Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 59.30 kDa 
• Atom Count: 4310 
• Modelled Residue Count: 504 
• Deposited Residue Count: 512 
• Unique protein chains: 1

1YH3

Crystal structure of human CD38 extracellular domain

• PDB DOI: 10.2210/pdb1YH3/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2005-01-06 Released: 2005-09-27 
• Deposition Author(s): Liu, Q., Kriksunov, I.A., Graeff, R., Munshi, C., Lee, H.C., Hao, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.253 
• R-Value Work: 0.188 
• R-Value Observed: 0.192 

Literature

Crystal structure of human CD38 extracellular domain.

Liu, Q., Kriksunov, I.A., Graeff, R., Munshi, C., Lee, H.C., Hao, Q.

(2005) Structure 13: 1331-1339

• PubMed: 16154090 
• DOI: 10.1016/j.str.2005.05.012
• Primary Citation of Related Structures:  
  1YH3


• PubMed Abstract: 
  

Human CD38 is a multifunctional protein involved in diverse functions. As an enzyme, it is responsible for the synthesis of two Ca2+ messengers, cADPR and NAADP; as an antigen, it is involved in regulating cell adhesion, differentiation, and proliferation. Besides, CD38 is a marker of progression of HIV-1 infection and a negative prognostic marker of B-CLL. We have determined the crystal structure of the soluble extracellular domain of human CD38 to 1.9 A resolution. The enzyme's overall topology is similar to the related proteins CD157 and the Aplysia ADP-ribosyl cyclase, except with large structural changes at the two termini. The extended positively charged N terminus has lateral associations with the other CD38 molecule in the crystallographic asymmetric unit. The analysis of the CD38 substrate binding models revealed two key residues that may be critical in controlling CD38's multifunctionality of NAD hydrolysis, ADP-ribosyl cyclase, and cADPR hydrolysis activities.

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Organizational Affiliation: 

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyl cyclase 1	A, B	256	Homo sapiens	Mutation(s): 4  Gene Names: CD38 EC: 3.2.2.5 (PDB Primary Data), 3.2.2.6 (UniProt), 2.4.99.20 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P28907 (Homo sapiens) Explore P28907  Go to UniProtKB:  P28907
PHAROS:  P28907 GTEx:  ENSG00000004468

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.253 
• R-Value Work: 0.188 
• R-Value Observed: 0.192 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.839	α = 108.27
b = 51.491	β = 90.47
c = 66.439	γ = 97.29

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-06 
• Released Date: 2005-09-27 
Deposition Author(s): Liu, Q., Kriksunov, I.A., Graeff, R., Munshi, C., Lee, H.C., Hao, Q.

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2021-10-20
  Changes: Advisory, Database references