3F1I | pdb_00003f1i

Human ESCRT-0 Core Complex

• PDB DOI: https://doi.org/10.2210/pdb3F1I/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-28 Released: 2009-03-24 
• Deposition Author(s): Ren, X., Kloer, D.P., Kim, Y., Ghirlando, R., Saidi, L., Hummer, G., Hurley, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.253 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Hybrid Structural Model of the Complete Human ESCRT-0 Complex.

Ren, X., Kloer, D.P., Kim, Y.C., Ghirlando, R., Saidi, L.F., Hummer, G., Hurley, J.H.

(2009) Structure 17: 406-416

• PubMed: 19278655 
• DOI: https://doi.org/10.1016/j.str.2009.01.012
• Primary Citation Related Structures: 
  3F1I


• PubMed Abstract: 
  

  The human Hrs and STAM proteins comprise the ESCRT-0 complex, which sorts ubiquitinated cell surface receptors to lysosomes for degradation. Here we report a model for the complete ESCRT-0 complex based on the crystal structure of the Hrs-STAM core complex, previously solved domain structures, hydrodynamic measurements, and Monte Carlo simulations. ESCRT-0 expressed in insect cells has a hydrodynamic radius of RH = 7.9 nm and is a 1:1 heterodimer. The 2.3 Angstroms crystal structure of the ESCRT-0 core complex reveals two domain-swapped GAT domains and an antiparallel two-stranded coiled-coil, similar to yeast ESCRT-0. ESCRT-0 typifies a class of biomolecular assemblies that combine structured and unstructured elements, and have dynamic and open conformations to ensure versatility in target recognition. Coarse-grained Monte Carlo simulations constrained by experimental RH values for ESCRT-0 reveal a dynamic ensemble of conformations well suited for diverse functions.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content 

• Total Structure Weight: 29.32 kDa 
• Atom Count: 1,642 
• Modeled Residue Count: 199 
• Deposited Residue Count: 252 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor-regulated tyrosine kinase substrate	A [auth H]	98	Homo sapiens	Mutation(s): 0  Gene Names: Hepatocyte growth factor regulated tyrosine kinase substrate (HGS), HGS, HRS
UniProt & NIH Common Fund Data Resources
Find proteins for O14964 (Homo sapiens) Explore O14964  Go to UniProtKB:  O14964
PHAROS:  O14964 GTEx:  ENSG00000185359

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal transducing adapter molecule 1	B [auth S], C	77	Homo sapiens	Mutation(s): 0  Gene Names: Signal transducing adaptor molecule (STAM), STAM, STAM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92783 (Homo sapiens) Explore Q92783  Go to UniProtKB:  Q92783
PHAROS:  Q92783 GTEx:  ENSG00000136738

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.253 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.059	α = 90
b = 78.059	β = 90
c = 152.849	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
XSCALE	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Ren, X., Kloer, D.P., Kim, Y., Ghirlando, R., Saidi, L., Hummer, G., Hurley, J.H.

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references