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- PDB-6yc0: Crystal structure of the steady-state-SMX activated state of the ... -

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Basic information

Entry
Database: PDB / ID: 6yc0
TitleCrystal structure of the steady-state-SMX activated state of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0
ComponentsSodium pumping rhodopsin
KeywordsMEMBRANE PROTEIN / rhodopsin / ion pumping / retinal / sodium pump / intermediate state
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / EICOSANE / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Sodium pumping rhodopsin
Function and homology information
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 Biology (GRAL)ANR-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
DepositionMar 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 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 1.2Dec 13, 2023Group: 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_related_exp_data_set / pdbx_struct_conn_angle / 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 / _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.pdbx_ptnr1_label_alt_id / _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
Revision 1.3Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)174,14380
Polymers154,0385
Non-polymers20,10575
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33750 Å2
ΔGint-178 kcal/mol
Surface area43410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.210, 240.340, 138.370
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 / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 3 - 271 / Label seq-ID: 1 - 269

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15BB
25CC
16BB
26DD
17BB
27EE
18CC
28DD
19CC
29EE
110DD
210EE

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

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Sodium pumping rhodopsin


Mass: 30807.639 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

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Non-polymers , 7 types, 302 molecules

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


Mass: 356.540 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 21 / 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
#5: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H28O
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H34O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 3.65 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8 / Details: 1.2 M NaMal pH 8.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→69.19 Å / Num. obs: 77967 / % possible obs: 100 % / Redundancy: 894.5 % / CC1/2: 0.988 / CC star: 0.997 / R split: 0.152 / Net I/σ(I): 11.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 640.6 % / Mean I/σ(I) obs: 0.72 / Num. unique obs: 7691 / CC1/2: 0.488 / CC star: 0.81 / R split: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6xyt

6xyt


Resolution: 2.7→50.01 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.951 / SU B: 16.843 / SU ML: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.843 / ESU R Free: 0.289
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 3067 4.9 %RANDOM
Rwork0.1916 ---
obs0.193 58999 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 249.8 Å2 / Biso mean: 60.461 Å2 / Biso min: 22.15 Å2
Baniso -1Baniso -2Baniso -3
1-5.95 Å20 Å20 Å2
2---9.07 Å20 Å2
3---3.11 Å2
Refinement stepCycle: final / Resolution: 2.7→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10769 0 741 227 11737
Biso mean--109.12 67.1 -
Num. residues----1345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.01313515
X-RAY DIFFRACTIONr_bond_other_d00.01712896
X-RAY DIFFRACTIONr_angle_refined_deg1.0751.65218175
X-RAY DIFFRACTIONr_angle_other_deg1.0411.61529748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.11151565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.26422.66609
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.98151978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.8651525
X-RAY DIFFRACTIONr_chiral_restr0.0370.21644
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214653
X-RAY DIFFRACTIONr_gen_planes_other00.023036
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A87210.04
12B87210.04
21A87060.04
22C87060.04
31A86800.05
32D86800.05
41A87180.04
42E87180.04
51B87000.05
52C87000.05
61B86770.05
62D86770.05
71B87210.04
72E87210.04
81C86720.05
82D86720.05
91C86930.04
92E86930.04
101D86780.04
102E86780.04
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 229 -
Rwork0.365 4279 -
all-4508 -
obs--100 %

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