[English] 日本語
Yorodumi
- PDB-6wvh: Human VKOR with Brodifacoum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wvh
TitleHuman VKOR with Brodifacoum
ComponentsVitamin K epoxide reductase, termini restrained by green fluorescent protein
KeywordsOXIDOREDUCTASE / FLUORESCENT PROTEIN / Vitamin K epoxide Reductase (VKOR) / Vitamin K / warfarin / superwarfarin / Brodifacoum / 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 / quinone binding / xenobiotic metabolic process / bioluminescence ...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 / quinone binding / xenobiotic metabolic process / bioluminescence / generation of precursor metabolites and energy / bone development / blood coagulation / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Vitamin K epoxide reductase complex subunit 1 / VKOR domain / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / de novo design (two linked rop proteins) / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein ...Vitamin K epoxide reductase complex subunit 1 / VKOR domain / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / de novo design (two linked rop proteins) / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Brodifacoum / 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: 1.99 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 6, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,1556
Polymers88,3952
Non-polymers1,7604
Water8,305461
1
A: Vitamin K epoxide reductase, termini restrained by green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4344
Polymers44,1971
Non-polymers1,2363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vitamin K epoxide reductase, termini restrained by green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7212
Polymers44,1971
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.576, 82.593, 78.610
Angle α, β, γ (deg.)93.417, 97.481, 104.685
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEU(chain 'A' and (resid 2 through 297 or resid 299 through 384))AA2 - 642 - 64
12VALVALGLUGLU(chain 'A' and (resid 2 through 297 or resid 299 through 384))AA68 - 29766 - 295
13SERSERHISHIS(chain 'A' and (resid 2 through 297 or resid 299 through 384))AA299 - 384297 - 382
24SERSERLEULEU(chain 'B' and (resid 2 through 158 or (resid 159...BB2 - 642 - 64
25VALVALGLUGLU(chain 'B' and (resid 2 through 158 or (resid 159...BB68 - 29766 - 295
26SERSERHISHIS(chain 'B' and (resid 2 through 158 or (resid 159...BB299 - 384297 - 382

-
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.: 2
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-UA7 / Brodifacoum / 3-[(1R,3S)-3-(4'-bromo[1,1'-biphenyl]-4-yl)-1,2,3,4-tetrahydronaphthalen-1-yl]-4-hydroxy-2H-1-benzopyran-2-one


Mass: 523.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H23BrO3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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: isolated from a natural source / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6.5
Details: 32% PEG400, 0.1 M ammonium acetate, 1% 1,2,3-heptanetriol, 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: Feb 11, 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: 1.99→50 Å / Num. obs: 63563 / % possible obs: 90.7 % / Redundancy: 2.3 % / Biso Wilson estimate: 23.86 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.055 / Rrim(I) all: 0.088 / Χ2: 1.15 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.032.20.41532600.7470.3430.5410.99591.7
2.03-2.072.30.37231410.8060.3050.4841.00691.3
2.07-2.112.30.32132150.8290.2640.4171.07291.3
2.11-2.152.30.28331660.8720.2330.3681.07690.8
2.15-2.22.30.23832030.9130.1960.311.10791
2.2-2.252.30.22732170.9110.1860.2951.12290.3
2.25-2.312.20.19629590.9270.1620.2561.17886.4
2.31-2.372.30.16431890.9480.1350.2131.22389.8
2.37-2.442.30.14832140.9570.1210.1931.20992.8
2.44-2.522.30.12332760.970.1010.161.25592.6
2.52-2.612.30.11331880.9720.0920.1461.18192.1
2.61-2.712.30.09931820.9790.080.1281.2190.3
2.71-2.842.20.08829840.9810.0720.1151.26885.1
2.84-2.992.30.07932230.9850.0640.1021.32792.9
2.99-3.172.30.06432810.9890.0510.0831.30693.7
3.17-3.422.30.05431960.9920.0430.0691.13291.4
3.42-3.762.30.04930200.9930.0390.0631.09285.9
3.76-4.312.30.0433220.9950.0320.0511.06694.5
4.31-5.432.20.03631190.9960.0280.0461.00289.2
5.43-502.30.03432080.9980.0270.0441.16191.7

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B3P

2b3p


Resolution: 1.99→30.47 Å / SU ML: 0.182 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.215 3223 5.07 %
Rwork0.1946 60321 -
obs0.1956 63544 90.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.69 Å2
Refinement stepCycle: LAST / Resolution: 1.99→30.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6123 0 98 461 6682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416375
X-RAY DIFFRACTIONf_angle_d0.79358636
X-RAY DIFFRACTIONf_chiral_restr0.0496955
X-RAY DIFFRACTIONf_plane_restr0.00491079
X-RAY DIFFRACTIONf_dihedral_angle_d18.34772270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.27521230.23632424X-RAY DIFFRACTION80.91
2.02-2.050.25681360.23542612X-RAY DIFFRACTION91.2
2.05-2.080.27171460.21492613X-RAY DIFFRACTION91.15
2.08-2.120.2351500.21272688X-RAY DIFFRACTION90.87
2.12-2.160.21651310.19962610X-RAY DIFFRACTION91.03
2.16-2.20.21741300.1962626X-RAY DIFFRACTION91.05
2.2-2.240.24841310.19742700X-RAY DIFFRACTION89.79
2.24-2.290.22841260.19412484X-RAY DIFFRACTION87
2.29-2.340.21131270.18712571X-RAY DIFFRACTION87.91
2.35-2.40.23821400.18962677X-RAY DIFFRACTION93.15
2.4-2.470.20211620.18542708X-RAY DIFFRACTION92.76
2.47-2.540.21521410.1882672X-RAY DIFFRACTION92.47
2.54-2.620.23141350.18882706X-RAY DIFFRACTION91.53
2.62-2.720.21671420.19252578X-RAY DIFFRACTION89.92
2.72-2.830.23631430.19532454X-RAY DIFFRACTION84.37
2.83-2.950.19851560.19052667X-RAY DIFFRACTION92.89
2.95-3.110.19571240.18672744X-RAY DIFFRACTION93.85
3.11-3.30.19551820.18282677X-RAY DIFFRACTION92.32
3.3-3.560.19841500.18252582X-RAY DIFFRACTION89.52
3.56-3.920.19941310.1862558X-RAY DIFFRACTION87.73
3.92-4.480.20121400.19122714X-RAY DIFFRACTION94.16
4.48-5.640.2421420.19832563X-RAY DIFFRACTION87.97
5.64-30.470.1971350.21112693X-RAY DIFFRACTION92.6
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)
11.356344051050.297989864784-0.1031556990032.36608707578-0.8151438740322.11954912562-0.0398384889032-0.05093757630680.05317658744790.0588618114275-0.0456809088627-0.0679022289903-0.0009653669973-0.003000308262140.06736365053880.08503115929930.0137541500088-0.025973128480.0913815939318-0.02937668400280.14885518799133.4361897738-59.580162345251.5315168055
22.88602280409-1.0730526498-0.08658959684512.182972978130.1346485882451.45973590771-0.101125889598-0.155929969937-0.1159074742970.4370658821160.1420731746160.1281529563790.197140047679-0.0367556527839-0.02036398311830.284976408070.0240833962666-0.007366981638530.178869466625-0.03424109026810.13638586909727.3973269334-13.592474599754.7034115916
31.368407139770.537683019315-0.6012142342682.28335291993-0.6068616035891.68385177559-0.00906269748874-0.07587707358610.07203152995730.161441589979-0.04968228540130.136107269754-0.138543644786-0.1186973392990.03874211750740.1596419480930.0313361108815-0.02922716421930.158361630166-0.04040601321420.19824010410628.0325393325-54.896958328855.7588372692
41.60282917643-0.6241432769570.2707865849241.81949682673-0.3536981826272.24395622429-0.04073502524760.05331972621860.128605934039-0.0680327239377-0.0493425756362-0.11817420353-0.05665905371320.04957792067860.06562868967220.0860018741292-0.03463922907150.0169560674820.09857078877320.00216077907510.13944502391933.6689076715.182871470520.5542762168
52.397826690970.7146338393170.2877318461312.576317200710.5279374525321.9247206704-0.1015990116110.1550759611760.0303408848705-0.481506872770.1840768825210.0717576596798-0.262327572425-0.131989590799-0.06584232757280.267221977492-0.02085285832230.02636076018540.19298747414-0.0122813510260.13960523053527.5305444596-30.402304790817.5796405891
60.41887661763-0.1818383002590.1126569361470.493863749118-0.3396338971271.37386807895-0.01383161094070.001931048811010.0492577964325-0.0650852069583-0.049147529717-0.03130499806710.0845299104146-0.07865217016420.08296728255630.183168406581-0.01686189750290.008424159806780.144253039211-0.01498498058960.19535521386728.008157371210.558764355713.6387823335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 151 )
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 296 )
3X-RAY DIFFRACTION3chain 'A' and (resid 297 through 384 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 151 )
5X-RAY DIFFRACTION5chain 'B' and (resid 152 through 298 )
6X-RAY DIFFRACTION6chain 'B' and (resid 299 through 392 )

+
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://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