5JKE
Crystal structure of human IZUMO1-JUNO complex (crystal form 3)
- PDB DOI: https://doi.org/10.2210/pdb5JKE/pdb
- Classification: CELL ADHESION
- Organism(s): Homo sapiens
- Expression System: Drosophila
- Mutation(s): No
- Deposited: 2016-04-26 Released: 2016-06-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.86 Å
- R-Value Free: 0.238
- R-Value Work: 0.203
- R-Value Observed: 0.204
This is version 1.4 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Izumo sperm-egg fusion protein 1 | 246 | Homo sapiens | Mutation(s): 0 Gene Names: IZUMO1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q8IYV9 (Homo sapiens) Explore Q8IYV9 Go to UniProtKB: Q8IYV9 | |||||
PHAROS: Q8IYV9 GTEx: ENSG00000182264 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8IYV9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Sperm-egg fusion protein Juno | 221 | Homo sapiens | Mutation(s): 0 Gene Names: IZUMO1R, FOLR4, JUNO |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for A6ND01 (Homo sapiens) Explore A6ND01 Go to UniProtKB: A6ND01 | |||||
PHAROS: A6ND01 GTEx: ENSG00000183560 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A6ND01 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | E [auth A], G [auth B], I [auth C], J [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| SO4 Query on SO4 | F [auth A], K [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| CL Query on CL | H [auth B], L [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.86 Å
- R-Value Free: 0.238
- R-Value Work: 0.203
- R-Value Observed: 0.204
- Space Group: P 2 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 64.182 | α = 90 |
| b = 141.776 | β = 90 |
| c = 144.861 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2016-06-22 Deposition Author(s): Ohto, U., Ishida, H., Shimizu, T.
Revision History (Full details and data files)
- Version 1.0: 2016-06-22
Type: Initial release - Version 1.1: 2016-06-29
Changes: Database references - Version 1.2: 2020-02-19
Changes: Data collection, Database references, Derived calculations - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
