[English] 日本語
Yorodumi
- PDB-6wv7: Human VKOR with Chlorophacinone -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wv7
TitleHuman VKOR with Chlorophacinone
ComponentsVitamin K epoxide reductase, termini restrained by green fluorescent protein
KeywordsOXIDOREDUCTASE / FLUORESCENT PROTEIN / Vitamin K epoxide Reductase (VKOR) / Vitamin K / warfarin / superwarfarin / vitamin K expoxide(KO) / Chlorophacinone / 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 / : ...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 / : / 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
Chlorophacinone / 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: 2.483 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
CitationJournal: 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.
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 / 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

-
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)89,1454
Polymers88,3952
Non-polymers7502
Water3,657203
1
A: Vitamin K epoxide reductase, termini restrained by green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5722
Polymers44,1971
Non-polymers3751
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)44,5722
Polymers44,1971
Non-polymers3751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.564, 82.567, 78.782
Angle α, β, γ (deg.)93.390, 97.360, 104.210
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 296 or (resid 297...
21(chain B and (resid 2 through 33 or (resid 34...

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
11SERSERGLNGLN(chain A and (resid 2 through 296 or (resid 297...AA2 - 2962 - 294
12GLUGLUGLUGLU(chain A and (resid 2 through 296 or (resid 297...AA297295
13SERSERHISHIS(chain A and (resid 2 through 296 or (resid 297...AA2 - 3842 - 382
14SERSERHISHIS(chain A and (resid 2 through 296 or (resid 297...AA2 - 3842 - 382
15SERSERHISHIS(chain A and (resid 2 through 296 or (resid 297...AA2 - 3842 - 382
16SERSERHISHIS(chain A and (resid 2 through 296 or (resid 297...AA2 - 3842 - 382
21SERSERGLYGLY(chain B and (resid 2 through 33 or (resid 34...BB2 - 332 - 33
22GLUGLUGLUGLU(chain B and (resid 2 through 33 or (resid 34...BB3434
23SERSERHISHIS(chain B and (resid 2 through 33 or (resid 34...BB2 - 3922 - 390
24SERSERHISHIS(chain B and (resid 2 through 33 or (resid 34...BB2 - 3922 - 390
25SERSERHISHIS(chain B and (resid 2 through 33 or (resid 34...BB2 - 3922 - 390
26SERSERHISHIS(chain B and (resid 2 through 33 or (resid 34...BB2 - 3922 - 390
27SERSERHISHIS(chain B and (resid 2 through 33 or (resid 34...BB2 - 3922 - 390

-
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-UAJ / Chlorophacinone / 2-[(2R)-2-(4-chlorophenyl)-2-phenylacetyl]-1H-indene-1,3(2H)-dione


Mass: 374.816 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H15ClO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: anticoagulant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6.5
Details: 33% PEG400, 5% DMSO, 0.1 M sodium acetate, 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: 2.483→50 Å / Num. obs: 31278 / % possible obs: 87.5 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.087 / Rrim(I) all: 0.123 / Χ2: 1.185 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.541.70.56315730.5240.5630.7961.11888.3
2.54-2.591.80.49915450.5550.4990.7061.02987.7
2.59-2.641.80.46315920.5870.4630.6551.11487.4
2.64-2.691.80.44915860.6150.4490.6351.15889
2.69-2.751.80.34215110.7340.3420.4841.13585.4
2.75-2.821.70.30614640.7780.3060.4331.15682.6
2.82-2.891.70.31115510.7740.3110.441.26585.9
2.89-2.961.80.24116270.8630.2410.341.17791.4
2.96-3.051.80.20516290.8870.2050.291.19889.9
3.05-3.151.80.16915810.910.1690.2391.34489.1
3.15-3.261.80.13915830.9380.1390.1971.28988.2
3.26-3.391.80.11115060.9640.1110.1581.2685.4
3.39-3.551.70.114980.9690.10.1421.34682.4
3.55-3.731.80.08416040.9770.0840.1191.27691.5
3.73-3.971.80.06916360.980.0690.0981.19890.3
3.97-4.271.80.05515600.9880.0550.0781.11386.9
4.27-4.71.70.04814640.990.0480.0681.28882.3
4.7-5.381.80.03916260.9920.0390.0551.10991.1
5.38-6.781.80.03615440.9930.0360.0511.07486.7
6.78-501.80.02115980.9980.0210.0291.07289.3

-
Processing

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

2b3p


Resolution: 2.483→34.742 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 1580 5.06 %
Rwork0.1997 29673 -
obs0.202 31253 86.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.17 Å2 / Biso mean: 39.7837 Å2 / Biso min: 16.13 Å2
Refinement stepCycle: final / Resolution: 2.483→34.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6114 0 84 203 6401
Biso mean--40.45 39.07 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066328
X-RAY DIFFRACTIONf_angle_d0.8448578
X-RAY DIFFRACTIONf_chiral_restr0.055954
X-RAY DIFFRACTIONf_plane_restr0.0051078
X-RAY DIFFRACTIONf_dihedral_angle_d14.3463664
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3596X-RAY DIFFRACTION8.299TORSIONAL
12B3596X-RAY DIFFRACTION8.299TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.483-2.56290.35521060.2918233575
2.5629-2.65450.34631390.2728276988
2.6545-2.76070.32321540.2427268286
2.7607-2.88630.27571520.2414262084
2.8863-3.03840.27371500.2243288291
3.0384-3.22860.23061600.2075272989
3.2286-3.47770.23711490.192259083
3.4777-3.82730.22541380.1835287291
3.8273-4.38020.20771430.1796273388
4.3802-5.5150.26471510.1786270387
5.515-34.7420.18331380.1761275888
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)
11.37520.6968-0.27662.8894-1.37512.7653-0.0723-0.07230.08720.1029-0.0717-0.1376-0.00540.09020.13070.15390.0386-0.04150.2003-0.0750.306533.3281-60.998951.3342
22.8976-0.8380.66613.30460.11011.9156-0.1059-0.0344-0.19050.31180.09270.16270.192-0.10870.01130.32170.0143-0.00940.2492-0.06830.237227.7828-15.006154.5223
31.79991.9172-1.32557.0851-3.45192.76530.1733-0.15720.32850.2034-0.21690.4159-0.2665-0.0994-0.01690.24970.0291-0.03370.3335-0.12130.353322.3823-56.878253.5687
46.7070.5783-1.79132.1093-0.76651.7821-0.0978-0.45860.88130.4450.1355-0.05920.05760.2713-0.0770.3229-0.0086-0.08480.2077-0.06250.432536.7227-55.204858.6589
52.1163-0.91210.62941.9016-0.142.8408-0.07480.19140.2251-0.1059-0.0403-0.2159-0.1170.21620.08710.1543-0.05840.02440.26510.03180.28834.209413.780320.1825
62.5547-0.39130.21638.181.79193.6647-0.19240.2628-0.5415-0.48540.3953-0.11410.0598-0.28-0.27320.24670.01430.01310.3767-0.04190.315229.2652-39.782922.0407
74.06191.21490.27172.65080.9893.9684-0.27410.25020.1095-0.81310.29370.2083-0.455-0.42010.01190.53440.0625-0.06770.3975-0.05050.296826.7889-27.301214.4293
84.3547-2.97234.02786.1679-5.01935.88480.2401-0.0101-0.04-0.2273-0.12370.3250.3642-0.1378-0.15080.2627-0.01980.05140.254-0.06630.287723.21679.828618.2196
95.2257-1.57472.33631.7798-1.61824.05920.05990.2376-0.381-0.0618-0.0351-0.18910.17310.43740.09450.25140.02740.00850.1955-0.01250.250337.51387.635912.8597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 151 )A2 - 151
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 296 )A152 - 296
3X-RAY DIFFRACTION3chain 'A' and (resid 297 through 350 )A297 - 350
4X-RAY DIFFRACTION4chain 'A' and (resid 351 through 384 )A351 - 384
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 151 )B2 - 151
6X-RAY DIFFRACTION6chain 'B' and (resid 152 through 206 )B152 - 206
7X-RAY DIFFRACTION7chain 'B' and (resid 207 through 296 )B207 - 296
8X-RAY DIFFRACTION8chain 'B' and (resid 297 through 350 )B297 - 350
9X-RAY DIFFRACTION9chain 'B' and (resid 351 through 384 )B351 - 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