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- EMDB-65925: Cryo-EM structure of GGCX-MGP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65925
TitleCryo-EM structure of GGCX-MGP complex
Map data
Sample
  • Complex: Cryo-EM structure of complex D
    • Protein or peptide: Vitamin K-dependent gamma-carboxylase
    • Protein or peptide: Matrix Gla protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate
  • Ligand: CHOLESTEROL
  • Ligand: (1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione
KeywordsVitamin K-dependent gamma-carboxylase binding to its substrate MGP / MEMBRANE PROTEIN
Function / homology
Function and homology information


structural constituent of bone / peptidyl-glutamate 4-carboxylase / gamma-glutamyl carboxylase activity / negative regulation of testosterone biosynthetic process / negative regulation of bone development / Defective gamma-carboxylation of F9 / vitamin binding / vitamin K metabolic process / negative regulation of neurotransmitter secretion / regulation of bone mineralization ...structural constituent of bone / peptidyl-glutamate 4-carboxylase / gamma-glutamyl carboxylase activity / negative regulation of testosterone biosynthetic process / negative regulation of bone development / Defective gamma-carboxylation of F9 / vitamin binding / vitamin K metabolic process / negative regulation of neurotransmitter secretion / regulation of bone mineralization / type B pancreatic cell proliferation / cartilage condensation / extracellular matrix structural constituent / Gamma-carboxylation of protein precursors / ossification / protein modification process / protein maturation / cellular response to insulin stimulus / blood coagulation / glucose homeostasis / extracellular matrix / cell differentiation / endoplasmic reticulum lumen / calcium ion binding / endoplasmic reticulum membrane / extracellular exosome / membrane
Similarity search - Function
Matrix Gla protein / Osteocalcin/matrix Gla protein / : / Osteocalcin, C-terminal domain / Vitamin K-dependent gamma-carboxylase / HTTM / : / : / HTTM domain / Vitamin K-dependent gamma-carboxylase, lumenal domain ...Matrix Gla protein / Osteocalcin/matrix Gla protein / : / Osteocalcin, C-terminal domain / Vitamin K-dependent gamma-carboxylase / HTTM / : / : / HTTM domain / Vitamin K-dependent gamma-carboxylase, lumenal domain / Horizontally Transferred TransMembrane Domain / RmlC-like cupin domain superfamily / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / RmlC-like jelly roll fold
Similarity search - Domain/homology
Matrix Gla protein / Vitamin K-dependent gamma-carboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsQian HW / Zhang WJ
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Cryo-EM structure of GGcX-MGP complex
Authors: Qian HW / Zhang WJ
History
DepositionAug 21, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65925.png

Downloads & links

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Map

FileDownload / File: emd_65925.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.173
Minimum - Maximum-1.2596924 - 1.5949111
Average (Standard dev.)0.0008716264 (±0.037372153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65925_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65925_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of complex D

EntireName: Cryo-EM structure of complex D
Components
  • Complex: Cryo-EM structure of complex D
    • Protein or peptide: Vitamin K-dependent gamma-carboxylase
    • Protein or peptide: Matrix Gla protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate
  • Ligand: CHOLESTEROL
  • Ligand: (1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione

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Supramolecule #1: Cryo-EM structure of complex D

SupramoleculeName: Cryo-EM structure of complex D / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Vitamin K-dependent gamma-carboxylase

MacromoleculeName: Vitamin K-dependent gamma-carboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidyl-glutamate 4-carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.275875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SRIGKLLGFE WTDLSSWRRL VTLLNRPTDP ASLAVFRFLF GFLMVLDIPQ ERGLSSLDRK YLDGLDVCRF PLLDALRPLP LDWMYLVYT IMFLGALGMM LGLCYRISCV LFLLPYWYVF LLDKTSWNNH SYLYGLLAFQ LTFMDANHYW SVDGLLNAHR R NAHVPLWN ...String:
SRIGKLLGFE WTDLSSWRRL VTLLNRPTDP ASLAVFRFLF GFLMVLDIPQ ERGLSSLDRK YLDGLDVCRF PLLDALRPLP LDWMYLVYT IMFLGALGMM LGLCYRISCV LFLLPYWYVF LLDKTSWNNH SYLYGLLAFQ LTFMDANHYW SVDGLLNAHR R NAHVPLWN YAVLRGQIFI VYFIAGVKKL DADWVEGYSM EYLSRHWLFS PFKLLLSEEL TSLLVVHWGG LLLDLSAGFL LF FDVSRSI GLFFVSYFHC MNSQLFSIGM FSYVMLASSP LFCSPEWPRK LVSYCPRRLQ QLLPLKAAPQ PSVSCVYKRS RGK SGQKPG LRHQLGAAFT LLYLLEQLFL PYSHFLTQGY NNWTNGLYGY SWDMMVHSRS HQHVKITYRD GRTGELGYLN PGVF TQSRR WKDHADMLKQ YATCLSRLLP KYNVTEPQIY FDIWVSINDR FQQRIFDPRV DIVQAAWSPF QRTSWVQPLL MDLSP WRAK LQEIKSSLDN HTEVVFIADF PGLHLENFVS EDLGNTSIQL LQGEVTVELV AEQKNQTLRE GEKMQLPAGE YHKVYT TSP SPSCYMYVYV NTTELALEQD LAYLQELKEK VENGSETGPL PPELQPLLEG EVKGGPEPTP LVQTFLRRQQ RLQEIER RR NTPFHERFFR FLLRKLYVFR RSFLMTCISL RNLILGRPSL EQLAQEVTYA NLRPF

UniProtKB: Vitamin K-dependent gamma-carboxylase

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Macromolecule #2: Matrix Gla protein

MacromoleculeName: Matrix Gla protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.336689 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LCYESHESMS YELNPFINRR NANTFISP

UniProtKB: Matrix Gla protein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 5 / Number of copies: 2 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #6: (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate

MacromoleculeName: (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate
type: ligand / ID: 6 / Number of copies: 1 / Formula: MX7
Molecular weightTheoretical: 700.966 Da
Chemical component information

ChemComp-MX7:
(2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate

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Macromolecule #7: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #8: (1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca...

MacromoleculeName: (1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione
type: ligand / ID: 8 / Number of copies: 1 / Formula: A1AT1
Molecular weightTheoretical: 460.648 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / 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: 1.7 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 138030
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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