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Yorodumi- PDB-7e70: Time-resolved serial femtosecond crystallography reveals early st... -
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-Basic information
Entry | Database: PDB / ID: 7.0E+70 | ||||||
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Title | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 250 microsecond structure | ||||||
Components | Archaeal-type opsin 1,Archaeal-type opsin 2 | ||||||
Keywords | MEMBRANE PROTEIN / Channelrhodopsin / Rhodopsin | ||||||
Function / homology | Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / endoplasmic reticulum / plasma membrane / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Archaeal-type opsin 2 / Archaeal-type opsin 1 Function and homology information | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Oda, K. / Nomura, T. / Nakane, T. / Yamashita, K. / Inoue, K. / Ito, S. / Vierock, J. / Hirata, K. / Maturana, A.D. / Katayama, K. ...Oda, K. / Nomura, T. / Nakane, T. / Yamashita, K. / Inoue, K. / Ito, S. / Vierock, J. / Hirata, K. / Maturana, A.D. / Katayama, K. / Ikuta, T. / Ishigami, I. / Izume, T. / Umeda, R. / Eguma, R. / Oishi, S. / Kasuya, G. / Kato, T. / Kusakizako, T. / Shihoya, W. / Shimada, H. / Takatsuji, T. / Takemoto, M. / Taniguchi, R. / Tomita, A. / Nakamura, R. / Fukuda, M. / Miyauchi, H. / Lee, Y. / Nango, E. / Tanaka, R. / Tanaka, T. / Sugahara, M. / Kimura, T. / Shimamura, T. / Fujiwara, T. / Yamanaka, Y. / Owada, S. / Joti, Y. / Tono, K. / Ishitani, R. / Hayashi, S. / Kandori, H. / Hegemann, P. / Iwata, S. / Kubo, M. / Nishizawa, T. / Nureki, O. | ||||||
Citation | Journal: Elife / Year: 2021 Title: Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Authors: Oda, K. / Nomura, T. / Nakane, T. / Yamashita, K. / Inoue, K. / Ito, S. / Vierock, J. / Hirata, K. / Maturana, A.D. / Katayama, K. / Ikuta, T. / Ishigami, I. / Izume, T. / Umeda, R. / Eguma, ...Authors: Oda, K. / Nomura, T. / Nakane, T. / Yamashita, K. / Inoue, K. / Ito, S. / Vierock, J. / Hirata, K. / Maturana, A.D. / Katayama, K. / Ikuta, T. / Ishigami, I. / Izume, T. / Umeda, R. / Eguma, R. / Oishi, S. / Kasuya, G. / Kato, T. / Kusakizako, T. / Shihoya, W. / Shimada, H. / Takatsuji, T. / Takemoto, M. / Taniguchi, R. / Tomita, A. / Nakamura, R. / Fukuda, M. / Miyauchi, H. / Lee, Y. / Nango, E. / Tanaka, R. / Tanaka, T. / Sugahara, M. / Kimura, T. / Shimamura, T. / Fujiwara, T. / Yamanaka, Y. / Owada, S. / Joti, Y. / Tono, K. / Ishitani, R. / Hayashi, S. / Kandori, H. / Hegemann, P. / Iwata, S. / Kubo, M. / Nishizawa, T. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e70.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e70.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 7e70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e70_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 7e70_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7e70_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 7e70_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/7e70 ftp://data.pdbj.org/pub/pdb/validation_reports/e7/7e70 | HTTPS FTP |
-Related structure data
Related structure data | 7c86C 7e6xC 7e6yC 7e6zC 7e71C 3ug9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1768368 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39692.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) Gene: acop1, cop4, acop2, COP4, CSOB, CHLRE_02g085257v5, CHLREDRAFT_182032 Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q93WP2, UniProt: Q8RUT8 | ||||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||
#3: Chemical | ChemComp-RET / | ||||||
#4: Chemical | ChemComp-OLC / ( #5: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.07 % Description: This is a time-resolved study and two sets of structure factors are deposited: extrapolated and observed data. Data collection statistics is about the latter but we used the former for ...Description: This is a time-resolved study and two sets of structure factors are deposited: extrapolated and observed data. Data collection statistics is about the latter but we used the former for refinement, where some reflections were rejected. |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.9 Details: 100 mM MES, pH 6.9, 100 mM Na formate, and 30% PEG500DM |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MPCCD / Detector: CCD / Date: Oct 12, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.77 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→39.41 Å / Num. obs: 16730 / % possible obs: 100 % / Redundancy: 110 % / CC1/2: 0.9812 / R split: 0.132 / Net I/σ(I): 4.87 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ug9 Resolution: 2.5→14.96 Å / Cor.coef. Fo:Fc: 0.76 / Cor.coef. Fo:Fc free: 0.717 / SU B: 101.397 / SU ML: 2.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.722 / ESU R Free: 0.661 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 326.5 Å2 / Biso mean: 57.917 Å2 / Biso min: 2.71 Å2
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Refinement step | Cycle: final / Resolution: 2.5→14.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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