[English] 日本語
Yorodumi
- PDB-6rf0: Crystal structure of the light-driven sodium pump KR2 in the pent... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rf0
TitleCrystal structure of the light-driven sodium pump KR2 in the pentameric "dry" form
ComponentsSodium pumping rhodopsin
KeywordsMEMBRANE PROTEIN / light-driven sodium pump / ion translocation / retinal / rhodopsin
Function / homology
Function and homology information


Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
EICOSANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Sodium pumping rhodopsin
Similarity search - Component
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKovalev, K. / Polovinkin, V. / Gushchin, I. / Borshchevskiy, V. / Gordeliy, V.
Funding support France, Russian Federation, 5items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0029-02 France
Russian Foundation for Basic Research6.3157.2017/PP Russian Federation
French Infrastructure for Integrated Structural BiologyANR-10-INSB-05-02 France
Grenoble Alliance for Integrated Structural Cell BiologyANR-10-LABX-49-01 France
Russian Science FoundationRSF 16-15-00242 Russian Federation
CitationJournal: Sci Adv / Year: 2019
Title: Structure and mechanisms of sodium-pumping KR2 rhodopsin.
Authors: Kovalev, K. / Polovinkin, V. / Gushchin, I. / Alekseev, A. / Shevchenko, V. / Borshchevskiy, V. / Astashkin, R. / Balandin, T. / Bratanov, D. / Vaganova, S. / Popov, A. / Chupin, V. / Buldt, ...Authors: Kovalev, K. / Polovinkin, V. / Gushchin, I. / Alekseev, A. / Shevchenko, V. / Borshchevskiy, V. / Astashkin, R. / Balandin, T. / Bratanov, D. / Vaganova, S. / Popov, A. / Chupin, V. / Buldt, G. / Bamberg, E. / Gordeliy, V.
History
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sodium pumping rhodopsin
B: Sodium pumping rhodopsin
C: Sodium pumping rhodopsin
D: Sodium pumping rhodopsin
E: Sodium pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,20330
Polymers163,0585
Non-polymers6,14525
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26130 Å2
ΔGint-170 kcal/mol
Surface area41570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.184, 239.719, 131.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUVALVALAA4 - 2764 - 276
21GLUGLUVALVALBB4 - 2764 - 276
12GLUGLUGLUGLUAA4 - 2774 - 277
22GLUGLUGLUGLUCC4 - 2774 - 277
13GLUGLUVALVALAA4 - 2764 - 276
23GLUGLUVALVALDD4 - 2764 - 276
14GLUGLUVALVALAA4 - 2764 - 276
24GLUGLUVALVALEE4 - 2764 - 276
15GLUGLUVALVALBB4 - 2764 - 276
25GLUGLUVALVALCC4 - 2764 - 276
16GLUGLUVALVALBB4 - 2764 - 276
26GLUGLUVALVALDD4 - 2764 - 276
17GLNGLNGLUGLUBB3 - 2773 - 277
27GLNGLNGLUGLUEE3 - 2773 - 277
18GLUGLUALAALACC4 - 2784 - 278
28GLUGLUALAALADD4 - 2784 - 278
19GLUGLUVALVALCC4 - 2764 - 276
29GLUGLUVALVALEE4 - 2764 - 276
110GLUGLUVALVALDD4 - 2764 - 276
210GLUGLUVALVALEE4 - 2764 - 276

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Sodium pumping rhodopsin


Mass: 32611.580 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dokdonia eikasta (bacteria) / Gene: NaR / Production host: Escherichia coli (E. coli) / References: UniProt: N0DKS8

-
Non-polymers , 5 types, 66 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C20H42
#5: Chemical
ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H28O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.36 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 3.4 M Sodium Malonate pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3→47.28 Å / Num. obs: 41018 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.304 / Rpim(I) all: 0.127 / Rrim(I) all: 0.33 / Net I/σ(I): 5.7 / Num. measured all: 271542
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.126.61.4753021845620.6620.6181.6011.4100
10.82-47.285.40.06251949550.9960.0310.0716.998.5

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XTO

4xto


Resolution: 3→47.32 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.902 / SU B: 21.126 / SU ML: 0.359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.411
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 2059 5 %RANDOM
Rwork0.2166 ---
obs0.2184 38937 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 140.36 Å2 / Biso mean: 43.925 Å2 / Biso min: 19.03 Å2
Baniso -1Baniso -2Baniso -3
1-5.3 Å20 Å20 Å2
2---6.49 Å20 Å2
3---1.19 Å2
Refinement stepCycle: final / Resolution: 3→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10841 0 206 41 11088
Biso mean--55.55 36.14 -
Num. residues----1370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01411328
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710507
X-RAY DIFFRACTIONr_angle_refined_deg0.591.65315355
X-RAY DIFFRACTIONr_angle_other_deg0.7661.68924216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.63751363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26123.362473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.243151676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.7131520
X-RAY DIFFRACTIONr_chiral_restr0.0280.21458
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022516
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A95490.08
12B95490.08
21A96050.09
22C96050.09
31A95300.09
32D95300.09
41A95820.09
42E95820.09
51B94860.09
52C94860.09
61B94790.09
62D94790.09
71B96080.08
72E96080.08
81C95830.09
82D95830.09
91C95250.08
92E95250.08
101D95220.08
102E95220.08
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 136 -
Rwork0.326 2846 -
all-2982 -
obs--100 %

+
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