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- EMDB-65921: Cryo-EM structure of GGCX-BGP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65921
TitleCryo-EM structure of GGCX-BGP complex
Map data
Sample
  • Complex: Cryo-EM structure of human complex A
    • Protein or peptide: Osteocalcin
  • Protein or peptide: Vitamin K-dependent gamma-carboxylase
  • 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 / MEMBRANE PROTEIN
Function / homology
Function and homology information


response to hydroxyisoflavone / hydroxyapatite binding / structural constituent of bone / cellular response to zinc ion starvation / peptidyl-glutamate 4-carboxylase / gamma-glutamyl carboxylase activity / negative regulation of testosterone biosynthetic process / peptidyl-glutamic acid carboxylation / negative regulation of bone development / type B pancreatic cell proliferation ...response to hydroxyisoflavone / hydroxyapatite binding / structural constituent of bone / cellular response to zinc ion starvation / peptidyl-glutamate 4-carboxylase / gamma-glutamyl carboxylase activity / negative regulation of testosterone biosynthetic process / peptidyl-glutamic acid carboxylation / negative regulation of bone development / type B pancreatic cell proliferation / response to macrophage colony-stimulating factor / regulation of testosterone biosynthetic process / Defective gamma-carboxylation of F9 / vitamin binding / vitamin K metabolic process / positive regulation of neurotransmitter secretion / response to vitamin K / regulation of osteoclast differentiation / cellular response to vitamin D / negative regulation of neurotransmitter secretion / regulation of bone mineralization / response to vitamin D / regulation of bone resorption / response to zinc ion / response to testosterone / bone mineralization / RUNX2 regulates osteoblast differentiation / response to gravity / response to mechanical stimulus / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / skeletal system development / regulation of cellular response to insulin stimulus / response to glucocorticoid / stem cell differentiation / response to activity / protein modification process / brain development / protein maturation / bone development / hormone activity / cellular response to growth factor stimulus / response to estrogen / Golgi lumen / cognition / cellular response to insulin stimulus / osteoblast differentiation / blood coagulation / glucose homeostasis / vesicle / response to ethanol / perikaryon / learning or memory / cell adhesion / response to xenobiotic stimulus / endoplasmic reticulum lumen / calcium ion binding / lipid binding / dendrite / endoplasmic reticulum membrane / structural molecule activity / : / extracellular region / membrane / cytoplasm
Similarity search - Function
Osteocalcin / Osteocalcin/matrix Gla protein / : / Osteocalcin, C-terminal domain / Vitamin K-dependent gamma-carboxylase / HTTM / : / : / HTTM domain / Vitamin K-dependent gamma-carboxylase, lumenal domain ...Osteocalcin / 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
Osteocalcin / Vitamin K-dependent gamma-carboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsQian HW / Zhang WJ
Funding support China, 1 items
OrganizationGrant numberCountry
Other governmentKY9100000034 China
CitationJournal: To Be Published
Title: Cryo-EM structure of GGCX-BGP complex
Authors: Qian HW / Zhang WJ
History
DepositionAug 20, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65921.png

Downloads & links

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Map

FileDownload / File: emd_65921.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: 0.266
Minimum - Maximum-1.3675997 - 1.9421159
Average (Standard dev.)-0.000066040666 (±0.053886313)
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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Additional map: #1

Fileemd_65921_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65921_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_65921_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of human complex A

EntireName: Cryo-EM structure of human complex A
Components
  • Complex: Cryo-EM structure of human complex A
    • Protein or peptide: Osteocalcin
  • Protein or peptide: Vitamin K-dependent gamma-carboxylase
  • 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 human complex A

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

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Macromolecule #1: Osteocalcin

MacromoleculeName: Osteocalcin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.983948 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GAAFVSKQEG SEVVKRQRRY LYQWLGAPVP YPDPLERRRE VCELNPDCDE LADHIGFQEA YRRFYGPV

UniProtKB: Osteocalcin

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Macromolecule #2: Vitamin K-dependent gamma-carboxylase

MacromoleculeName: Vitamin K-dependent gamma-carboxylase / type: protein_or_peptide / ID: 2 / 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 #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: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 193004
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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