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Yorodumi- PDB-5iib: Crystal structure of red abalone egg VERL repeat 3 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iib | |||||||||||||||||||||
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Title | Crystal structure of red abalone egg VERL repeat 3 in complex with sperm lysin at 1.64 A resolution (crystal form II) | |||||||||||||||||||||
Components |
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Keywords | CELL ADHESION / FERTILIZATION / EGG-SPERM INTERACTION / GAMETE RECOGNITION / SPERM RECEPTOR / EGG COAT / VITELLINE ENVELOPE / ZP DOMAIN / ZP-N DOMAIN / SPERM ACROSOME / EGG COAT PENETRATION | |||||||||||||||||||||
Function / homology | Function and homology information vitelline envelope / acrosomal lumen / sperm-egg recognition / single fertilization / extracellular region / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Haliotis rufescens (red abalone) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | |||||||||||||||||||||
Authors | Raj, I. / Sadat Al-Hosseini, H. / Nishimura, K. / De Sanctis, D. / Jovine, L. | |||||||||||||||||||||
Funding support | Sweden, 6items
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Citation | Journal: Cell / Year: 2017 Title: Structural Basis of Egg Coat-Sperm Recognition at Fertilization. Authors: Raj, I. / Sadat Al Hosseini, H. / Dioguardi, E. / Nishimura, K. / Han, L. / Villa, A. / de Sanctis, D. / Jovine, L. #1: Journal: Mol. Biol. Evol. / Year: 2011 Title: The molecular basis of sex: linking yeast to human. Authors: Swanson, W.J. / Aagaard, J.E. / Vacquier, V.D. / Monne, M. / Sadat Al Hosseini, H. / Jovine, L. #2: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2006 Title: Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs. Authors: Aagaard, J.E. / Yi, X. / MacCoss, M.J. / Swanson, W.J. #3: Journal: Gene / Year: 2002 Title: Full-length sequence of VERL, the egg vitelline envelope receptor for abalone sperm lysin. Authors: Galindo, B.E. / Moy, G.W. / Swanson, W.J. / Vacquier, V.D. #4: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2000 Title: 1.35 and 2.07 A resolution structures of the red abalone sperm lysin monomer and dimer reveal features involved in receptor binding. Authors: Kresge, N. / Vacquier, V.D. / Stout, C.D. #5: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 1997 Title: The abalone egg vitelline envelope receptor for sperm lysin is a giant multivalent molecule. Authors: Swanson, W.J. / Vacquier, V.D. #6: Journal: J. Cell Biol. / Year: 1995 Title: Crystal structure and subunit dynamics of the abalone sperm lysin dimer: egg envelopes dissociate dimers, the monomer is the active species. Authors: Shaw, A. / Fortes, P.A. / Stout, C.D. / Vacquier, V.D. #7: Journal: Science / Year: 1993 Title: The crystal structure of lysin, a fertilization protein. Authors: Shaw, A. / McRee, D.E. / Vacquier, V.D. / Stout, C.D. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iib.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iib.ent.gz | 126.7 KB | Display | PDB format |
PDBx/mmJSON format | 5iib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iib_validation.pdf.gz | 938.4 KB | Display | wwPDB validaton report |
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Full document | 5iib_full_validation.pdf.gz | 941.2 KB | Display | |
Data in XML | 5iib_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 5iib_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/5iib ftp://data.pdbj.org/pub/pdb/validation_reports/ii/5iib | HTTPS FTP |
-Related structure data
Related structure data | 5ii4C 5ii5C 5ii6C 5ii7C 5ii8C 5ii9C 5iiaC 5iicC 5mr2C 5mr3C 2lisS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 16295.218 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haliotis rufescens (red abalone) / Cell line (production host): HEK-293S / Production host: Homo sapiens (human) / References: UniProt: P04552 |
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#2: Protein | Mass: 14432.386 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haliotis rufescens (red abalone) / Gene: VERL / Cell line (production host): HEK-293S / Production host: Homo sapiens (human) / References: UniProt: Q8WR62 |
-Sugars , 2 types, 3 molecules
#3: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose |
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#5: Sugar | Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C8H15NO6 / Source: (gene. exp.) Haliotis rufescens (red abalone) / Plasmid: pHLsec / Cell line (production host): HEK-293S / Production host: Homo sapiens (human) |
-Non-polymers , 2 types, 127 molecules
#4: Chemical | ChemComp-EPE / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.6 M ammonium sulfate, 0.1 M citric acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→32.25 Å / Num. obs: 39159 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 34.67 Å2 / Rmerge(I) obs: 0.04848 / Net I/σ(I): 12.43 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 5.5 % / Rmerge(I) obs: 2.087 / Mean I/σ(I) obs: 0.85 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LIS Resolution: 1.64→32.25 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.47
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Solvent computation | Shrinkage radii: 0.5 Å / VDW probe radii: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→32.25 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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