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- PDB-6yc1: Crystal structure of the H30A mutant of the light-driven sodium p... -

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Basic information

Entry
Database: PDB / ID: 6yc1
TitleCrystal structure of the H30A mutant 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 / (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: 2.2 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 1.2Jul 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)181,35796
Polymers153,7035
Non-polymers27,65491
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40110 Å2
ΔGint-124 kcal/mol
Surface area43000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.089, 239.733, 135.132
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: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 275 / Label seq-ID: 1 - 273

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 / Sugars , 2 types, 10 molecules ABCDE

#1: Protein
Sodium pumping rhodopsin


Mass: 30740.572 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 , 5 types, 653 molecules

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


Mass: 356.540 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-RET / RETINAL


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


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.45 Å3/Da / Density % sol: 64.39 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→48.01 Å / Num. obs: 106450 / % possible obs: 98.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.049 / Rrim(I) all: 0.132 / Net I/σ(I): 11.5 / Num. measured all: 758221
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
2.2-2.247.42.0993876652610.4890.8272.2590.999.2
12.05-48.015.90.02642597170.9990.0120.02946.497.1

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Processing

Software
NameVersionClassification
Aimless0.7.2data 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: 2.2→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 7.103 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.167
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 5267 5 %RANDOM
Rwork0.1814 ---
obs0.1827 100998 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 168.2 Å2 / Biso mean: 47.815 Å2 / Biso min: 23.17 Å2
Baniso -1Baniso -2Baniso -3
1-4.77 Å20 Å20 Å2
2---4.48 Å20 Å2
3----0.29 Å2
Refinement stepCycle: final / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10911 0 1215 567 12693
Biso mean--86.56 55.03 -
Num. residues----1365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01312440
X-RAY DIFFRACTIONr_bond_other_d00.01712328
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.69916543
X-RAY DIFFRACTIONr_angle_other_deg1.0681.69328572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.30651380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73222.639523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.496151766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3591520
X-RAY DIFFRACTIONr_chiral_restr0.0410.21507
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212899
X-RAY DIFFRACTIONr_gen_planes_other00.022654
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A98290.05
12B98290.05
21A98440.04
22C98440.04
31A98250.04
32D98250.04
41A98370.04
42E98370.04
51B98330.05
52C98330.05
61B98140.04
62D98140.04
71B97920.05
72E97920.05
81C98260.04
82D98260.04
91C98400.05
92E98400.05
101D98180.04
102E98180.04
LS refinement shellResolution: 2.2→2.256 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 403 -
Rwork0.337 7322 -
all-7725 -
obs--99.22 %

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