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

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Basic information

Entry
Database: PDB / ID: 6rez
TitleCrystal structure of the light-driven sodium pump KR2 in the pentameric form, pH 5.0
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: 2.6 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 / pdbx_struct_conn_angle / 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 / _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 / _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

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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)166,11751
Polymers154,0385
Non-polymers12,07946
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34200 Å2
ΔGint-104 kcal/mol
Surface area43090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.241, 241.392, 135.109
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
11LEULEUAA3 - 2751 - 273
21LEULEUBB3 - 2751 - 273
12LEULEUAA3 - 2751 - 273
22LEULEUCC3 - 2751 - 273
13LYSLYSAA3 - 2711 - 269
23LYSLYSDD3 - 2711 - 269
14LEULEUAA3 - 2751 - 273
24LEULEUEE3 - 2751 - 273
15LEULEUBB3 - 2751 - 273
25LEULEUCC3 - 2751 - 273
16LYSLYSBB3 - 2711 - 269
26LYSLYSDD3 - 2711 - 269
17LEULEUBB3 - 2751 - 273
27LEULEUEE3 - 2751 - 273
18LYSLYSCC3 - 2711 - 269
28LYSLYSDD3 - 2711 - 269
19LEULEUCC3 - 2751 - 273
29LEULEUEE3 - 2751 - 273
110LYSLYSDD3 - 2711 - 269
210LYSLYSEE3 - 2711 - 269

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 , 5 types, 143 molecules

#2: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C20H42
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-RET / RETINAL


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


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 3.42 Å3/Da / Density % sol: 64.01 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 3.4 M Sodium Malonate pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→48.08 Å / Num. obs: 64789 / % possible obs: 98.9 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.041 / Rrim(I) all: 0.096 / Net I/σ(I): 9.7 / Num. measured all: 356146
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
2.6-2.665.71.7462582745590.4480.7941.9240.999.8
11.91-48.084.70.03133637120.9990.0150.03531.594.2

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XTN chain D

4xtn


Resolution: 2.6→48.13 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 11.37 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.259
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 3301 5.1 %RANDOM
Rwork0.191 ---
obs0.1928 61464 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 209.53 Å2 / Biso mean: 72.949 Å2 / Biso min: 44.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.87 Å20 Å20 Å2
2---5.76 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 2.6→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10900 0 422 97 11419
Biso mean--93.42 73.52 -
Num. residues----1362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01411699
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711084
X-RAY DIFFRACTIONr_angle_refined_deg0.5421.66815775
X-RAY DIFFRACTIONr_angle_other_deg0.7611.7425634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.45651385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1623.636495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.428151756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6431520
X-RAY DIFFRACTIONr_chiral_restr0.0310.21460
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212727
X-RAY DIFFRACTIONr_gen_planes_other00.022546
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A99300.04
12B99300.04
21A99550.04
22C99550.04
31A98450.04
32D98450.04
41A99180.04
42E99180.04
51B99240.04
52C99240.04
61B98190.04
62D98190.04
71B98670.05
72E98670.05
81C98380.04
82D98380.04
91C99240.04
92E99240.04
101D98370.04
102E98370.04
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 243 -
Rwork0.368 4527 -
all-4770 -
obs--99.67 %

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