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- EMDB-62758: Vitamin K-dependent gamma-carboxylase apo status -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62758
TitleVitamin K-dependent gamma-carboxylase apo status
Map data
Sample
  • Complex: Vitamin K-dependent gamma-carboxylase in apo status
    • Protein or peptide: Vitamin K-dependent gamma-carboxylase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
  • Ligand: CHOLESTEROL HEMISUCCINATE
Keywordsapo / MEMBRANE PROTEIN
Function / homology
Function and homology information


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 / Gamma-carboxylation of protein precursors / protein maturation ...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 / Gamma-carboxylation of protein precursors / protein maturation / protein modification process / blood coagulation / endoplasmic reticulum lumen / endoplasmic reticulum membrane / membrane
Similarity search - Function
Vitamin K-dependent gamma-carboxylase / HTTM / : / : / HTTM domain / Vitamin K-dependent gamma-carboxylase, lumenal domain / Horizontally Transferred TransMembrane Domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
Vitamin K-dependent gamma-carboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsYao D / Wu K / Lan P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Vitamin K-dependent gamma-carboxylase apo status
Authors: Yao D / Wu K / Lan P
History
DepositionDec 16, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62758.png

Downloads & links

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Map

FileDownload / File: emd_62758.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 192 pix.
= 211.2 Å		1.1 Å/pix.
x 192 pix.
= 211.2 Å		1.1 Å/pix.
x 192 pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-3.4714434 - 5.5836167
Average (Standard dev.)0.0023547804 (±0.10199766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 211.20001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62758_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_62758_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 : Vitamin K-dependent gamma-carboxylase in apo status

EntireName: Vitamin K-dependent gamma-carboxylase in apo status
Components
  • Complex: Vitamin K-dependent gamma-carboxylase in apo status
    • Protein or peptide: Vitamin K-dependent gamma-carboxylase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: Vitamin K-dependent gamma-carboxylase in apo status

SupramoleculeName: Vitamin K-dependent gamma-carboxylase in apo status / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 87.655641 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAVSAGSART SPSSDKVQKD KAELISGPRQ DSRIGKLLGF EWTDLSSWRR LVTLLNRPTD PASLAVFRFL FGFLMVLDIP QERGLSSLD RKYLDGLDVC RFPLLDALRP LPLDWMYLVY TIMFLGALGM MLGLCYRISC VLFLLPYWYV FLLDKTSWNN H SYLYGLLA ...String:
MAVSAGSART SPSSDKVQKD KAELISGPRQ DSRIGKLLGF EWTDLSSWRR LVTLLNRPTD PASLAVFRFL FGFLMVLDIP QERGLSSLD RKYLDGLDVC RFPLLDALRP LPLDWMYLVY TIMFLGALGM MLGLCYRISC VLFLLPYWYV FLLDKTSWNN H SYLYGLLA FQLTFMDANH YWSVDGLLNA HRRNAHVPLW NYAVLRGQIF IVYFIAGVKK LDADWVEGYS MEYLSRHWLF SP FKLLLSE ELTSLLVVHW GGLLLDLSAG FLLFFDVSRS IGLFFVSYFH CMNSQLFSIG MFSYVMLASS PLFCSPEWPR KLV SYCPRR LQQLLPLKAA PQPSVSCVYK RSRGKSGQKP GLRHQLGAAF TLLYLLEQLF LPYSHFLTQG YNNWTNGLYG YSWD MMVHS RSHQHVKITY RDGRTGELGY LNPGVFTQSR RWKDHADMLK QYATCLSRLL PKYNVTEPQI YFDIWVSIND RFQQR IFDP RVDIVQAAWS PFQRTSWVQP LLMDLSPWRA KLQEIKSSLD NHTEVVFIAD FPGLHLENFV SEDLGNTSIQ LLQGEV TVE LVAEQKNQTL REGEKMQLPA GEYHKVYTTS PSPSCYMYVY VNTTELALEQ DLAYLQELKE KVENGSETGP LPPELQP LL EGEVKGGPEP TPLVQTFLRR QQRLQEIERR RNTPFHERFF RFLLRKLYVF RRSFLMTCIS LRNLILGRPS LEQLAQEV T YANLRPFEAV GELNPSNTDS SHSNPPESNP DPVHSEF

UniProtKB: Vitamin K-dependent gamma-carboxylase

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / 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 #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #5: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Image recordingFilm or detector model: GATAN K3 (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: 0.9 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 166899
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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