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- PDB-6yc2: Crystal structure of the light-driven sodium pump KR2 in the pent... -

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Basic information

Entry
Database: PDB / ID: 6yc2
TitleCrystal structure 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 / ALANINE / EICOSANE / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Sodium pumping rhodopsin
Function and homology information
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2Jan 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 / 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.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

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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)164,70842
Polymers155,3755
Non-polymers9,33337
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29420 Å2
ΔGint-89 kcal/mol
Surface area41660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.540, 240.130, 138.580
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
11SERSERAA3 - 2701 - 268
21SERSERBB3 - 2701 - 268
12SERSERAA3 - 2701 - 268
22SERSERCC3 - 2701 - 268
13LEULEUAA3 - 2691 - 267
23LEULEUDD3 - 2691 - 267
14SERSERAA3 - 2701 - 268
24SERSEREE3 - 2701 - 268
15SERSERBB3 - 2701 - 268
25SERSERCC3 - 2701 - 268
16LEULEUBB3 - 2691 - 267
26LEULEUDD3 - 2691 - 267
17SERSERBB3 - 2701 - 268
27SERSEREE3 - 2701 - 268
18LEULEUCC3 - 2691 - 267
28LEULEUDD3 - 2691 - 267
19SERSERCC3 - 2701 - 268
29SERSEREE3 - 2701 - 268
110LEULEUDD3 - 2691 - 267
210LEULEUEE3 - 2691 - 267

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: 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

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Non-polymers , 6 types, 258 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C20H42
#4: 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
#5: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8 / Details: 1.2 NaMal pH 8.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→48.86 Å / Num. obs: 78232 / % possible obs: 100 % / Redundancy: 16.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.052 / Rrim(I) all: 0.213 / Net I/σ(I): 10.6 / Num. measured all: 1274833 / Scaling rejects: 23
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
2.5-2.5516.62.4817358644410.770.6162.5581.1100
12.75-48.86130.05986106600.9970.0190.06235.998.4

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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: 2.5→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 7.636 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.188
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 3762 4.8 %RANDOM
Rwork0.1631 ---
obs0.1643 74296 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 171.64 Å2 / Biso mean: 49.11 Å2 / Biso min: 30.69 Å2
Baniso -1Baniso -2Baniso -3
1-3.8 Å20 Å20 Å2
2---5.36 Å20 Å2
3---1.56 Å2
Refinement stepCycle: final / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10769 0 372 221 11362
Biso mean--83.31 56.26 -
Num. residues----1341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01311479
X-RAY DIFFRACTIONr_bond_other_d00.01710926
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.62815492
X-RAY DIFFRACTIONr_angle_other_deg1.1291.55525198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.70451356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.67622.548522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.576151739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4851520
X-RAY DIFFRACTIONr_chiral_restr0.050.21434
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212520
X-RAY DIFFRACTIONr_gen_planes_other00.022572
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A93990.05
12B93990.05
21A94090.04
22C94090.04
31A93480.05
32D93480.05
41A94000.05
42E94000.05
51B93880.05
52C93880.05
61B93410.06
62D93410.06
71B93790.05
72E93790.05
81C93230.05
82D93230.05
91C94190.04
92E94190.04
101D93560.05
102E93560.05
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 283 -
Rwork0.296 5369 -
all-5652 -
obs--99.98 %

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