5JKD
Crystal structure of human IZUMO1-JUNO complex (crystal form 2)
- PDB DOI: https://doi.org/10.2210/pdb5JKD/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: 2.90 Å
- R-Value Free: 0.251 
- R-Value Work: 0.220 
- R-Value Observed: 0.222 
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 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | C [auth A], D [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CL Query on CL | E [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.251 
- R-Value Work: 0.220 
- R-Value Observed: 0.222 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 145.604 | α = 90 |
b = 65.377 | β = 104.24 |
c = 77.199 | 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