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Yorodumi- PDB-6rx1: Crystal structure of human syncytin 1 in post-fusion conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rx1 | ||||||
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Title | Crystal structure of human syncytin 1 in post-fusion conformation | ||||||
Components | Syncytin-1 | ||||||
Keywords | MEMBRANE PROTEIN / HUMAN PLACENTAL PROTEIN / MEMBRANE FUSION / ENDOGENOUS RETROVIRUS / HERV-W / SYNCYTIN | ||||||
Function / homology | Function and homology information syncytium formation by plasma membrane fusion / syncytium formation / myoblast fusion / anatomical structure morphogenesis / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ruigrok, K. / Backovic, M. / Vaney, M.C. / Rey, F.A. | ||||||
Funding support | France, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2019 Title: X-ray Structures of the Post-fusion 6-Helix Bundle of the Human Syncytins and their Functional Implications. Authors: Ruigrok, K. / Vaney, M.C. / Buchrieser, J. / Baquero, E. / Hellert, J. / Baron, B. / England, P. / Schwartz, O. / Rey, F.A. / Backovic, M. #1: Journal: J.Mol.Biol. / Year: 2005 Title: Crystal structure of a pivotal domain of human syncytin-2, a 40 million years old endogenous retrovirus fusogenic envelope gene captured by primates. Authors: Renard, M. / Varela, P.F. / Letzelter, C. / Duquerroy, S. / Rey, F.A. / Heidmann, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rx1.cif.gz | 34.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rx1.ent.gz | 21.9 KB | Display | PDB format |
PDBx/mmJSON format | 6rx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/6rx1 ftp://data.pdbj.org/pub/pdb/validation_reports/rx/6rx1 | HTTPS FTP |
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-Related structure data
Related structure data | 6rx3C 1y4mS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12614.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The following sequence MHHHHHHENLYFQS at the N-terminal of the protein sequence is from an expression tag with the 1st residue MET as the initiating methionine. The 3 first residues 'TST' ...Details: The following sequence MHHHHHHENLYFQS at the N-terminal of the protein sequence is from an expression tag with the 1st residue MET as the initiating methionine. The 3 first residues 'TST' from the protein sequence are disordered in density. Source: (gene. exp.) Homo sapiens (human) / Gene: ERVW-1, ERVWE1 / Plasmid: PET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UQF0 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.16 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 30% v/v 2-propanol, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.070638 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 17, 2016 |
Radiation | Monochromator: cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a KirkpatrickBaez pair of focussing mirrors Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.070638 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→43.1 Å / Num. obs: 7752 / % possible obs: 99.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 30 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.08 / Rrim(I) all: 0.15 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 622 / CC1/2: 0.47 / Rpim(I) all: 0.81 / Rrim(I) all: 1.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y4M Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.212 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.164
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Displacement parameters | Biso max: 154.08 Å2 / Biso mean: 50.38 Å2 / Biso min: 30.2 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.35 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
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