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- PDB-7e4g: Crystal structure of schizorhodopsin 4 -

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Basic information

Entry
Database: PDB / ID: 7e4g
TitleCrystal structure of schizorhodopsin 4
Componentsschizorhodopsin 4
KeywordsMEMBRANE PROTEIN / rhodopsin / inward proton pump
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / metal ion binding / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Rhodopsin, retinal binding site / 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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Uncharacterized protein
Similarity search - Component
Biological speciesAsgard group archaeon (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShihoya, W. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Crystal structure of schizorhodopsin reveals mechanism of inward proton pumping.
Authors: Higuchi, A. / Shihoya, W. / Konno, M. / Ikuta, T. / Kandori, H. / Inoue, K. / Nureki, O.
History
DepositionFeb 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 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: schizorhodopsin 4
B: schizorhodopsin 4
C: schizorhodopsin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,36648
Polymers73,3263
Non-polymers13,03945
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-199 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.000, 61.140, 98.750
Angle α, β, γ (deg.)90.000, 99.350, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

ZN

21A-306-

SO4

31B-301-

ZN

41A-451-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein schizorhodopsin 4


Mass: 24442.080 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asgard group archaeon (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A524F8J2*PLUS

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Non-polymers , 5 types, 189 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 20% PEG500DME, 100 mM Na-acetate, pH 4.75, 250 mM MgSO4. and 10 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.56 Å / Num. obs: 36552 / % possible obs: 99.56 % / Redundancy: 21 % / Biso Wilson estimate: 26.14 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.3841 / Rpim(I) all: 0.07358 / Rrim(I) all: 0.3922 / Net I/σ(I): 6.81
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 19.2 % / Rmerge(I) obs: 3.282 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 3615 / CC1/2: 0.39 / CC star: 0.749 / Rpim(I) all: 0.7221 / Rrim(I) all: 3.369 / % possible all: 98.42

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M0K

1m0k


Resolution: 2.1→49.56 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 1724 4.73 %
Rwork0.2021 34719 -
obs0.2037 36443 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.33 Å2 / Biso mean: 36.6858 Å2 / Biso min: 8.19 Å2
Refinement stepCycle: final / Resolution: 2.1→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4799 0 839 144 5782
Biso mean--59.15 38.16 -
Num. residues----588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.160.33841400.29282803294398
2.16-2.230.30621430.25862842298599
2.23-2.310.27081430.24929043047100
2.31-2.40.29691430.231628753018100
2.4-2.510.28071430.211329013044100
2.51-2.650.24521450.207329043049100
2.65-2.810.2431420.188528823024100
2.81-3.030.23411450.185229123057100
3.03-3.330.20511430.189728983041100
3.33-3.820.21331470.181829413088100
3.82-4.810.20081440.173729053049100
4.81-49.560.22941460.20882952309898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2839-0.5504-2.09482.74490.74435.9183-0.2069-0.1988-0.545-0.0047-0.19260.4584-0.0317-0.02940.41120.1362-0.0268-0.02690.20530.00460.3571-26.3202-22.840322.2644
22.68150.6457-1.34622.32710.3526.6207-0.04380.15060.092-0.10750.11990.09480.6301-0.1513-0.11630.12750.0199-0.05170.1669-0.02740.2391-21.0974-15.295219.6269
30.7516-0.20850.4451.0688-0.53197.0732-0.1329-0.00980.25520.1851-0.0919-0.08570.18370.21520.16050.13680.0177-0.0090.21180.02750.222-13.9969-12.3629.712
41.12820.43230.72921.04681.43379.3966-0.0557-0.0239-0.0297-0.0025-0.06630.1875-0.3272-0.28210.20030.1560.00220.02240.18510.00880.2703-8.0189-6.408326.0747
52.0071-0.5385-0.76762.2084-1.03037.94110.29380.170.1955-0.15670.1691-0.0477-0.28310.3598-0.35380.13670.02610.01920.2042-0.00620.2965-0.1631-9.949320.1765
69.47026.25646.10529.42496.70197.488-0.47980.05740.18190.12940.22520.62491.3470.17420.2220.5398-0.0087-0.03830.5467-0.16910.4779-3.5078-18.329944.5873
72.94420.01670.40731.91450.6372.8553-0.059-0.1128-0.17830.11750.0175-0.04660.20580.04410.07870.16110.0289-0.02240.1052-0.02140.2253-11.2919-23.228823.0522
82.9581-1.69010.32593.4948-1.92928.356-0.00240.2804-0.31140.0977-0.0966-0.36240.0480.38010.18210.1195-0.0151-0.03660.20890.00250.35966.49424.535521.536
91.1654-0.4596-0.38813.33431.23258.2548-0.0639-0.1590.15570.261-0.0651-0.25080.27440.36580.02220.1513-0.0283-0.040.18830.04510.3422-0.47272.326827.6932
102.2685-0.0710.41751.42170.23362.19870.06-0.0914-0.0548-0.01020.0077-0.0559-0.04670.0176-0.08440.194-0.0047-0.00850.18140.00740.292-13.334313.436522.2329
113.4516-0.82710.85663.0479-0.81663.0628-0.0942-0.20810.42410.2894-0.0382-0.1226-0.3732-0.08840.0510.1529-0.02580.00290.1773-0.04610.307-1.756917.736124.2555
123.83060.88090.65633.91650.91315.9603-0.0087-0.16210.4736-0.0393-0.11250.0534-0.4126-0.27850.29490.21060.0403-0.00020.1711-0.03050.3168-33.433518.942222.1997
133.42910.73180.36142.459-1.11372.13-0.1304-0.37670.34820.3419-0.24620.0179-0.3278-0.72590.22370.17110.0012-0.02630.2567-0.06570.42-28.522913.797127.7606
142.0854-0.7251-0.43232.4702-0.27745.3115-0.02740.0863-0.03850.03210.0692-0.06760.0894-0.0235-0.10570.148-0.0363-0.01170.1955-0.01270.2355-30.75553.809721.4161
150.4672-0.48640.76561.5157-1.85138.336-0.1198-0.09740.19570.2357-0.0122-0.0782-0.45710.2020.0730.1760.0205-0.02360.2262-0.02910.3431-28.3009-5.090925.9864
162.475-0.5565-0.57192.88971.34615.9130.09640.2231-0.1196-0.15230.1923-0.183-0.0579-0.1716-0.30970.134-0.0312-0.0240.2091-0.01870.3268-35.1732-10.218219.6372
174.3025-0.78350.39897.1921-1.58675.8316-0.1748-1.02270.11621.5199-0.27610.4709-0.8864-0.28360.26530.8239-0.09130.20840.5834-0.14051.0589-43.1231-3.205841.1951
181.8668-0.10830.30281.79720.21472.78350.0711-0.2604-0.3321-0.0223-0.02610.12580.0599-0.1092-0.00010.1448-0.0087-0.00110.22630.03270.3218-42.11310.507119.2965
192.3323-0.58410.31042.8816-0.86972.109-0.1797-0.15740.14680.2666-0.13250.43940.3224-0.10390.09230.10050.03540.00730.2431-0.01280.4204-40.368611.212724.5156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 64 )A25 - 64
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 89 )A65 - 89
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 112 )A90 - 112
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 137 )A113 - 137
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 144 )A138 - 144
7X-RAY DIFFRACTION7chain 'A' and (resid 145 through 199 )A145 - 199
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 23 )B1 - 23
9X-RAY DIFFRACTION9chain 'B' and (resid 24 through 50 )B24 - 50
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 137 )B51 - 137
11X-RAY DIFFRACTION11chain 'B' and (resid 138 through 199 )B138 - 199
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 24 )C1 - 24
13X-RAY DIFFRACTION13chain 'C' and (resid 25 through 49 )C25 - 49
14X-RAY DIFFRACTION14chain 'C' and (resid 50 through 89 )C50 - 89
15X-RAY DIFFRACTION15chain 'C' and (resid 90 through 112 )C90 - 112
16X-RAY DIFFRACTION16chain 'C' and (resid 113 through 136 )C113 - 136
17X-RAY DIFFRACTION17chain 'C' and (resid 137 through 145 )C137 - 145
18X-RAY DIFFRACTION18chain 'C' and (resid 146 through 172 )C146 - 172
19X-RAY DIFFRACTION19chain 'C' and (resid 173 through 197 )C173 - 197

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