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- PDB-6gf7: Molecular basis of egg coat filament cross-linking: Zn-SAD struct... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gf7 | |||||||||||||||
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Title | Molecular basis of egg coat filament cross-linking: Zn-SAD structure of the partially deglycosylated ZP1 ZP-N1 domain homodimer | |||||||||||||||
![]() | Zona pellucida sperm-binding protein 1,Zona pellucida sperm-binding protein 1 | |||||||||||||||
![]() | CELL ADHESION / Zona pellucida / ZP1 / ZP-N domain / ZP module / ZP domain / egg coat filament cross-linking / egg coat penetration by sperm | |||||||||||||||
Function / homology | ![]() egg coat / structural constituent of egg coat / acrosin binding / prevention of polyspermy / binding of sperm to zona pellucida / collagen-containing extracellular matrix / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Nishimura, K. / Jovine, L. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of egg coat cross-linking sheds light on ZP1-associated female infertility. Authors: Nishimura, K. / Dioguardi, E. / Nishio, S. / Villa, A. / Han, L. / Matsuda, T. / Jovine, L. #1: Journal: J. Mol. Biol. / Year: 1985 Title: Mouse egg extracellular coat is a matrix of interconnected filaments possessing a structural repeat. Authors: Greve, J.M. / Wassarman, P.M. #2: Journal: Development / Year: 1999 Title: Abnormal zonae pellucidae in mice lacking ZP1 result in early embryonic loss. Authors: Rankin, T. / Talbot, P. / Lee, E. / Dean, J. #3: Journal: Biol. Reprod. / Year: 2001 Title: Morphological and biochemical changes of isolated chicken egg-envelope during sperm penetration: degradation of the 97-kilodalton glycoprotein is involved in sperm-driven hole formation on the egg-envelope. Authors: Takeuchi, Y. / Cho, R. / Iwata, Y. / Nishimura, K. / Kato, T. / Aoki, N. / Kitajima, K. / Matsuda, T. #4: Journal: Biochem. J. / Year: 2004 Title: A newly identified zona pellucida glycoprotein, ZPD, and dimeric ZP1 of chicken egg envelope are involved in sperm activation on sperm-egg interaction. Authors: Okumura, H. / Kohno, Y. / Iwata, Y. / Mori, H. / Aoki, N. / Sato, C. / Kitajima, K. / Nadano, D. / Matsuda, T. #5: Journal: N. Engl. J. Med. / Year: 2014 Title: Mutant ZP1 in familial infertility. Authors: Huang, H.L. / Lv, C. / Zhao, Y.C. / Li, W. / He, X.M. / Li, P. / Sha, A.G. / Tian, X. / Papasian, C.J. / Deng, H.W. / Lu, G.X. / Xiao, H.M. #6: Journal: FEBS Open Bio / Year: 2015 Title: Identification of distinctive interdomain interactions among ZP-N, ZP-C and other domains of zona pellucida glycoproteins underlying association of chicken egg-coat matrix. Authors: Okumura, H. / Sato, T. / Sakuma, R. / Fukushima, H. / Matsuda, T. / Ujita, M. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.5 KB | Display | ![]() |
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PDB format | ![]() | 43 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461 KB | Display | ![]() |
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Full document | ![]() | 463 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15485.485 Da / Num. of mol.: 2 / Mutation: N121Q, G140H(6), G149S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.6 M LiCl, 0.1 M tri-sodium citrate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2825 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→53.323 Å / Num. obs: 15254 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 70.95 Å2 / CC1/2: 1 / Rpim(I) all: 0.041 / Rrim(I) all: 0.103 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.7→2.82 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1896 / CC1/2: 0.51 / Rpim(I) all: 0.852 / Rrim(I) all: 1.627 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→53.323 Å
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Refine LS restraints |
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LS refinement shell |
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