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- PDB-6xyt: Crystal structure of the O-state of the light-driven sodium pump ... -

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Basic information

Entry
Database: PDB / ID: 6xyt
TitleCrystal structure of the O-state of the light-driven sodium pump KR2 in the pentameric form, pH 8.0
ComponentsSodium pumping rhodopsin
KeywordsMEMBRANE PROTEIN / rhodopsin / ion pumping / retinal / sodium pump / intermediate state
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 / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Sodium pumping rhodopsin
Similarity search - Component
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKovalev, K. / Gushchin, I. / Gordeliy, V.
Funding support France, Russian Federation, 5items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0029-02 France
French National Research AgencyANR-10-INBS-05-02 France
Grenoble Alliance for Integrated Structural Cell BiologyANR-17-EURE-0003 France
Russian Science Foundation16-15-00242 Russian Federation
Russian Science Foundation6.3157.2017/PP Russian Federation
CitationJournal: Nat Commun / Year: 2020
Title: Molecular mechanism of light-driven sodium pumping.
Authors: Kovalev, K. / Astashkin, R. / Gushchin, I. / Orekhov, P. / Volkov, D. / Zinovev, E. / Marin, E. / Rulev, M. / Alekseev, A. / Royant, A. / Carpentier, P. / Vaganova, S. / Zabelskii, D. / ...Authors: Kovalev, K. / Astashkin, R. / Gushchin, I. / Orekhov, P. / Volkov, D. / Zinovev, E. / Marin, E. / Rulev, M. / Alekseev, A. / Royant, A. / Carpentier, P. / Vaganova, S. / Zabelskii, D. / Baeken, C. / Sergeev, I. / Balandin, T. / Bourenkov, G. / Carpena, X. / Boer, R. / Maliar, N. / Borshchevskiy, V. / Buldt, G. / Bamberg, E. / Gordeliy, V.
History
DepositionJan 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)179,84594
Polymers155,3755
Non-polymers24,46989
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38610 Å2
ΔGint-120 kcal/mol
Surface area42710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.157, 240.629, 135.039
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: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA3 - 2711 - 269
21LYSLYSBB3 - 2711 - 269
12LYSLYSAA3 - 2711 - 269
22LYSLYSCC3 - 2711 - 269
13ASNASNAA3 - 2721 - 270
23ASNASNDD3 - 2721 - 270
14ASNASNAA3 - 2721 - 270
24ASNASNEE3 - 2721 - 270
15LYSLYSBB3 - 2731 - 271
25LYSLYSCC3 - 2731 - 271
16LYSLYSBB3 - 2711 - 269
26LYSLYSDD3 - 2711 - 269
17LYSLYSBB3 - 2711 - 269
27LYSLYSEE3 - 2711 - 269
18LYSLYSCC3 - 2711 - 269
28LYSLYSDD3 - 2711 - 269
19LYSLYSCC3 - 2711 - 269
29LYSLYSEE3 - 2711 - 269
110ASNASNDD3 - 2721 - 270
210ASNASNEE3 - 2721 - 270

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

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Components

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Protein / Sugars , 2 types, 10 molecules ABCDE

#1: Protein
Sodium pumping rhodopsin


Mass: 31075.068 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
#5: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 380 molecules

#2: Chemical...
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C18H34O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.43 Å3/Da / Density % sol: 64.13 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 0.7 M Sodium Malonate pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.06 Å / Num. obs: 123865 / % possible obs: 99.8 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.022 / Rrim(I) all: 0.081 / Net I/σ(I): 20.1 / Num. measured all: 1708461
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
2.1-2.14142.768584361330.560.7572.8631.199.9
11.5-48.0611.20.02901280410.0060.02189.796

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6REW

6rew
PDB Unreleased entry


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.971 / SU B: 5.768 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.137
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 6234 5 %RANDOM
Rwork0.1789 ---
obs0.1798 117421 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 193.84 Å2 / Biso mean: 57.586 Å2 / Biso min: 28.83 Å2
Baniso -1Baniso -2Baniso -3
1-5 Å20 Å2-0 Å2
2---5.51 Å20 Å2
3---0.51 Å2
Refinement stepCycle: final / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10865 0 1185 299 12349
Biso mean--97.3 62.28 -
Num. residues----1355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01312310
X-RAY DIFFRACTIONr_bond_other_d00.01712084
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.6916379
X-RAY DIFFRACTIONr_angle_other_deg1.1081.67428002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.93351364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93422.629525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.024151748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2911520
X-RAY DIFFRACTIONr_chiral_restr0.0440.21488
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212872
X-RAY DIFFRACTIONr_gen_planes_other00.022644
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A96940.05
12B96940.05
21A97200.04
22C97200.04
31A97530.04
32D97530.04
41A97570.04
42E97570.04
51B98090.05
52C98090.05
61B97500.05
62D97500.05
71B97270.05
72E97270.05
81C97220.05
82D97220.05
91C97270.05
92E97270.05
101D98000.04
102E98000.04
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 448 -
Rwork0.356 8553 -
all-9001 -
obs--99.81 %

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