2YW8 | pdb_00002yw8

Crystal structure of human RUN and FYVE domain-containing protein

• PDB DOI: https://doi.org/10.2210/pdb2YW8/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2007-04-20 Released: 2008-04-22 
• Deposition Author(s): Wang, H., Kishishita, S., Murayama, K., Takemoto, C., Terada, T., Shirouzu, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.224 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human RUN and FYVE domain-containing protein

Wang, H., Kishishita, S., Murayama, T., Takemoto, C., Terada, T., Chen, L., Fu, Z.Q., Chrzas, J., Wang, B.C., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 9.57 kDa 
• Atom Count: 528 
• Modeled Residue Count: 61 
• Deposited Residue Count: 82 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RUN and FYVE domain-containing protein 1	A	82	Homo sapiens	Mutation(s): 0  Gene Names: RUFY1, RABIP4, ZFYVE12 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q96T51 (Homo sapiens) Explore Q96T51  Go to UniProtKB:  Q96T51
PHAROS:  Q96T51 GTEx:  ENSG00000176783

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.224 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.15	α = 90
b = 115.15	β = 90
c = 115.15	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Wang, H., Kishishita, S., Murayama, K., Takemoto, C., Terada, T., Shirouzu, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description