8W90 | pdb_00008w90

crystal structure of CD4-D1D2 with Nb457

• PDB DOI: https://doi.org/10.2210/pdb8W90/pdb

• Classification: ANTIVIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Vicugna pacos, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-09-04 Released: 2024-09-04 
• Deposition Author(s): Wang, X.Y., Wang, Y.X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 

Starting Models: experimental

Literature

Structure of CD4-D1D2 domain and nanobody Nb457 at 1.78 Angstroms resolution

Wang, X.Y., Wang, Y.X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 102.93 kDa 
• Atom Count: 6,936 
• Modeled Residue Count: 878 
• Deposited Residue Count: 936 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NB457	A, C, E	134	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD4	B, D, F	178	Homo sapiens	Mutation(s): 0  Gene Names: CD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens) Explore P01730  Go to UniProtKB:  P01730
PHAROS:  P01730 GTEx:  ENSG00000010610

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.082	α = 90
b = 141.978	β = 97.931
c = 81.662	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Wang, X.Y., Wang, Y.X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary