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- PDB-13ib: Structure of GGCX-BGP-Anisindione complex -

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Basic information

Entry
Database: PDB / ID: 13ib
TitleStructure of GGCX-BGP-Anisindione complex
Components
  • Osteocalcin
  • Vitamin K-dependent gamma-carboxylase
KeywordsMEMBRANE PROTEIN / vitamin K
Function / homology
Function and homology information


response to hydroxyisoflavone / hydroxyapatite binding / structural constituent of bone / type B pancreatic cell proliferation / 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 ...response to hydroxyisoflavone / hydroxyapatite binding / structural constituent of bone / type B pancreatic cell proliferation / 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 / 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 / negative regulation of neurotransmitter secretion / cellular response to vitamin D / regulation of bone mineralization / response to vitamin D / regulation of bone resorption / bone mineralization / response to zinc ion / response to testosterone / RUNX2 regulates osteoblast differentiation / response to gravity / skeletal system development / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / response to mechanical stimulus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / stem cell differentiation / regulation of cellular response to insulin stimulus / response to glucocorticoid / 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 / osteoblast differentiation / blood coagulation / glucose homeostasis / cellular response to insulin stimulus / 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
: / CHOLESTEROL / Chem-POV / Osteocalcin / Vitamin K-dependent gamma-carboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsWang, R. / Qi, X. / Zhou, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR230054 United States
CitationJournal: To Be Published
Title: gamma-glutamyl carboxylase inhibition by Anisindione
Authors: Zhou, N. / Wang, R. / Chen, B. / Li, J. / TIe, J.-K. / Liu, F. / Qi, X.
History
DepositionMay 7, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin K-dependent gamma-carboxylase
B: Osteocalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8978
Polymers98,6312
Non-polymers2,2666
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Vitamin K-dependent gamma-carboxylase / Gamma-glutamyl carboxylase / Peptidyl-glutamate 4-carboxylase / Vitamin K gamma glutamyl carboxylase


Mass: 87655.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGCX, GC / Production host: Homo sapiens (human)
References: UniProt: P38435, peptidyl-glutamate 4-carboxylase
#2: Protein Osteocalcin / Bone Gla protein / BGP / Gamma-carboxyglutamic acid-containing protein


Mass: 10975.558 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BGLAP / Production host: Homo sapiens (human) / References: UniProt: P02818

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Sugars , 2 types, 3 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 3 molecules

#5: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#6: Chemical ChemComp-A1AT0 / anisindione / 2-(4-methoxyphenyl)-1H-indene-1,3(2H)-dione


Mass: 252.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GGCX-BGP-Anisindione complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1crYOLOparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3207368 / Num. of class averages: 757035 / Symmetry type: POINT
RefinementHighest resolution: 2.68 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046199
ELECTRON MICROSCOPYf_angle_d0.5428412
ELECTRON MICROSCOPYf_dihedral_angle_d6.095973
ELECTRON MICROSCOPYf_chiral_restr0.041911
ELECTRON MICROSCOPYf_plane_restr0.0051047

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