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- PDB-6wv6: Human VKOR with phenindione -

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Basic information

Entry
Database: PDB / ID: 6wv6
TitleHuman VKOR with phenindione
ComponentsVitamin K epoxide reductase, termini restrained by green fluorescent protein
KeywordsOXIDOREDUCTASE / FLUORESCENT PROTEIN / Vitamin K epoxide Reductase (VKOR) / Vitamin K / warfarin / superwarfarin / phenindione / vitamin K expoxide(KO) / membrane protein
Function / homology
Function and homology information


peptidyl-glutamic acid carboxylation / vitamin-K-epoxide reductase (warfarin-insensitive) activity / Metabolism of vitamin K / vitamin-K-epoxide reductase (warfarin-sensitive) / vitamin-K-epoxide reductase (warfarin-sensitive) activity / vitamin K metabolic process / positive regulation of coagulation / regulation of blood coagulation / quinone binding / response to organonitrogen compound ...peptidyl-glutamic acid carboxylation / vitamin-K-epoxide reductase (warfarin-insensitive) activity / Metabolism of vitamin K / vitamin-K-epoxide reductase (warfarin-sensitive) / vitamin-K-epoxide reductase (warfarin-sensitive) activity / vitamin K metabolic process / positive regulation of coagulation / regulation of blood coagulation / quinone binding / response to organonitrogen compound / xenobiotic metabolic process / bioluminescence / generation of precursor metabolites and energy / bone development / response to organic cyclic compound / blood coagulation / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Vitamin K epoxide reductase complex subunit 1 / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Phenindione / Green fluorescent protein / Green fluorescent protein / Vitamin K epoxide reductase complex subunit 1
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLiu, S. / Sukumar, N. / Li, W.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL121718 United States
Other privateForefront of Science Award United States
Other privateMCII 2020-854 United States
National Institutes of Health/National Eye Institute (NIH/NEI)R21 EY028705 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM131008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
Citation
Journal: Science / Year: 2021
Title: Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation.
Authors: Liu, S. / Li, S. / Shen, G. / Sukumar, N. / Krezel, A.M. / Li, W.
#1: Journal: To Be Published
Title: Termini restraining of small membrane proteins enables structure determination at atomic resolution
Authors: Liu, S. / Li, S. / Yang, Y. / Li, W.
History
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitamin K epoxide reductase, termini restrained by green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1334
Polymers44,1971
Non-polymers9353
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.019, 84.878, 42.558
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Vitamin K epoxide reductase, termini restrained by green fluorescent protein / Vitamin K1 2 / 3-epoxide reductase subunit 1


Mass: 44197.434 Da / Num. of mol.: 1
Fragment: GPF (UNP residues 1-144) + VKOR + GFP (UNP residues 146-231)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: gfp, VKORC1, VKOR, MSTP134, MSTP576, UNQ308/PRO351 / Production host: Komagataella pastoris (fungus)
References: UniProt: A0A059PIQ0, UniProt: Q9BQB6, UniProt: P42212*PLUS, vitamin-K-epoxide reductase (warfarin-sensitive)
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-UAS / Phenindione / 2-phenyl-1H-indene-1,3(2H)-dione


Mass: 222.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: anticoagulant, antagonist*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6.5
Details: 34% PEG400, 80 mM lithium sulfate, 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 15647 / % possible obs: 97.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.079 / Rrim(I) all: 0.142 / Χ2: 1.156 / Net I/σ(I): 6.8 / Num. measured all: 45677
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.752.70.6467380.730.4460.7891.14894.4
2.75-2.82.70.6477690.6740.4540.7950.99996.5
2.8-2.852.70.5957580.7510.4160.7311.08896.8
2.85-2.913.10.5317620.7370.350.6391.06998.4
2.91-2.973.10.4517740.8370.2960.5421.09897.6
2.97-3.043.10.387860.860.250.4571.08797.2
3.04-3.123.10.3067510.880.20.3681.12198.4
3.12-3.230.2697740.9140.180.3261.1596.8
3.2-3.330.227950.9410.1460.2661.16198.8
3.3-3.42.90.2167710.9330.1470.2631.15497.3
3.4-3.522.60.1717760.9570.1230.2121.17996.4
3.52-3.663.10.147680.9720.0930.1691.16998.7
3.66-3.833.10.1298110.9770.0850.1551.16798.9
3.83-4.0330.1027850.9880.0670.1231.07798.6
4.03-4.2930.0887900.9870.0580.1061.02397.2
4.29-4.622.70.0887630.9840.0630.112.14994.5
4.62-5.0830.0657990.9910.0420.0781.11698.8
5.08-5.8130.0638040.9930.0410.0761.10197.8
5.81-7.322.70.0598100.9910.040.0721.01894.4
7.32-502.80.048630.9990.0280.0491.18494.3

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B3P

2b3p


Resolution: 2.7→37.3 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 746 4.78 %
Rwork0.2261 14850 -
obs0.228 15596 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.43 Å2 / Biso mean: 50.9532 Å2 / Biso min: 17.95 Å2
Refinement stepCycle: final / Resolution: 2.7→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 57 33 3107
Biso mean--54.87 44.32 -
Num. residues----382
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.910.38071440.31372867301196
2.91-3.20.32971570.2542932308998
3.2-3.670.28171540.22422951310598
3.67-4.620.23311440.20582990313497
4.62-37.30.23641470.21433110325796
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1437-0.2670.14792.6822-0.39032.693-0.0531-0.15840.5465-0.17440.01080.0183-0.0741-0.07960.04290.3334-0.0266-0.03080.3455-0.05150.4159118.84477.411455.3917
27.8607-0.5544-0.90392.9643-0.37512.48030.08280.3958-0.1899-0.1139-0.02560.00960.060.1362-0.0150.3676-0.0022-0.05390.3544-0.00570.3515161.07169.334954.7382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resid 2 through 151 ) or (resid 299 through 385 ))A0
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 298 )A152 - 298

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