose (GDP-Man) is a key metabolite essential for protein glycosylation and glycophosphatidylinositol anchor synthesis, and aberrant cellular GDP-Man levels have been associated with multiple ...GDP-mannose (GDP-Man) is a key metabolite essential for protein glycosylation and glycophosphatidylinositol anchor synthesis, and aberrant cellular GDP-Man levels have been associated with multiple human diseases. How cells maintain homeostasis of GDP-Man is unknown. Here, we report the cryo-EM structures of human GMPPA-GMPPB complex, the protein machinery responsible for GDP-Man synthesis, in complex with GDP-Man or GTP. Unexpectedly, we find that the catalytically inactive subunit GMPPA displays a much higher affinity to GDP-Man than the active subunit GMPPB and, subsequently, inhibits the catalytic activity of GMPPB through a unique C-terminal loop of GMPPA. Importantly, disruption of the interactions between GMPPA and GMPPB or the binding of GDP-Man to GMPPA in zebrafish leads to abnormal brain development and muscle abnormality, analogous to phenotypes observed in individuals carrying GMPPA or GMPPB mutations. We conclude that GMPPA acts as a cellular sensor to maintain mannose homeostasis through allosterically regulating GMPPB.
History
DepositionOct 2, 2020-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0365
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0365
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d74
  • Surface level: 0.0365
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30601.png

Downloads & links

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Map

FileDownload / File: emd_30601.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.)
1.05 Å/pix.
x 240 pix.
= 252.48 Å		1.05 Å/pix.
x 240 pix.
= 252.48 Å		1.05 Å/pix.
x 240 pix.
= 252.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0365 / Movie #1: 0.0365
Minimum - Maximum-0.16953044 - 0.27797347
Average (Standard dev.)-5.2099636e-05 (±0.011680113)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 252.48001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0521.0521.052
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z252.480252.480252.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1700.278-0.000

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Supplemental data

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Sample components

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Entire : complex

EntireName: complex
Components
  • Complex: complex
    • Protein or peptide: Mannose-1-phosphate guanyltransferase alpha
    • Protein or peptide: Mannose-1-phosphate guanyltransferase beta
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: complex

SupramoleculeName: complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM

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Macromolecule #1: Mannose-1-phosphate guanyltransferase alpha

MacromoleculeName: Mannose-1-phosphate guanyltransferase alpha / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.341961 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MLKAVILIGG PQKGTRFRPL SFEVPKPLFP VAGVPMIQHH IEACAQVPGM QEILLIGFYQ PDEPLTQFLE AAQQEFNLPV RYLQEFAPL GTGGGLYHFR DQILAGSPEA FFVLNADVCS DFPLSAMLEA HRRQRHPFLL LGTTANRTQS LNYGCIVENP Q THEVLHYV ...String:
MLKAVILIGG PQKGTRFRPL SFEVPKPLFP VAGVPMIQHH IEACAQVPGM QEILLIGFYQ PDEPLTQFLE AAQQEFNLPV RYLQEFAPL GTGGGLYHFR DQILAGSPEA FFVLNADVCS DFPLSAMLEA HRRQRHPFLL LGTTANRTQS LNYGCIVENP Q THEVLHYV EKPSTFISDI INCGIYLFSP EALKPLRDVF QRNQQDGQLE DSPGLWPGAG TIRLEQDVFS ALAGQGQIYV HL TDGIWSQ IKSAGSALYA SRLYLSRYQD THPERLAKHT PGGPWIRGNV YIHPTAKVAP SAVLGPNVSI GKGVTVGEGV RLR ESIVLH GATLQEHTCV LHSIVGWGST VGRWARVEGT PSDPNPNDPR ARMDSESLFK DGKLLPAITI LGCRVRIPAE VLIL NSIVL PHKELSRSFT NQIIL

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Macromolecule #2: Mannose-1-phosphate guanyltransferase beta

MacromoleculeName: Mannose-1-phosphate guanyltransferase beta / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO / EC number: mannose-1-phosphate guanylyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.878316 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MKALILVGGY GTRLRPLTLS TPKPLVDFCN KPILLHQVEA LAAAGVDHVI LAVSYMSQVL EKEMKAQEQR LGIRISMSHE EEPLGTAGP LALARDLLSE TADPFFVLNS DVICDFPFQA MVQFHRHHGQ EGSILVTKVE EPSKYGVVVC EADTGRIHRF V EKPQVFVS ...String:
MKALILVGGY GTRLRPLTLS TPKPLVDFCN KPILLHQVEA LAAAGVDHVI LAVSYMSQVL EKEMKAQEQR LGIRISMSHE EEPLGTAGP LALARDLLSE TADPFFVLNS DVICDFPFQA MVQFHRHHGQ EGSILVTKVE EPSKYGVVVC EADTGRIHRF V EKPQVFVS NKINAGMYIL SPAVLQRIQL QPTSIEKEVF PIMAKEGQLY AMELQGFWMD IGQPKDFLTG MCLFLQSLRQ KQ PERLCSG PGIVGNVLVD PSARIGQNCS IGPNVSLGPG VVVEDGVCIR RCTVLRDARI RSHSWLESCI VGWRCRVGQW VRM ENVTVL GEDVIVNDEL YLNGASVLPH KSIGESVPEP RIIM

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 12 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115375
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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