[English] 日本語
Yorodumi
- PDB-6wv5: Human VKOR C43S mutant with vitamin K1 epoxide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wv5
TitleHuman VKOR C43S mutant with vitamin K1 epoxide
ComponentsVitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein
KeywordsOXIDOREDUCTASE / FLUORESCENT PROTEIN / Vitamin K epoxide Reductase (VKOR) / Vitamin K / warfarin / superwarfarin / 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
Chem-UAV / 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: 2.8 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6502
Polymers44,1811
Non-polymers4691
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18690 Å2
Unit cell
Length a, b, c (Å)88.927, 88.927, 229.889
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Vitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein / Vitamin K1 2 / 3-epoxide reductase subunit 1


Mass: 44181.371 Da / Num. of mol.: 1
Fragment: GPF (UNP residues 1-144) + VKOR + GFP (UNP residues 146-231)
Mutation: C43S
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-UAV / (2R,3R)-2-hydroxy-3-methyl-2-[(2E,7S)-3,7,11,15-tetramethylhexadec-2-en-1-yl]-2,3-dihydronaphthalene-1,4-dione


Mass: 468.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C31H48O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.94 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6.5
Details: 25% PEG400, 0.1 M ammonium citrate dibasic, 0.1 M MES, pH 6.5

-
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: Jul 15, 2017
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: 2.8→50 Å / Num. obs: 15792 / % possible obs: 94.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 57.98 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.056 / Rrim(I) all: 0.095 / Χ2: 1.19 / Net I/σ(I): 9.5 / Num. measured all: 35949
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.852.20.4257840.7520.3340.5451.05896.8
2.85-2.92.30.388010.7950.2890.4820.96495.5
2.9-2.962.20.3637920.8220.280.4631.10994.7
2.96-3.022.30.2817550.8930.2090.3541.19491.7
3.02-3.082.10.2437750.9060.1750.3031.37988.6
3.08-3.152.30.2437900.9030.1810.3061.35195.5
3.15-3.232.30.1998130.9270.150.2511.26797.2
3.23-3.322.20.1758120.9480.1320.2221.44797
3.32-3.422.30.1378210.9710.10.1721.33296.5
3.42-3.532.30.1257970.980.0920.1571.45495.1
3.53-3.652.20.1127840.9760.0840.1421.26995.3
3.65-3.82.20.0947330.9840.0660.1161.14887.4
3.8-3.972.30.0837830.9860.060.1041.03394.9
3.97-4.182.30.0718260.9880.0520.0891.0696.9
4.18-4.442.30.0658060.9890.0490.0821.09995.4
4.44-4.792.30.0567730.9920.0410.071.10793.6
4.79-5.272.30.057570.9950.0340.0621.17689.7
5.27-6.032.40.058190.9930.0360.0621.13997.7
6.03-7.592.30.0437690.9930.0340.0551.11991.8
7.59-502.40.03380210.0260.0431.13894.9

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B3P

2b3p


Resolution: 2.8→39.478 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 31.77
RfactorNum. reflection% reflection
Rfree0.2704 792 5.04 %
Rwork0.2311 --
obs0.2331 15728 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.12 Å2 / Biso mean: 62.1792 Å2 / Biso min: 33.14 Å2
Refinement stepCycle: final / Resolution: 2.8→39.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 57 0 2992
Biso mean--67.38 --
Num. residues----370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053033
X-RAY DIFFRACTIONf_angle_d0.5434111
X-RAY DIFFRACTIONf_chiral_restr0.041460
X-RAY DIFFRACTIONf_plane_restr0.003518
X-RAY DIFFRACTIONf_dihedral_angle_d14.81757
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.97540.32521320.3166251795
2.9754-3.2050.31221240.2731244793
3.205-3.52740.28581500.2553253796
3.5274-4.03740.25221350.2356245293
4.0374-5.08490.25051330.1999244593
5.0849-39.4780.26561180.2139253895
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)
11.03380.3254-1.70811.2728-2.07276.06860.1224-0.04890.10420.0021-0.2113-0.097-0.25870.34150.0190.44990.0026-0.09760.39840.03160.40553.5187-29.348-89.5884
22.0964-0.34590.42891.3096-0.08495.7861-0.3126-0.12050.19150.3766-0.0045-0.1495-0.76140.14940.02390.6228-0.085-0.10820.44820.01170.39673.7598-29.3277-52.5185
3-0.4499-0.4632-0.66621.1471-2.51165.69610.0887-0.140.13070.1084-0.2783-0.2483-0.49150.83280.18420.6181-0.1186-0.07320.61530.05570.49969.6011-31.1931-82.2385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 181 )A3 - 181
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 266 )A182 - 266
3X-RAY DIFFRACTION3chain 'A' and (resid 267 through 384 )A267 - 384

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more