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- PDB-6rf0: Crystal structure of the light-driven sodium pump KR2 in the pent... -

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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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)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: _ / Refine code: _

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

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Components

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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

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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


Mass: 282.547 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C20H42
#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.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.27 Å3/Da / Density % sol: 62.36 %
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: 0.976 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

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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 %

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